An ancestral signalling pathway is conserved in plant lineages forming intracellular symbioses

Supplementary methods

OneKP transcriptome annotation

A total of 264 transcriptomes from non-angiosperm species were collected from the 1KP project (https://db.cngb.org/onekp/). For each transcriptome, ORFs were predicted using TransDecoder v5.5.0 (http://transdecoder.github.io) with default parameters. Then, predicted ORFs were subjected to BLASTp v2.7.1+66 and PFAM searches against the Uniprot (accessed 11/2018) and PFAM v3267 database. Results of BLAST and PFAM searches were used to improve final annotation and coding-sequence prediction.

Phylogeny and sequence analysis

Phylogenetic analysis of candidate genes. Homologs of each candidate genes (Supplementary Table 2) were retrieved from the SymDB database with the tBLASTn algorithm v2.9.0+66 with e- value no greater than 1e-10 (e-value threshold was adapted for highly duplicated gene families) and using the protein sequence from Medicago truncatula as query. To remove short and partial transcript that are abundant in the transcriptomes from the 1KP project, shorter transcript than 60% of the M. truncatula query were removed prior alignment. Sequences were aligned using MAFFT v7.40768 with default parameter and the resulting alignments trimmed using trimAl v1.2rev5769 to remove all positions with more than 20% of gaps. Cleaned alignments were subjected to Maximum Likelihood (ML) approach using the IQ-TREE software v1.6.770. Prior to ML analysis, best-fitted evolutionary model was tested for each alignment using ModelFinder71 as implemented in IQ-TREE. Branch support was tested with 10,000 replicates of SH-alrt72. From these initial phylogenies, clade containing the candidate genes were extracted, removing distant homologs, and a new phylogenetic analysis performed as described above. Trees were visualized and annotated using the iTOL v4.4.273. Following gene phylogenies, for genes missing from sequenced genomes, the tBLASTn search was repeated on the genome assembly. This lead to the identification of a number of non-annotated genes that are summarized in Supplementary Table 6, and included in Figure 1 and Supplementary Figure 1.

Synteny analysis. For the genes for which orthologs/homologs were not found in in the genome and transcriptome of M. polymorpha ssp. ruderalis, more detailed searches in the genomes of M. polymorpha ssp. ruderalis, M. polymorpha ssp. polymorpha and M. polymorpha ssp. monitvagans were conducted. To do this, the coding sequences of the respective M. paleacea genes were used as queries for a BLASTn search against the genome assemblies of all three M. polymorpha subspecies. The genomic regions were then aligned with the corresponding M. paleacea genomic regions for comparisons using Mauve 2.3.1 and visualized in Geneious. Following this, gene syntenic analysis was performed by mapping the respective transcriptome onto the M. polymorpha ssp. ruderalis and M. paleacea genomic regions upstream and downstream of each gene using Geneious. The identities of the preceding and subsequent genes were confirmed by aligning the M. paleacea and M. polymorpha ssp. ruderalis sequences using MAFFT68. Their functional identity was confirmed using BLAST through searches against the SWISSPROT database and using Pfam.

Analysis of the Nelumbo CCaMK locus. Reference coding sequence of Medicago truncatula CCaMK was used as query to search for homolog sequence in three different Nelumbo nucifera genome assemblies74,75. Search was performed using the BLASTn+, with an e-value threshold set at 1e-10 and default parameters. For each hit in the BLAST results, 5 kb of upstream and downstream sequences were extracted using custom Python script. Extracted sequences were then aligned using MAFFT68 with the genomic reference and the coding sequences of M. truncatula and Oryza sativa.

Signature of selection on CCaMK and CYCLOPS in mosses. With the exception of Takakia lepidozioides, mosses are not mycorrhizal76. We investigated the selection acting on CCaMK and CYCLOPS on the branch before the radiation of mosses but after the divergence of T. lepidozioides (foreground branch). We adopted branch models77 to identify differential signatures of selective pressure acting on the sequences between the foreground branch and the rest of the tree (i.e. background branches) and branch-site models78 to identify differential signatures of selective pressures acting on specific sites between foreground and background branches. These models are implemented in the codeml program79 using ete-evol program80. In addition to the branch model, we also used the RELAX program81 to look for relaxation (K<1) or intensification (K>1) of the strength of selection acting on the non-mycorrhizal mosses (mosses clade without T. lepidozioides) compared to the rest of the tree. These methods calculate different synonymous and nonsynonymous substitution rates (ω = 푑N ) using the phylogenetic tree topology for both 푑S foreground and background branches. Because (i) the programs used do not accept gap in codon sequences and (ii) there is a negative correlation between the number of sequences and the number of ungapped positions, we used different number of sequences for each analysis. Protein sequences from CCaMK and CYCLOPS orthologs were aligned using MUSCLE v3.8.382. Short sequences were excluded to maximize sequence number while limiting gapped positions compared to CCaMK/CYCLOPS sequences of T. lepidozioides using a custom R script83. We opted for 124 sequences for CCaMK and 121 sequences for CYCLOPS corresponding to 1092 and 552 nucleotide positions, respectively (Supplementary Table 3). We used likelihood-ratio test (LRT) to assess significance between models ran with codeml. For the branch model, we compare likelihoods from the “b_free” and “M0” models to determine if the ratios are different between

77 background and foreground branches (p-val>0.05 : ωf oreground and ωbackground are not different, p- val<0.05 : ωf oreground and ωbackground are different). We also compared likelihoods from the “b_free” and “b_neut” models to determine if the ratio on the foreground branch is not neutral77 (p-val>0.05: no signature of selection on foreground (neutral), p-val<0.05 and ωf oreground<1: signature of negative/relaxed selection on foreground, p-val<0.05 and ωf oreground>1: signature of positive selection on foreground). For the branch-site model, we compare likelihoods from the “bsA” and “M1” models to determine if the selection pressure is relaxed on sites on the foreground branch78 (p-val<0.05: signature of relaxed selection on sites on foreground). We also compared likelihoods from the “bsA” and “bsA1” models to determine if there are sites under positive selection on the foreground branch78 (p-val<0.05: signature of positive selection on specific sites on foreground).

MpoCCaMK and MpoCYCLOPS pseudogenes in wild populations

Plant material and DNA extraction. Samples from a total of 35 accessions of Marchantia polymorpha (Supplementary Table 4) were collected. Approximately 0.1 g of cleaned young thalli was reduced to a fine powder in liquid nitrogen and cleaned as follow. First, 1 ml of cleaning STE buffer (Sucrose 0.25 M, Tris-HCl 0.03 M at pH=7.5 and EDTA 0.05M at pH=7.5) was added to the powder and the mixture was thoroughly vortexed. After 5 min of centrifugation at 14, 000 rpm for 5 min, the supernatant was removed. Washes with STE buffer were repeated until the red coloration was completely gone. Subsequent DNA extraction was performed using a CTAB method58.

PCR and sequencing. Putative MpoCCaMK and MpoCYCLOPS genomic sequences (1 kb) were amplified by PCR using GoTaq polymerase (Promega) according to manufacturer’s protocol. Primers used were (MpoCCAMK fwd GGTCATCTTGTACATTCTCCT, rev CTTGCTACTGAAGATACTTGCA; MpoCYCLOPS fwd CAGCACCCTCAAAACTTAGAGT, MpoCYCLOPS rev CCCAGCTGTTACCTTAAGAAG). After amplification, PCR products were sent for Sanger sequencing at Eurofins (Germany) using the PCR forward and reverse primers of the two genes. Sanger sequences were assembled using the Tracy software v0.5.5 and aligned using MUSCLE82 v3.8.3 with genomic CCaMK and CYCLOPS sequences from the three Marchantia polymorpha subspecies.

Mycorrhization assays

Material and growth conditions. Thalli of Marchantia paleacea, Marchantia polymorpha ssp. ruderalis (TAK1), Marchantia polymorpha ssp. polymorpha (MppBR5) and Marchantia polymorpha ssp. montivagans (MpmSA2) were grown on a substrate containing 50% Oil‐Dri UK (Damolin, Etrechy, France) and 50% sand (0.7–1.3 mm) in 9x9x8 cm pots (5 thalli per pot, 5 pots per species/subspecies). Each pot was inoculated with 1000 sterile spores of Rhizophagus irregularis DAOM 197198 (Agronutrition Labège, France), grown at a 16h/8h photoperiod at 22°C/20°C and watered once a week with ½ Long Ashton medium containing 7.5 μM of phosphate84.

Microscopic phenotyping. After 8 weeks of colonization, thalli were harvested Sections of the thalli were made by hand or using a Leica vt1000s vibratome (100µm sections) on thalli included in 6% agarose. Sections were cleared in 10% KOH overnight and ink colored one hour in 5% Sheaffer ink, 5% acetic acid. Sections were observed under a microscope and pictures of representative sections were taken with a Zeiss Axiozoom V16 microscope.

Molecular phenotyping. After 8 weeks of colonization, portions of 5 thalli per condition were harvested and frozen in liquid nitrogen. DNA was extracted from frozen thalli material as described in Edwards85. PCR was performed using GoTaq polymerase (Promega) following manufacturer instructions on the M. polymorpha Elongation factor-1 alpha (Mapoly0024s0116, fwd CGACCACTGGTCACCTTATC, rev AACCTCAGTGGTCAGACCG) and on the Rhizophagus irregularis Elongation factor-1 alpha (Rhiir2_1_GeneCatalog_transcripts_20160502.nt, fwd TGTTGCTTTCGTCCCAATATC, rev CTCAACACACATCGGTTTGG)

Medicago truncatula root assays

Plasmid construction. The Golden Gate modular cloning system was used to prepare the plasmids as described in Schiessl et al86. Levels 0 and 1 used in this study are listed in Supplemental Table 6 and held for distribution in the ENSA project core collection (https://www.ensa.ac. uk/). We used L1 plasmid piCH4781187, L1 construct L1M-R1-pAtUBI-DSred-t35S23 and L2 acceptor backbone EC50507. Sequences were domesticated (listed in Supplemental Table 7) synthesized and cloned into pMS (GeneArt, Thermo Fisher Scientific, Waltham, USA). Activation of pENOD11:GUS by CCaMK orthologs. Constructs containing CCaMK-K were transformed in A. rhizogenes A4TC24 by electroporation. Transformed strains were grown at 28°C in Luria-Bertani medium supplemented with rifampicin and kanamycin (20 µg/mL). M. truncatula pENOD11:GUS L416 roots88, were transformed with the different CCaMK-K as described by Boisson-Dernier et al.89, and grown on Fahraeus medium for 2 months, selected with the DsRed marker present in all the constructs and GUS stained as in Vernié et al90. Trans-complementation assays. The MedtruCCaMK null allele dmi3-191 and MedtruCYCLOPS null allele ipd3-192 were used in this study. Roots were transformed as described above with the various CCaMK and CYCLOPS constructs respectively (Supplementary Table 7). For nodulation assays, M. truncatula plants with DsRed positive roots were transferred in pots containing Zeolite substrate (50% fraction 1.0-2,5mm, 50% fraction 0,5-1.0-mm, Symbiom) and watered with liquid Fahraeus medium. Wild-type S. meliloti RCR2011 pXLGD4 (GMI6526) was grown at 28°C in tryptone yeast medium supplemented with 6 mM calcium chloride and 10 µg/mL tetracycline, rinsed with water and diluted at OD600=0.02. Each pot was inoculated with 10 ml of bacterial suspension. Two independent biological replicates were conducted for ccamk and cyclops complementation assays. For ccamk, one biological assay was harvested at 26DPI and scored for the ratio of infected nodules after X-Gal staining, and one at 42DPI scored for the total nodule number. For cyclops, one biological assay was harvested at 32DPI and one at 49 DPI, both were scored for infected nodules after X-Gal staining and the ratio of fully infected nodules out of the total number of nodules was calculated and used on the box plot (both biological replicates combined).

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Symbiosis Genes type AMS RAD1 STR STR2 RAM1 ABCB12 ABCB20 DHY HYP2 KinF HYP4 pp2a DnaJ CCaMK CYCLOPS SymRK EPP1 HYP3 CCD RFCa RFCb KinG1 KinG2 VAPYRIN LIN CASTOR EXO70 FatM NFP SEC SYN CYTB561 GRAS HEP TAU OM Cyanobacteria RNS Ericoid-like EcM Data TypeData Amborella trichopoda Spirodela polyrhiza Zostera marina Apostasia shenzhenica Phalaenopsis equestris Dendrobium catenatum Ananas comosus Musa acuminata Oryza sativa Hordeum vulgare Brachypodium distachyon Setaria italica Sorghum bicolor Zea mays PH207 Nelumbo nucifera Dianthus caryophyllus Beta vulgaris ssp. vulgaris KWS2320 Chenopodium quinoa Spinacia oleracea Helianthus annuus Daucus carota Fraxinus excelsior Utricularia gibba Nicotiana benthamiana Petunia axillaris Capsicum annuum cvCM334 Solanum lycopersicum Solanum pennellii Citrus clementina Citrus sinensis Gossypium raimondii Theobroma cacao Carica papaya Tarenaya hassleriana Eutrema salsugineum Brassica oleraceae capitata Brassica rapa FPsc Boechera stricta Capsella grandiflora Capsella rubella Arabidopsis thaliana Arabidopsis lyrata Arabidopsis halleri Cephalotus follicularis Manihot esculenta Ricinus communis Populus trichocarpa Cercis canadensis Chamaecrista fasciculata Mimosa pudica Castanospermum australe Lupinus angustifolius Angiosperms Nissolia schottii Arachis ipaensis Arachis duranensis Arachis hypogaea Lotus japonicus Cicer arietinum ICC4958 Medicago truncatula Trifolium pratense Trifolium subterraneum Cajanus cajan Glycine max Phaseolus vulgaris Vigna angularis Vigna radiata Vigna unguiculata Castanea mollissima Quercus robur Juglans regia Casuarina glauca Alnus glutinosa Datisca glomerata Begonia fuchsioides Momordica charantia Cucurbita maxima Cucurbita moschata Cucurbita pepo Citrullus lanatus subsp. vulgaris 97103 Lagenaria siceraria Cucumis melo Cucumis sativus PI183967 Morus notabilis Ziziphus jujuba cv. Dongzao Discaria trinervis Humulus lupulus Trema orientalis Parasponia andersonii Dryas drummondii Rubus occidentalis Rosa chinensis Potentilla micrantha Fragaria vesca Fragaria x ananassa Malus domestica Pyrus x bretschneideri Pyrus communis Prunus avium Prunus mume Prunus dulcis Prunus persica Cycas micholitzii Dioon edule Encephalartos barteri Stangeria eriopus Ginkgo biloba Ephedra sinica Gnetum montanum Welwitschia mirabilis Cedrus libani Keteleeria evelyniana Abies lasiocarpa Pseudolarix amabilis Tsuga heterophylla Nothotsuga longibracteata Larix speciosa Pseudotsuga menziesii Pseudotsuga wilsoniana Picea abies Picea engelmannii Cathaya argyrophylla Picea glauca Picea sitchensis Pinus parviflora Pinus sylvestris Pinus pinaster Pinus jeffreyi Pinus ponderosa Pinus taeda Pinus radiata Araucaria rulei Wollemia nobilis Agathis robusta Agathis macrophylla Phyllocladus hypophyllus Lepidothamnus sp. Prumnopitys andina Sundacarpus amarus Manoao colensoi Lagarostrobos franklinii Parasitaxus usta Halocarpus bidwillii Saxegothaea conspicua Microcachrys tetragona Acmopyle pancheri Dacrycarpus compactus Gymnosperms Dacrydium balansae Falcatifolium taxoides Nageia nagi Retrophyllum minus Podocarpus coriaceus Podocarpus rubens Sciadopitys verticillata Cephalotaxus harringtonia Amentotaxus argotaenia Torreya nucifera Torreya taxifolia Austrotaxus spicata Pseudotaxus chienii Taxus baccata Taxus cuspidata Cunninghamia lanceolata Taiwania cryptomerioides Athrotaxis cupressoides Metasequoia glyptostroboides Sequoiadendron giganteum Glaucum Sequoia sempervirens Cryptomeria japonica Taxodium distichum Glyptostrobus pensilis Austrocedrus chilensis Papuacedrus papuana Pilgerodendron uviferum Widdringtonia cedarbergensis Diselma archeri Neocallitropsis pancheri Callitris gracilis Callitris macleayana Thujopsis dolabrata Thuja plicata Chamaecyparis lawsoniana Fokienia hodginsii Juniperus scopulorum Cupressus dupreziana Calocedrus decurrens Microbiota decussata Platycladus orientalis Tetraclinis sp. Equisetum hyemale Equisetum diffusum Tmesipteris parva Psilotum nudum Botrypus virginianus Sceptridium dissectum Ophioglossum petiolatum Ophioglossum vulgatum Marattia sp. Angiopteris evecta Osmunda sp. Osmundastrum cinnamomeum Osmunda javanica Osmunda regalis Crepidomanes venosum Hymenophyllum bivalve Hymenophyllum cupressiforme Dipteris conjugata Sticherus lobatus Anemia tomentosa Lygodium japonicum Pilularia globulifera Salvinia cucullata Azolla cf. caroliniana Azolla filiculoides Thyrsopteris elegans Cyathea spinulosa Plagiogyria japonica Culcita macrocarpa Lindsaea linearis Lindsaea microphylla Dennstaedtia davallioides Cryptogramma acrostichoides Pityrogramma trifoliata Pteris ensiformis Pteris vittata Adiantum aleuticum Adiantum raddianum Monilophytes Vittaria appalachiana Vittaria lineata Gaga arizonica Argyrochosma nivea Myriopteris rufa Notholaena montieliae Parahemionitis cordata Didymochlaena truncatula Leucostegia immersa Athyrium filix-femina Bolbitis repanda Polystichum acrostichoides Nephrolepis exaltata Davallia fejeensis Phlebodium pseudoaureum Phymatosorus grossus Pleopeltis polypodioides Polypodium hesperium Polypodium amorphum Polypodium glycyrrhiza Thelypteris acuminata Woodsia ilvensis Woodsia scopulina Homalosorus pycnocarpos Asplenium nidus Asplenium platyneuron Blechnum spicant Onoclea sensibilis Deparia lobato-crenata Diplazium wichurae Gymnocarpium dryopteris Cystopteris reevesiana Cystopteris utahensis Cystopteris fragilis Cystopteris protrusa Pseudolycopodiella caroliniana Diphasiastrum digitatum Dendrolycopodium obscurum Lycopodium annotinum Lycopodium deuterodensum Lycopodiella appressa Phylloglossum drummondii Huperzia selago Huperzia squarrosa Huperzia lucidula Huperzia myrsinites Isoetes sp. Lycophytes Isoetes tegetiformans Selaginella selaginoides Selaginella kraussiana Selaginella lepidophylla Selaginella wallacei Selaginella acanthonota Selaginella stauntoniana Selaginella willdenowii Selaginella moellendorffii Selaginella apoda Leiosporoceros dussii Anthoceros angustus Phaeoceros carolinianus Paraphymatoceros hallii Megaceros flagellaris Hornworts Nothoceros aenigmaticus Nothoceros vincentianus mixed species Treubia lacunosa Blasia sp. Sphaerocarpos texanus Lunularia cruciata Marchantia emarginata Marchantia polymorpha Marchantia paleacea Conocephalum conicum Monoclea gottschei Ricciocarpos natans Pallavicinia lyellii Pellia cf. epiphylla Pellia neesiana Metzgeria crassipilis Liverworts Ptilidium pulcherrimum Radula lindenbergiana Porella navicularis Porella pinnata Frullania sp. Frullania spp. Scapania nemorosa Barbilophozia barbata Schistochila sp. Bazzania trilobata Calypogeia fissa Odontoschisma prostratum Takakia lepidozioides Sphagnum palustre Sphagnum lescurii Sphagnum recurvum Sphagnum fallax Andreaea rupestris Tetraphis pellucida Atrichum angustatum Polytrichum commune Diphyscium foliosum Buxbaumia aphylla Encalypta streptocarpa Physcomitrella patens Physcomitrium sp. Timmia austriaca Racomitrium elongatum Racomitrium varium Syntrichia princeps Leucobryum albidum Leucobryum glaucum Ceratodon purpureus Scouleria aquatica Dicranum scoparium Mosses Hedwigia ciliata Philonotis fontana Plagiomnium insigne Rosulabryum cf. capillare Bryum argenteum Orthotrichum lyellii Aulacomnium heterostichum Fontinalis antipyretica Thuidium delicatulum Leucodon brachypus Leucodon julaceus Rhynchostegium serrulatum Pseudotaxiphyllum elegans Stereodon subimponens Calliergon cordifolium Claopodium rostratum Neckera douglasii Anomodon attenuatus Climacium dendroides Loeskeobryum brevirostre

AMS loss Ortholog Absent (in genome) Symbiosis Genome Homolog (inc. paralog) Not Detected (in transcriptome) No symbiosis Transcriptome Not determined Supplementary Figure 2: Maximum likelihood tree of RAD1.

Ambtri evm 27.model.AmTr v1.0 scaffold00049.33

Horvul HORVU3Hr1G088820.1

Horvul HORVU3Hr1G088780.2

Orysat LOC Os01g67670.1 Musacu GSMUA Achr8T01180 001 Orysat LOC Os01g67650.1

Psechi 2081916 YLPM Conifers.p1

Psinud 2017449 QVMR Eusporangiate Monilophytes.p1 Bradis Bradi2g57940.1 Ausspi 2077149 BTTS Conifers.p1 Taxbac 2003837 WWSS Conifers.p1 Anacom Aco004673.1

Podcor 2050823 SCEB Conifers.p1

Marpal 2014890 LFVP Liverworts 2 samples combined.p1 Marpal 2011252 IHWO Liverworts mycorrizal.p1

Setita Seita.5G418700.1 Sorbic Sobic.003G392800.1

Zeamay Zm00008a013022

Daucar DCAR 031178

Riccom 29929.m004746

Manesc Manes.13G013600.1

Thecac Thecc1EG010708t1

Citsin orange1.1g037028m

Ginbil Gb 25388 Citcle Ciclev10031305m

Querob Qrob P0094610.2

Jugreg g19108.t1

Casgla Casgl41S01891 Selmoe 83811 Alnglu Alngl16107S17488 Marpal scaff8805 FGenesh3.1 Luncru 2014175 TXVB Liverworts.p1 Alnglu Alngl16107S17478

Zizjuj lcl NC 029688.1 XP 015894512.1 26725 Scanem 2015448 IRBN Liverworts.p1 Drydru Drydr13S00526

100 Maldom MDP0000464809

Calfis 2018351 RTMU Liverworts.p1 84.3

99.4

92.7 96.8 Pyrcom PCP044084.1

100 100 Pruavi Pav sc0002479.1 g590.1.mk Marpal scaff3964 FGenesh2.1 Prumum lcl NC 024127.1 XP 008222011.1 6861 96.5

100 100

99.4 95.4 95.7 Prudul Prudul26A009965P1

100 98.9 Pruper Prupe.1G237500.1 99.7

94.5 89.5 Rubocc Bras G07211 99.7

99.3 100 Roschi RchiOBHm Chr4g0431901 98.7 88.8 99 Potmic 28337 t 100 Vigang vigan.Vang11g07370.1 Fraves FvH4 4g24820.1

98.5 100 Fraana FAN iscf00002238.1.g00002.1 Vigrad Vradi07g14730.1 99.4 Fraana FAN iscf00078592.1.g00001.1 94.1 93.8 98.6 Vigung Vigun03g315800.1 97.8

99.9 99.7 100 Fraana FAN iscf00155624.1.g00001.1 100 Phavul Phvul.003G208600.1 87.9 100 Daucar DCAR 007469 100

99 Daucar DCAR 026212 Cajcaj Ccajan 11226 94.9 100 99.8 100 100 Glymax Glyma.17G127500.1 Helann HanXRQChr05g0154681 100 96.4 Helann HanXRQChr16g0497891 98.1 100 Glymax Glyma.05G045300.1 99.9 94.8 99.5 Helann HanXRQChr09g0272901 Trisub lcl DF973985.1 GAU43614.1 32672 100 100 Fraexc FRAEX38873 v2 000040660.1 99.7 Tripra Tp57577 TGAC v2 mRNA38803 Fraexc FRAEX38873 v2 000003780.1 100 98.4 91.3 95.9 Capann CA03g24270 Medtru MtrunA17 Chr4g0057891 97.9 100 Cicari Ca 21067.1 100 Sollyc Solyc03g110950.1.1 85.9 Solpen Sopen03g030140.1 100 96.5 Lotjap Lj4g3v1389110.1 Nicben Niben101Scf15120g01016.1 97.7 Nissch Nissc5453S10500 95.5 97.1 99.4 100 Nicben Niben101Scf04328g00054.1 100 96.5 100 Petaxi Peaxi162Scf01390g00037.1 85.7 99 Casaus Castanospermum11400-PA Petaxi Peaxi162Scf00089g00027.1 Cercan Cerca4S03608 84.2

100 100 Petaxi Peaxi162Scf01390g00007.1

100 Mimpud Mimpu7210S04424 Zizjuj lcl NC 029683.1 XP 015882278.1 14060

90.3 99 Chafas Chafa3254S09087 89.8 Distri Distr238S19353

100 99.9 99.9 100 99.5 Mornot L484 006916

98.5 Mimpud Mimpu8656S28022 99.3 94.3 99.9

98.6 99.9 99.7 Parand lcl JXTB01000326.1 PON45613.1 25726

Casgla Casgl177S03923 100 99.8 100 Treori lcl JXTC01000150.1 PON85303.1 18973

100 100 98.8 98.8 100 Alnglu Alngl50020S41686Jugreg g6040.t1 86.6 Drydru Drydr295S10168

Rubocc Bras G01975

100 Roschi RchiOBHm Chr7g0190881

Potmic 29102 t Cucsat evm.model.Chr1.80 Fraves FvH4 5g07610.1

Pruavi Pav sc0000261.1 g150.1.mk Cucmel MELO3C026237.2.1 Citlan Cla019248 Lagsic Lsi06G016090.1 Prumum lcl NC 024132.1 XP 008239620.1 23255

Pruper Prupe.5G156100.1

Prudul Prudul26A022858P1

Pyrcom PCP039959.1

Pyrbre lcl NW 008988474.1 XP 009336573.1 33581

Pyrbre lcl NW 008988108.1 XP 009359535.1 12358

Pyrcom PCP023344.1

Cucpep Cp4.1LG04g15890.1 Maldom MDP0000431628

Maldom MDP0000258655

Maldom MDP0000259403

Manesc Manes.14G054900.1

Cucmax CmaCh11G000570.1

Cucmos CmoCh11G000590.1

Begfuc Begfu10926S06942 Begfuc Begfu786S13893

Datglo Datgl1085S18072 Datglo Datgl621S11923

Gosrai Gorai.006G270800.1 Citcle Ciclev10019777m Thecac Thecc1EG014574t1

Citsin orange1.1g040125m Riccom 30147.m013794

Poptri Potri.012G093900.1

Poptri Potri.015G091200.1

Momcha lcl NW 019104494.1 XP 022135579.1 6548

Tree scale: 0.1 Supplementary Figure 3: Maximum likelihood tree of STR1/STR2.

Casmol snap masked-scaffold02140-abinit-gene-0.12-mRNA-1 Parand lcl JXTB01000130.1 PON60443.1 15242 Treori lcl JXTC01000362.1 PON60712.1 28403

Zizjuj lcl NC 029683.1 XP 015883601.1 15458

Roschi RchiOBHm Chr7g0178121 Roschi RchiOBHm Chr3g0493261

Humlup HL.SW.v1.0.G008675.1 Humlup HL.SW.v1.0.G008677.1 Ambtri evm 27.model.AmTr v1.0 scaffold00060.152 Humlup HL.SW.v1.0.G008676.1

Rubocc Bras G03627

Mornot L484 004555 Mornot L484 004554 Alnglu Alngl13943S00925

Potmic 8648 t

Begfuc Begfu13278S46660 Casgla Casgl66S20855 Jugreg g28179.t1 Begfuc Begfu1494S01078 Jugreg g43297.t1

Zeamay Zm00008a036926 Sorbic Sobic.007G095100.1 Horvul HORVU5Hr1G060690.4

Fraana FAN icon20124905.1.g00001.1 Fraves FvH4 5g17530.1 Fraana FAN iscf00177692.1.g00001.1 Fraana FAN iscf00297730.1.g00001.1 Fraana FAN iscf00233882.1.g00001.1 Drydru Drydr192S07836 Setita Seita.6G098800.1 Pruavi Pav sc0000103.1 g860.1.mk Prumum lcl NC 024132.1 XP 008240289.1 23887 Prudul Prudul26A015441P1 Musacu GSMUA Achr9T27200 001 Pruper Prupe.5G235100.1 Maldom MDP0000243323 Pyrbre lcl NW 008988114.1 XP 018503790.1 12882 Orysat LOC Os09g23640.1 Pyrcom PCP015737.1 Bradis Bradi4g29810.2 Selsta 2011171 ZZOL Lycophytes.p2 Maldom MDP0000755262 Maldom MDP0000847967 Pyrcom PCP009903.1 Marpal 2015253 LFVP Liverworts 2 samples combined.p1 Pyrbre lcl NW 008988083.1 XP 009356016.1 9140 Marpal 2011583 IHWOSelwil Liverworts2013634 KJYC mycorrizal.p1 Lycophytes.p2 Cercan Cerca449S24705 Anacom Aco001046.1 Chafas Chafa4242S09852 Selkra 2008979 ZFGK Lycophytes.p1 Mimpud Mimpu1109S05408 Chafas Chafa95284S29316 Nissch Nissc3167S21270 Aradur Aradu.CH84G

99.9 Arahyp arahy.Tifrunner.gnm1.ann1.H0WU6V.1 99.5 80.2

87.7

Selmoe 134275 99.1 100 Araipa Araip.55F8V

100 Arahyp arahy.Tifrunner.gnm1.ann1.K59KPA.1

100 100 97.1 Casaus Castanospermum15031-PA Marpal scaff13491 FGenesh2.1 100 98.2 Luncru 2011164 TXVB Liverworts.p1 99.7

97.2 Nissch Nissc524419S09916

100 99.6 100 98.3 100 98.5 Lotjap Lj4g3v3115140.1 Cicari Ca 15399.1

99.3 100 Medtru MtrunA17 Chr8g0393191 89.4 99.5 100 98.9

99.3 Trisub lcl DF973126.1 GAU12786.1 1844 96.1 99.9 100 99.6 Tripra Tp57577 TGAC v2 mRNA1489 100 89.8 100 Cajcaj Ccajan 23099 99.9 99.3 Glymax Glyma.05G247100.1 94.5 Outgroup 100 Glymax Glyma.08G055500.1 99.9 99.4 100 Phavul Phvul.002G331200.1 99.9 94.5 100 Vigung Vigun03g002500.1 100 Vigrad Vradi01g02650.1

99 97.3 Vigang vigan.Vang10g00290.1 94.5 10099.9 100 Datglo Datgl554S11232 98.9 Solpen Sopen09g036340.1 100 Momcha lcl NW 019104497.1 XP 022137340.1 8922 99 88.9 99.6 Sollyc Solyc09g098410.1.1 98.9 Cucmax CmaCh18G000790.1 100 Cucpep Cp4.1LG09g11180.1 Nicben Niben101Scf03036g07014.1Capann CA03g03110 100 Cucsat evm.model.Chr1.717 100 Cucmel MELO3C002142.2.1 Petaxi Peaxi162Scf00286g00240.1 100 100 99.6 100 Citlan Cla018446 100 94.9 Nicben Niben101Scf05548g02015.1 87.2 100 90.2 Lagsic Lsi02G002440.1 STR1 100 Poptri Potri.012G045100.1 Petaxi Peaxi162Scf00378g00624.1 100 89.3 Poptri Potri.015G036100.2 Nicben Niben101Scf05548g02014.1 100 Manesc Manes.06G004300.1 100 100 Fraexc FRAEX38873 v2 000347150.2 99.9 Riccom 29653.m000293 99.2 Fraexc FRAEX38873 v2 000347150.1 99.5 100 Carpap evm.model.supercontig 3.375 99.9 Thecac Thecc1EG012911t1 Fraexc FRAEX38873 v2 000006480.1 100 Gosrai Gorai.007G108700.1 98.7 82.9 100 Helann HanXRQChr11g0324351 100 Gosrai Gorai.008G290900.1

Helann HanXRQChr15g0474021 99.8 97.9 Citcle Ciclev10033370m 100 Citcle Ciclev10007469m Helann HanXRQChr11g0324341 99 96.9 Citsin orange1.1g003437m Daucar DCAR 021457 99.4 100 Fraexc FRAEX38873 v2 000260100.2 100 Manesc Manes.13G104000.1 99.8 86.5 100 Fraexc FRAEX38873 v2 000260100.1 Riccom 28333.m000560 100 Daucar DCAR 011619 Poptri Potri.007G004800.1 STR2 Daucar DCAR 003539 100 95.4 100 Helann HanXRQChr12g0375201 Gosrai Gorai.007G230200.1 97.7 100 Petaxi Peaxi162Scf00282g00221.1 100 100 Thecac Thecc1EG000922t1 100 100 Capann CA08g10400 98.1 92.9 100 Citsin orange1.1g039035m 89.7 Solpen Sopen01g041100.1 99.9 95.6 Citcle Ciclev10026941m 100 100 Sollyc Solyc01g097430.2.1 99.7 83 99.4 Nicben Niben101Scf01696g06031.1 100 100 Nicben Niben101Scf02792g01032.1 Alnglu Alngl603S33202 Carpap evm.model.supercontig 755.4 99.8 Nicben Niben101Scf01696g06047.1 Alnglu Alngl2271S20974 Luncru 2074553 TXVB Liverworts.p1 Marpal 2009148 IHWO Liverworts mycorrizal.p1 Casgla Casgl291S14103Jugreg g49004.t1 100 100 99.8 99.9 99.1 Marpal 2012505 LFVP Liverworts 2 samples combined.p1 Jugreg g12291.t1 99.8 82.1 99.7 100 96.4 Marpal scaff5479 FGenesh8.1 Selkra 2041662 ZFGK Lycophytes.p1 100 99.6 Selwil 2001723 KJYC Lycophytes.p1 99.8 Selmoe 90494 Querob Qrob P0386870.2 100 100 Selapo 2007686 LGDQ Lycophytes.p1 Linlin 2097259 NOKI Leptosporangiate Monilophytes.p1 Cucsat evm.model.Chr6.3080 97.2 99.6 Cryacr 2067547 WQML Leptosporangiate Monilophytes.p1 CucmelLagsic MELO3C007696.2.1 Lsi01G008290.1Citlan Cla014087 100 99.9 Anacom Aco010077.1 100 100 Musacu GSMUA Achr4T27670 001 100 99 Bradis Bradi2g26560.1 Casmol augustus masked-scaffold15843-abinit-gene-0.0-mRNA-1 99.4 100 Horvul HORVU3Hr1G066220.2 99.7 100 99.9 95.8 98.2 87.2 100 82.9 Setita Seita.5G287400.1 93.2 99.3 100 95.2 Cucmos CmoCh07G005930.1 100 99 Sorbic Sobic.003G271300.1 96.7

97.2 99.8 94.4 99.7 95.5 88.5 Cucpep Cp4.1LG19g10300.1 99.9 Zeamay Zm00008a014037

100 100 99.9 Ambtri evm 27.model.AmTr v1.0 scaffold00046.166

100 98.7 Cucmax CmaCh07G005880.1 91.1 Begfuc Begfu848S14152 Datglo Datgl115S01120 100 Zizjuj lcl NC 029686.1 XP 015890494.1 22594 Araipa Araip.9Z02C Distri Distr3496S22917 Mornot L484 016115 Araipa Araip.90JFZ Humlup HL.SW.v1.0.G008704.1 Humlup HL.SW.v1.0.G008705.1 Parand lcl JXTB01000482.1 PON38886.1 30915 Treori lcl JXTC01000034.1 PON97101.1 7152 Drydru Drydr87S24490 Rubocc Bras G11212 Aradur Aradu.XYY87 Roschi RchiOBHm Chr7g0221691 Roschi RchiOBHm Chr7g0218751 Potmic 17353 t Momcha lcl NW 019104492.1 XP 022132948.1 4903 Fraana FAN icon19358323.1.g00001.1 Fraves FvH4 5g29080.1 Arahyp arahy.Tifrunner.gnm1.ann1.8ZQ67F.1 Fraana FAN icon20593788.1.g00001.1 Fraana FAN iscf00173852.1.g00001.1 Fraana FAN iscf00345394.1.g00001.1 Pruavi Pav sc0002388.1 g050.1.mk Prumum lcl NC 024126.1 XP 008236580.1 1962 Pruper Prupe.6G208600.1 Prudul Prudul26A025593P1 Maldom MDP0000153802 Nissch Nissc524545S10090 Vigrad Vradi11g09080.1

Cajcaj Ccajan 12296 Arahyp arahy.Tifrunner.gnm1.ann1.NS7HT9.1 Vigung Vigun02g088600.1 Vigang vigan.Vang0002ss02220.1 Arahyp arahy.Tifrunner.gnm1.ann1.C2LWE2.1 Phavul Phvul.002G143300.1 Cicari Ca 24301.1

Glymax Glyma.01G020000.1 Glymax Glyma.09G202400.1

Lotjap Lj2g3v1467930.1 Lotjap Lj0g3v0104499.1 Cercan Cerca9S31707

Chafas Chafa70S26063 Pyrcom PCP025048.1

Pyrcom PCP029502.1

Medtru MtrunA17 Chr5g0411621

Maldom MDP0000211382

Tripra Tp57577 TGAC v2 mRNA38248 Mimpud Mimpu26253S21137

Trisub lcl DF973800.1 GAU40328.1 29386

Casaus Castanospermum23650-PA

Pyrbre lcl NW 008988912.1 XP 009345867.1 42031

Pyrbre lcl NW 008988155.1 XP 009364791.1 17169

Tree scale: 0.1 Supplementary Figure 4: Maximum likelihood tree of RAM1.

Tree scale: 0.1

Parand lcl JXTB01000122.1 PON61262.1 14641

Treori lcl JXTC01000045.1 PON95419.1 8942

Humlup HL.SW.v1.0.G029910.1

Distri Distr1117S12120

Zeamay Zm00008a015347

Sorbic Sobic.005G123000.1 Mornot L484 005656

Setita Seita.8G129500.1

Bradis Bradi4g18390.1 Ambtri evm 27.model.AmTr v1.0 scaffold00016.177 Orysat LOC Os11g31100.1

ijjlcl NCZizjuj 029687.1 XP 024933321.1 26212

Zizjuj lcl NW 015453618.1 XP 024924028.1 36247 Musacu GSMUA Achr6T20830 001 Rubocc Bras G03769

Roschi RchiOBHm Chr2g0176081

Anacom Aco003635.1 Potmic 27311 t

Fraves FvH4 6g53920.1

Tmepar 2001218 ALVQ Eusporangiate Monilophytes.p1 Fraana FAN iscf00315581.1.g00001.1

Parhal 2010384 FAJB Hornworts.p1 Drydru Drydr690S13573

Pruavi Pav sc0001080.1 g690.1.mk

Prumum lcl NC 024129.1 XP 008231070.1 15356

Prudul Prudul26A019943P1

Pruper Prupe.3G309800.1

97.5 Maldom MDP0000441376 Taklep 2080055 SKQD Mosses.p1 93.5

Selmoe 88990 Pyrcom PCP007261.1

Maldom MDP0000263576

100 Pyrcom PCP022669.1 87 100 99.8

100 100 Pyrbre lcl NW 008988793.1 XP 009344215.1 40553

99.5 100

100 98.5 Pyrbre lcl NW 008989490.1 XP 009350709.1 46450

99.6 99.8 100 Sollyc Solyc02g094340.1.1 99.8 99.3 Pyrbre lcl NW 008988356.1 XP 009378007.1 29287

92.7 100 99.993.3 Begfuc Begfu1780S22682

Solpen Sopen02g038990.1 90.3

96.4 83.5 99 Begfuc Begfu2539S27580 Capann CA02g31050 100 100

99.8 98.3 Momcha lcl NW 019104493.1 XP 022133663.1 6389 Nicben Niben101Scf38644g00002.1 100 90.5 Cucmax CmaCh04G029840.1

82.3 Nicben Niben101Scf02188g02020.1 98.8 100 Cucmos CmoCh04G031040.1 100 100

94.5 Petaxi Peaxi162Scf00420g00650.1 98.2 Cucpep Cp4.1LG01g26010.1

99.4 100 Cucmel MELO3C008170.2.1 99.9 Fraexc FRAEX38873 v2 000038020.1 97.8 91.5 99.9 Cucsat evm.model.Chr2.2522

89.4 Fraexc FRAEX38873 v2 000295380.1 99.7 98 Citlan Cla011849 100 99.9 Daucar DCAR 015927 100 85.9 Lagsic Lsi03G004130.1

99.6 99 89.8 Daucar DCAR 014493 100 Carpap evm.model.supercontig 70.116 100 99.4 99.5 Cercan Cerca69S04384

97 100 95.5 86 86.9 Helann HanXRQChr09g0256471 100 Mimpud Mimpu25419S20895 99 100

100 100 Helann HanXRQChr15g0486991 100 Chafas Chafa8363S27424 85.7

100

Citsin orange1.1g045762m 100 84 Casaus Castanospermum27502-PA

100

96 Citcle Ciclev10018153m 99.6 Medtru MtrunA17 Chr7g0224271

Cicari Ca 05630.1

Thecac Thecc1EG017269t1 Tripra Tp57577 TGAC v2 mRNA8863

Trisub lcl DF973265.1 GAU23211.1 12269 Gosrai Gorai.006G044300.1 Nissch Nissc6072S29437

Arahyp arahy.Tifrunner.gnm1.ann1.8PQZ09.1 Manesc Manes.11G083500.1 Riccom 30131.m007029 Aradur Aradu.N7IXY

Arahyp arahy.Tifrunner.gnm1.ann1.SRU6K5.1

Jugreg g44947.t1 Araipa Araip.N9QES

Poptri Potri.001G326000.1 Cajcaj Ccajan 30022

Cajcaj Ccajan 30026 Jugreg g44947.t2 Glymax Glyma.19G096400.1

Glymax Glyma.16G053000.1

Phavul Phvul.001G089900.2

Jugreg g49241.t1

Casgla Casgl74S21680

Alnglu Alngl140824S16233

Querob Qrob P0187370.2

Vigrad Vradi0146s00200.1

Vigung Vigun01g073400.1

Vigang vigan.Vang04g12880.1

Casmol maker-scaffold23116-augustus-gene-0.5-mRNA-1 Supplementary Figure 5: Maximum likelihood tree of ABCB12.

Fraexc FRAEX38873 v2 000112370.1

Helann HanXRQChr04g0094461

Helann HanXRQChr09g0277141

Zeamay Zm00008a007925

Sorbic Sobic.006G014800.1 Daucar DCAR 022660

Setita Seita.7G029100.1 Orysat LOC Os03g08380.1 Horvul HORVU4Hr1G077060.4

Musacu GSMUA Achr2T07290 001 Ambtri evm 27.model.AmTr v1.0 scaffold00007.341

Bradis Bradi1g72517.2 Fraexc FRAEX38873 v2 000156330.1 Petaxi Peaxi162Scf00038g01953.1

Nicben Niben101Scf18000g00029.1

Capann CA03g35390

Sollyc Solyc03g122070.1.1

Solpen Sopen03g040850.1

100 Anacom Aco003987.1 Sollyc Solyc03g122050.1.1

100 Poptri Potri.001G165000.1

Manesc Manes.11G015600.1

Phacar 2001981 WCZBParhal Hornworts 2057582 gametophyte.p1 FAJB Hornworts.p1 Riccom 29727.m000475

100 Thecac Thecc1EG029206t1 Ginbil Gb 07563 100

Phacar 2025234 RXRQ Hornworts sporophyte.p1 Gosrai Gorai.011G057300.1

100 99.8 100 100 Carpap evm.model.supercontig 25.158 95.5

100

100 99.9

99.6 Citsin orange1.1g000406m

99.7

99.9 Citcle Ciclev10027300m

100 100 Chafas Chafa874S27754 100

98.7

100 98.6 Mimpud Mimpu22231S19975

100 Cercan Cerca15S15461 100 100

Maldom MDP0000254397 Mimpud Mimpu6012S26048 100

Maldom MDP0000399961 Chafas Chafa95477S29793

Pyrbre lcl NW 008988363.1 XP 018507797.1 29629 100 100 Casaus Castanospermum26517-PA 100 100 82.5 Nissch Nissc1777S16564 100 100 Pyrcom PCP026406.1 100 99.2 Arahyp arahy.Tifrunner.gnm1.ann1.BB2RVD.1

100 99.8 Pyrbre lcl NW 008988479.1 XP 009336717.1 33737 98.8 Araipa Araip.3CT26 100 100 100 Pyrcom PCP029438.1 100 Arahyp arahy.Tifrunner.gnm1.ann1.WYBN0Q.2 100 95.8

Aradur Aradu.FXB1F Maldom MDP0000248803 98.9 97.9 100 100 Cajcaj Ccajan 00541

Prudul Prudul26A013685P1 98.6

100 Glymax Glyma.16G011000.1 100 Pruper Prupe.3G036400.1 99.5 99.4 Phavul Phvul.010G126200.1 99.8 91.4 100 100 97.1 Vigung Vigun10g161000.1

100 Prumum lcl NC 024129.1 XP 008228350.2 12621 Vigrad Vradi09g02720.1 Drydru Drydr490S22706 100 99.7 100 Potmic 4601 t 100 99.3 Vigang vigan.Vang0071ss00950.1 100

100 100 100 100 Lotjap Lj3g3v2576200.1

93.1 100 100 Fraves FvH4 6g35260.1 99.4

99.2 Lotjap Lj3g3v2576200.2

100

100 98.6 Cicari Ca 19418.1

100 Medtru MtrunA17 Chr8g0344651 Roschi RchiOBHm Chr2g0146621 99.9

100

99.1 99.9 Tripra Tp57577 TGAC v2 mRNA17252

98.5

100 88.8 100 Trisub lcl DF973513.1 GAU33025.1 22083

Querob Qrob P0599690.2 Treori lcl JXTC01000058.1 PON93473.1 10752 Casmol maker-scaffold16925-snap-gene-0.10-mRNA-1 Mornot L484 005037 Humlup HL.SW.v1.0.G013029.1 Casgla Casgl31S15253

Parand lcl JXTB01000368.1 PON43566.1 27259 Alnglu Alngl9958S38225

Jugreg g46195.t1

Jugreg g34733.t1

Datglo Datgl534S31625 Distri Distr1387S14172 Begfuc Begfu724S40358

Momcha lcl NW 019104489.1 XP 022148825.1 2230

Cucmos CmoCh08G007880.1

Cucmel MELO3C024330.2.1 Zizjuj lcl NC 029679.1 XP 015901521.1 3504 Citlan Cla015527

Lagsic Lsi02G028790.1 Cucsat evm.model.Chr7.2194

Cucpep Cp4.1LG12g09410.1

Cucmos CmoCh17G006490.1

Cucmax CmaCh17G006690.1 Cucpep Cp4.1LG17g04260.1

Cucmax CmaCh08G008150.1

Tree scale: 0.1 Supplementary Figure 6: Maximum likelihood tree of ABCB20.

Marpal 2086054 LFVP Liverworts 2 samples combined.p1

Ambtri evm 27.model.AmTr v1.0 scaffold00018.111

Marpal 2068120 IHWO Liverworts mycorrizal.p1

Musacu GSMUA Achr10T07980 001 Musacu GSMUA

Marpal 2005644 LFVP Liverworts 2 samples combined.p1

Taicry 2002350 QSNJ Conifers.p1 Marpal scaff16487 FGenesh3.1 Marpal 2005646 LFVP Liverworts 2 samples combined.p1 Taicry 2002351 QSNJ Conifers.p1

Marpal 2005643 LFVP Liverworts 2 samples combined.p1 Parhal 2006821 FAJB Hornworts.p1

Marpal 2005645 LFVP Liverworts 2 samples combined.p1

Selmoe 75690

Anacom Aco013278.1 Selmoe 84555 Setita Seita.6G060300.1 Sorbic Sobic.007G042600.1

Zeamay Zm00008a037305

Orysat LOC Os08g05690.1

Marpal scaff149 FGenesh3.1 Bradis Bradi3g17020.1

Horvul HORVU7Hr1G071870.23

Orysat LOC Os08g05710.1

100 Bradis Bradi3g17010.1

100 Horvul HORVU0Hr1G015570.6 Ricnat 2002405Marpol WJLO Mapoly0023s0157.1 Liverworts.p1

99.9 Setita Seita.6G060200.1 100

Sorbic Sobic.007G042700.1 BlaspNW c332454 g2 i5 m.123922 99.2 Zeamay Zm00008a015573 100 100 100 100 BlaspNW c332454 g2 i3 m.123913 95.8 Helann HanXRQChr15g0497031

99

Daucar DCAR 020392 BlaspNW c332454 g2 i2 m.123910

100 Fraexc FRAEX38873 v2 000081070.1

Nicben Niben101Scf01063g11014.1

Nicben Niben101Scf04231g01028.1 97.1 Petaxi Peaxi162Scf00815g00244.1 100

100 99.3 100 Nicben Niben101Scf02249g01017.1 100

100 Capann CA06g21480 Fraana FAN iscf00078156.1.g00001.1 100 Sollyc Solyc06g072960.1.1

100

99.2 Solpen Sopen06g029310.1 Fraves FvH4 7g33380.1 100

96.1 Citcle Ciclev10006992m 92.8 Fraves FvH4 7g32320.1 99.8 88.4 97.7 Citsin orange1.1g048639m 100 100 100 Fraves FvH4 7g32300.1 100 100 99.8 Poptri Potri.015G000200.2 100 96.6 Potmic 23394 t Manesc Manes.05G196700.1 100 100 100 Roschi RchiOBHm Chr1g0383351 Riccom 30098.m001722 100 83.7 Carpap evm.model.supercontig 3.192 Rubocc Bras G09002 89.7 97.4 Thecac Thecc1EG007638t1 Drydru Drydr2S17589 100 Gosrai Gorai.005G214200.1 99 83.9 98.5 100 Pruper Prupe.2G322600.1 Gosrai Gorai.013G066600.1

100 100 Prudul Prudul26A005897P1 Jugreg g38700.t1 99.9

99.9 Casgla Casgl64S05807

99.2 95.1 Alnglu Alngl31122S23751 Prumum lcl NC 024130.1 XP 016649811.1 18720 100 Begfuc Begfu3221S30918 Pruavi Pav sc0000138.1 g260.1.mk 99.9 92.6 100 Datglo Datgl615S32898 99.5 100 Pyrcom PCP003590.1 100 Momcha lcl NW 019104539.1 XP 022148546.1 18982 Pyrbre lcl NW 008988059.1 XP 018502044.1 5298 100 Momcha lcl NW 019104539.1 XP 022148639.1 18981 100 100 Maldom MDP0000322409 99.9 100 Citlan Cla006778

99.8 88.9 Lagsic Lsi10G001910.1 Humlup HL.SW.v1.0.G039634.1 100 100 99.4 Cucmel MELO3C024781.2.1 100 Humlup HL.SW.v1.0.G035520.1 Cucsat evm.model.Chr2.2682 99.5 100

91.8 82 Cucmax CmaCh20G009630.1 97.8 Cucmos CmoCh20G009740.1 100 Mornot L484 001860 95.5 99.2 100 Cucpep Cp4.1LG16g01580.1 100 100 100 Citlan Cla006779 Treori lcl JXTC01000174.1 PON83732.1 20542 82.1 100 100

94.6 Lagsic Lsi10G001920.1

99.9 100 Cucsat evm.model.Chr2.2683 100

97.4 Parand lcl JXTB01000131.1 PON60373.1 15361 89.9 Cucmel MELO3C024777.2.1 99.1

Distri Distr667S32393 Cercan Cerca188S16832 Casaus Castanospermum20799-PA

Nissch Nissc524351S35180

Arahyp arahy.Tifrunner.gnm1.ann1.V4QB5P.1

AraipaAraip.HUC28

Arahyp arahy.Tifrunner.gnm1.ann1.YLX2VM.1

Aradur Aradu.72QL5Aradur

Parand lcl JXTB01000131.1 PON60369.1 15357

Vigrad Vradi0239s00020.1 Treori lcl JXTC01000174.1 PON83729.1 20539

Vigung Vigun09g136900.1

Vigang vigan.Vang0200s00190.1 Cajcaj Ccajan 23678

Cicari Ca 14061.1 Zizjuj lcl NC 029681.1 XP 015878605.1 10299 Phavul Phvul.009G040700.1

Glymax Glyma.06G139500.1

Medtru MtrunA17 Chr3g0128391

Medtru MtrunA17 Chr3g0128381

Trisub lcl DF973925.1 GAU42575.1 31633

Tree scale: 0.1 Supplementary Figure 7: Maximum likelihood tree of DHY.

Faltax 2083855 PLYX Conifers 2 samples combined.p2

Ambtri evm 27.model.AmTr v1.0 scaffold00065.43

Acmpan 2016518 HILW Conifers.p1

Schisp. 2101977 LGOW Liverworts.p1Calfis 2175059 RTMU Liverworts.p1

Scanem 2153696 IRBN Liverworts.p1

Scanem 2155551 IRBN Liverworts.p1

Selwal 2170480 JKAA Lycophytes.p1

Stesub 2062467 LNSF Mosses.p1 Frusp. 2014807 TGKW Liverworts.p2

Blasp. 2015105 AEXY Liverworts.p8

Blasp. 2007494 AEXY Liverworts.p7

Scedis 2084875 EEAQ Eusporangiate Monilophytes.p1

Acmpan 2016517 HILW Conifers.p1

Musacu GSMUA Achr5T01910 001

Anacom Aco004973.1

Orysat LOC Os12g43740.1

Setita Seita.3G403100.1

Selsta 2001177 ZZOL Lycophytes.p3 Zeamay Zm00008a012002

Sorbic Sobic.008G187200.1

Bradis Bradi4g00850.1

Horvul HORVU5Hr1G001540.1

Selmoe 266637 Horvul HORVU5Hr1G001570.2

Horvul HORVU5Hr1G070420.1 Marpal scaff14690 FGenesh1.1 Humlup HL.SW.v1.0.G003017.1 Pelepi 2082972 PIUF Liverworts.p1 Parand lcl JXTB01000441.1 PON40343.1 29833

Treori lcl JXTC01000068.1 PON92181.1 12002

Sphfal Sphfalx0000s0484.1 Begfuc Begfu3394S49081 Taklep 2076344 SKQD Mosses.p1 Momcha lcl NW 019104527.1 XP 022146236.1 16988

Cucmax CmaCh20G008390.1 100

99.9

97.2 Cucmos CmoCh20G008490.1

Cucpep Cp4.1LG16g02480.1

100

100 94.9

93.3 100 Citlan Cla016575 99.6

90 98.5

98.5 Lagsic Lsi10G003840.1

Manesc Manes.13G108900.1 95.7 Cucmel MELO3C023311.2.1

99.8 97.2 Manesc Manes.12G117700.1 99.9 Cucsat evm.model.Chr2.1239 95.8 99.8 97.8 100 93 100 93.7 99.8 Datglo Datgl79S13405 82.4 Riccom 28976.m000162 99.2 99.2 100 Mornot L484 012991

Poptri Potri.007G007300.1 97.4 98.7 Distri Distr1269S00486 97.8 98 Carpap evm.model.supercontig 673.1 96.5 100 Zizjuj lcl NC 029686.1 XP 015890390.1 22524 90.7 100 Gosrai Gorai.011G108600.1 82.4 100 Zizjuj lcl NW 015453974.1 XP 015868188.1 38732 100 94.7 Pruavi Pav sc0005509.1 g020.1.mk Thecac Thecc1EG000843t1 99.8 100 88.6 95.5 88.4 Prumum lcl NC 024129.1 XP 008229466.1 13853

Citcle Ciclev10026237m 87.1 100 99 90 Prumum lcl NC 024126.1 XP 008237641.1 2038

Citsin orange1.1g040339m 94.2 99.9 Pruper Prupe.6G216500.1 80.9 100 91.6 99.9 100 Alnglu Alngl702S05658 Prudul Prudul26A008819P1 99.9

96.8 Maldom MDP0000465400 Alnglu Alngl60713S05274 100 87.7

100 Pyrbre lcl NW 008988133.1 XP 009362635.1 15171 99.6 98.3 Casgla Casgl230S24580 99.8 98.8

90.2 Pyrcom PCP001900.1 Jugreg g37078.t1 92.4 93.5 95.9 82.6 96.8 Maldom MDP0000243754 99.5

100 81.3 Pyrcom PCP011509.1 99.1 100 100

97.9

85

100 Pyrbre lcl NW 008988548.1 XP 009339171.1 35939 Querob Qrob P0665560.2 100

99.6 Drydru Drydr303S03250 Capann CA02g24810 Rubocc Bras G04279 Casmol augustus masked-scaffold11701-abinit-gene-0.0-mRNA-1 Roschi RchiOBHm Chr2g0108821 Sollyc Solyc02g092060.1.1 Roschi RchiOBHm Chr2g0108801

Roschi RchiOBHm Chr2g0108811

Potmic 7752 t Nicben Niben101Scf07169g02002.1 Fraves FvH4 1g18260.1

Nicben Niben101Scf00388g03007.1 Fraana FAN icon20001001.1.g00001.1

Daucar DCAR 014353 Fraana FAN iscf00236635.1.g00001.1

Petaxi Peaxi162Scf00096g00189.1 Fraana FAN iscf00350556.1.g00002.1

Fraana FAN iscf00223784.1.g00001.1

Cercan Cerca64S10245

Chafas Chafa7039S04036

Mimpud Mimpu22824S02300

Mimpud Mimpu3720S31545

Casaus Castanospermum09396-PA

Nissch Nissc37770S22489 Helann HanXRQChr12g0377021 Vigrad Vradi07g11470.1

Fraexc FRAEX38873 v2 000007560.1

Vigang vigan.Vang11g04880.1Vigung Vigun03g289800.1 Cajcaj Ccajan 24857

Phavul Phvul.003G232700.1 Cicari Ca 20833.1

Glymax Glyma.05G108500.1

Medtru MtrunA17 Chr4g0054341

Tripra Tp57577 TGAC v2 mRNA3820

Trisub lcl DF974372.1 GAU48015.1 37073

Tree scale: 0.1 Supplementary Figure 8: Maximum likelihood tree of HYP2.

Osmsp. 2075108 UOMY Leptosporangiate Monilophytes gametophyte.p1

Osmjav 2004426 VIBO Leptosporangiate Monilophytes.p1

Osmjav 2004425 VIBO Leptosporangiate Monilophytes.p1

Dioedu 2004916 WLIC Cycadales.p1 Nagnag 2114565 UUJS Conifers.p1 Athcup 2061543 XIRK Conifers.p1

Taicry 2062477 QSNJ Conifers.p1 Selkra 2006291 ZFGK Lycophytes.p1

Marpal 2085404 LFVP Liverworts 2 samples combined.p1 Pallye 2105920 YFGP Liverworts.p1

Marpol 2006960 JPYU Liverworts.p1

Marpol 2006959 JPYU Liverworts.p1 Marpal 2054495 HMHL Liverworts non mycorrizal.p1

Marpal 2067495 IHWO Liverworts mycorrizal.p1Marpol Mapoly0102s0044.1

Phaequ PEQU 35490

Musacu GSMUA AchrUn randomP14010 001

Anacom Aco011144.1

Orysat LOC Os01g74620.1

Setita Seita.7G002400.1

Zeamay Zm00008a037575

Bradis Bradi2g62790.2

Horvul HORVU2Hr1G017940.2

Horvul HORVU3Hr1G117950.1 Marema 2075554 TFYI Liverworts.p1 Horvul HORVU6Hr1G041980.2

Horvul HORVU7Hr1G022810.4 Ricnat 2007994 WJLO Liverworts.p1 Casaus Castanospermum01637-PA

Nissch Nissc3856S22661

BlaspNW c323463 g3 i2 m.57539 Arahyp arahy.Tifrunner.gnm1.ann1.QQ3HDC.1

Selapo 2041570 LGDQ Lycophytes.p1 Aradur Aradu.6896W

Arahyp arahy.Tifrunner.gnm1.ann1.VW3DCY.1

Taklep 2010049 SKQD Mosses.p1 Araipa Araip.SX8DW

Lotjap Lj6g3v0326360.1

Cicari Ca 13174.1

Medtru MtrunA17 Chr3g0107521

85.4 Tripra Tp57577 TGAC v2 mRNA29763

94.3 Trisub lcl DF973188.1 GAU18642.1 7700

96.2

94.5 99.6 99.1 Cajcaj Ccajan 32039

85.7 Lagsic Lsi02G012080.1 95 95.6 84.9 93.6 Glymax Glyma.11G187100.1 94.9 Citlan Cla008098 Glymax Glyma.18G052300.1 99.9

81.2 Cucsat evm.model.Chr1.471 96.9 100 Phavul Phvul.006G078700.1 98.6

85

90.6 99 96.9 Cucmel MELO3C020485.2.1 92.3 99.3 Vigung Vigun06g087400.1

88.2 Momcha lcl NW 019104784.1 XP 022158430.1 27806 99.2 94.5 Vigang vigan.Vang0994s00020.1 96.8 90.6 97.1 90.9 90.3 97 89.4 98.4 Vigrad Vradi10g03880.1 Cucmos CmoCh01G007620.1 99.8 100 Cercan Cerca30S21103 82.6 97.1 97.8 Cucmax CmaCh01G007330.1 99.8 Chafas Chafa16608S01100 100 83.2 87.6 Cucpep Cp4.1LG00g04350.1 99.8 96.5 Mimpud Mimpu7265S27136 98.4 89 98.7 100 99.3 Mimpud Mimpu1607S07443 Datglo Datgl32S28348 94.7 92.8

99.9 92.5 Casaus Castanospermum20930-PA 93.2 86.8 93 98.1 90.3 99.8 84.7 99.3 91.3 99.5 92 Lotjap Lj2g3v2437090.1 91.7 99.7 Treori lcl JXTC01000833.1 PON36401.1 34945 85.4 100 99.8 99.9 88.6 91.9 97.1 81.3 95.4 99.8 93.4 96.6 Lotjap Lj2g3v2437090.2 Parand lcl JXTB01000521.1 PON37689.1 31850 100 Cicari Ca 03735.1 Humlup HL.SW.v1.0.G007156.1 Mornot L484 010657 Medtru MtrunA17 Chr5g0432711

Tripra Tp57577 TGAC v2 mRNA18930

Trisub lcl DF973644.1 GAU36860.1 25918 Distri Distr875S28854 Zizjuj lcl NC 029680.1 XP 024926596.1 6071 Cajcaj Ccajan 05464

Glymax Glyma.02G236300.1 Maldom MDP0000163946

Glymax Glyma.14G204200.1 Maldom MDP0000141910 Phavul Phvul.008G247700.1 Pyrcom PCP002256.1 Vigung Vigun08g135000.1

Pyrcom PCP020082.1Potmic 14655 t Vigang vigan.Vang01g07660.1

Vigrad Vradi06g06400.1

Poptri Potri.019G130200.1

Poptri Potri.013G157100.1

Manesc Manes.02G211900.1

Riccom 29976.m000496

Rubocc Bras G10608 Jugreg g52056.t1 Fraana FAN iscf00136114.1.g00001.1 Jugreg g52275.t1

Roschi RchiOBHm Chr5g0073191 Casgla Casgl1124S03236 Alnglu Alngl15624S17124

Alnglu Alngl424755S10362

Gosrai Gorai.003G152600.1

Thecac Thecc1EG042288t1 Prudul Prudul26A004147P1 Jugreg g35940.t1

Pruper Prupe.6G041100.1

Drydru Drydr285S09818

Pruavi Pav sc0000206.1 g630.1.mk

Carpap evm.model.supercontig 2.297 Querob Qrob P0127090.2 Begfuc Begfu458S35767

Begfuc Begfu343S31841

Fraexc FRAEX38873 v2 000147110.2

Fraexc FRAEX38873 v2 000147110.1

Fraexc FRAEX38873 v2 000122770.1

Helann HanXRQChr16g0522641

Casmol maker-scaffold00541-snap-gene-0.48-mRNA-1

Tree scale: 1 Supplementary Figure 9: Maximum likelihood tree of KinF.

Osmsp. 2080049 UOMY Leptosporangiate Monilophytes gametophyte.p1

Marpal 2013151 LFVP Liverworts 2 samples combined.p1

Marpal 2013152 LFVP Liverworts 2 samples combined.p1 Marpal 2009947 HMHL Liverworts non mycorrizal.p1

Marpal 2006329 IHWO Liverworts mycorrizal.p1

Marpal 2006328 IHWO Liverworts mycorrizal.p1

Marpol 2009495 JPYU Liverworts.p1 Marpal scaff178 FGenesh2.1

Ricnat 2005853 WJLO Liverworts.p1 Marpol Mapoly0010s0174.1

Ricnat 2005852 WJLO Liverworts.p1

Concon 2044155 ILBQ Liverworts.p1

Sphtex 2044821 HERT Liverworts.p1

Selmoe 118910

Ambtri evm 27.model.AmTr v1.0 scaffold00024.199

Musacu GSMUA Achr9T27360 001

Anacom Aco020615.1

Orysat LOC Os09g27150.1

BlaspNW c328394 g3 i6 m.80024 Horvul HORVU5Hr1G061460.1

Bradis Bradi4g31517.1

BlaspNW c328394 g3 i9 m.80029 Setita Seita.2G221800.1 Zeamay Zm00008a008977

Sorbic Sobic.002G218200.1 BlaspNW c328394 g3 i7 m.80026 97.1 Daucar DCAR 000818

99.9 87.1 99.9 Helann HanXRQChr04g0097831 BlaspNW c328394 g3 i5 m.80022 Fraexc FRAEX38873 v2 000220000.1

BlaspNW c328394 g3 i3 m.80019 Petaxi Peaxi162Scf00101g00138.1

100 Nicben Niben101Scf11108g02005.1 BlaspNW c328394 g3 i4 m.80021 Nicben Niben101Scf11447g02008.1

BlaspNW c328394 g3 i8 m.80028 Capann CA03g02410

Sollyc Solyc08g062140.1.1

95.9 Solpen Sopen08g017660.1 99.7 85.9 Momcha lcl NW 019104488.1 XP 022136538.1 854

98.7 100 Cucpep Cp4.1LG06g02490.1 88.9 97.9 100

Cucmos CmoCh09G003600.1

Cucmax CmaCh09G003610.1 94.4 99.9 100 Vigrad Vradi05g11520.1 100

100 Citlan Cla007444 Vigang vigan.Vang05g03880.1 100 100 99.6 98.8 97.2 Cucsat evm.model.Chr4.2553

88.4 98.3 Vigung Vigun09g221600.1 98.6 Cucmel MELO3C016904.2.1 99.4 99.9 98.7 Phavul Phvul.009G081200.1 Jugreg g23547.t1 100 100 Alnglu Alngl6212S33526 Cajcaj Ccajan 29075 80.2 100 Querob Qrob P0472210.2 100 99.8 Glymax Glyma.06G055300.1 100 Casmol augustus masked-scaffold02840-abinit-gene-0.7-mRNA-1

Arahyp arahy.Tifrunner.gnm1.ann1.2W5J38.1 93.3 Poptri Potri.006G222600.2 100

Araipa Araip.93AXA 100 Manesc Manes.16G084200.1 92.8 88.5 98.1 Riccom 29739.m003601 Aradur Aradu.X6UYT 100 88 Thecac Thecc1EG037365t1 99.8

Arahyp arahy.Tifrunner.gnm1.ann1.85NTLH.1 Gosrai Gorai.009G041400.1 100

Nissch Nissc524354S25923 96.8 94.4 Carpap evm.model.supercontig 126.39

96.7 Citsin orange1.1g039082m 98.2 Trisub lcl DF973340.1 GAU26711.1 15769 100 91.1 100 Citcle Ciclev10010511m

99.9 Datglo Datgl2369S06008 Trisub lcl DF973340.1 GAU26712.1 15770

91 95.5 Begfuc Begfu216S09480 Tripra Tp57577 TGAC v2 mRNA41101 100 95.1 Zizjuj lcl NC 029684.1 XP 015884374.1 16340 99.5 100 99.5 100

Tripra Tp57577 TGAC v2 mRNA41097 93.2 100 Distri Distr1520S15090

99.9 100 91.1 Cicari Ca 15091.1 88 Medtru MtrunA17 Chr3g0136131 98.8 100 Mornot L484 018574

96.6 85.1 Parand lcl JXTB01000043.1 PON71748.1 7203

100 97.5 Vigrad Vradi06g13790.1 Treori lcl JXTC01000041.1 PON95954.1 8203

99.8 99.6 83.5 Maldom MDP0000446865

100 96.7

100 97 89.5 99.7 Pyrcom PCP034944.1 Vigang vigan.Vang01g15520.1 96.7 Vigung Vigun08g041400.1 Pyrbre lcl NW 008988041.1 XP 018504937.1 1598

97.2 Prumum lcl NC 024127.1 XP 008220552.1 5453

Phavul Phvul.001G039300.1 Pruper Prupe.1G406200.1

Prudul Prudul26A004007P1

Glymax Glyma.17G225400.1 Pruavi Pav sc0000069.1 g190.1.mk Drydru Drydr146S00872

Cajcaj Ccajan 38989 Rubocc Bras G04531

Glymax Glyma.14G099300.1 Roschi RchiOBHm Chr6g0311551

Fraana FAN iscf00203413.1.g00001.1

Fraves FvH4 2g31250.1

Fraana FAN icon20671696.1.g00001.1

Fraana FAN iscf00269630.1.g00001.1

Araipa Araip.UF0MQ

Aradur Aradu.T0K7A

Nissch Nissc4115S23139 Lotjap Lj5g3v0465920.1 Arahyp arahy.Tifrunner.gnm1.ann1.X266PE.1

Cercan Cerca259S19477 Mimpud Mimpu4886S24808 Chafas Chafa1046S13667

Arahyp arahy.Tifrunner.gnm1.ann1.T39EVL.1 Casaus Castanospermum17776-PA

Fraana FAN iscf00235482.1.g00001.1

Fraana FAN iscf00107021.1.g00001.1

Tree scale: 0.1 Supplementary Figure 10: Maximum likelihood tree of HYP4.

Phacar 2017449Phacar WCZB 2023067 Hornworts RXRQ gametophyte.p2 Hornworts sporophyte.p2 Hupluc 2094131 GKAG Lycophytes.p1

Lycapp 2015728Lycapp ULKT Lycophytes.p1

Ginbil 2035692 SGTW Ginkgoales.p1

Ausspi 2073193 BTTS Conifers.p1 Selsta 2011513 ZZOL Lycophytes.p3

Selsel 2009682 KUXM Lycophytes.p2 Sellep 2005718 ABIJ Lycophytes.p2

Parhal 2010687 FAJB Hornworts.p3 Phacar 2023088 RXRQ Hornworts sporophyte.p2 Parhal 2010686 FAJB Hornworts.p1 Phacar 2114146 WCZB Hornworts gametophyte.p1

Megfla 2003209 UCRN Hornworts.p4 Marpal 2083210 LFVP Liverworts 2 samples combined.p1 Megfla 2003211 UCRN Hornworts.p3 Megfla 2003210 UCRN Hornworts.p4 Marpal 2006026 IHWO Liverworts mycorrizal.p1

Ginbil Gb 14597 Marpal 2052362 HMHL Liverworts non mycorrizal.p1 Selmoe 130246

Taklep 2077271 SKQD Mosses.p1

Ginbil 2004676 SGTW Ginkgoales.p1 Ginbil Gb 12298 Ginbil 2004675 SGTW Ginkgoales.p1 Ginbil Gb 12297 Mictet 2064520 MHGD Conifers.p1 Linmic 2048371 YIXP Leptosporangiate Monilophytes.p1 Lygjap 2016157 PBUU Leptosporangiate Monilophytes.p1 Lygjap 2016156 PBUU Leptosporangiate Monilophytes.p1 Linlin 2015371 NOKI Leptosporangiate Monilophytes.p1 Marpal scaff8482 FGenesh2.1 Adirad 2013500 BMJR Leptosporangiate Monilophytes.p1 Adiale 2058646 WCLG Leptosporangiate Monilophytes.p1 Leuimm 2069625 WGTU Leptosporangiate Monilophytes.p1 Blespi 2201830 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Marema 2073611 TFYIMarpol Liverworts.p1 Mapoly0116s0005.1 Nepexa 2127963 NWWI Leptosporangiate Monilophytes.p2 Polamo 2001455 YLJA Leptosporangiate Monilophytes.p2 Marpol Mapoly0029s0149.1 Luncru 2072046 TXVB Liverworts.p1 Polgly 2076740 CJNT Leptosporangiate Monilophytes.p2 Orysat LOC Os05g49790.1 Concon 2042872 ILBQ Liverworts.p1 Setita Seita.3G138500.1 Zeamay Zm00008a026499 Sphtex 2043294 HERT Liverworts.p1 Sorbic Sobic.009G239800.1 Setita Seita.5G246800.1 Pelepi 2082727 PIUF Liverworts.p2 Zeamay Zm00008a014277 Pelnee 2103846 JHFI Liverworts.p2 Sorbic Sobic.003G240000.1 Orysat LOC Os01g46390.1 Pelnee 2016740 JHFI Liverworts.p2 Horvul HORVU3Hr1G058820.1 Bradis Bradi2g45340.1 Pallye 2012110 YFGP Liverworts.p1 Musacu GSMUA Achr2T20030 001 Anacom Aco005492.1 Dencat lcl NW 021318693.1 XP 020688908.1 4371 Ambtri evm 27.model.AmTr v1.0 scaffold00021.33 Momcha lcl NW 019104547.1 XP 022149634.1 20075 Cucmax CmaCh20G002190.1 Cucpep Cp4.1LG16g07540.1 Cucmos CmoCh20G002380.1

97.3

91.9 100 Lagsic Lsi02G025730.1

87 Citlan Cla015243 Pyrcom PCP044729.1 99.9 Cucmel MELO3C023553.2.1 Maldom MDP0000251135 Cucsat evm.model.Chr7.1887

Pyrbre lcl NW 008988063.1 XP 018502190.1 6139 92.7 Pyrcom PCP044901.1 Chafas Chafa543S10571 Casaus Castanospermum19665-PA

100 95.8 100

98.6 98.9 99.8 Nissch Nissc154422S00704 Maldom MDP0000139709 100 Pyrbre lcl NW 008988039.1 XP 009353291.1 573 99.8 99.7 Araipa Araip.IZQ8N 89.5 98.3 100 99.6 99.6 100

92.5 95.6 Arahyp arahy.Tifrunner.gnm1.ann1.E28A1S.1 92.1 99.9 95.8 99.8 89.4 93.2 98.4 85.7 92.2 Pyrcom PCP016955.1 94.1 98.4 Glymax Glyma.12G210200.1 89.6 91.2 83.3 88 86.4 91.5 98.3 Glymax Glyma.13G291100.1 Pyrcom PCP013914.1 99.6 90.3 99.8 86.7 93.4 99.5 99.5 95 92.9 Pyrbre lcl NW 008988063.1 XP 009352946.1 6140 86.7 Cajcaj Ccajan 23875 88.2 98.3 98.7 96.7 96.8 Vigung Vigun05g208900.1 93.7 94.8 Prudul Prudul26A025477P1 82.2 80.2 90.1 Phavul Phvul.005G095700.1 87.2 97.3 Pruper Prupe.4G060700.1 81 91.1 82.3 Vigrad Vradi0023s00490.1 99.2 87.3 99.9 Vigang vigan.Vang0184s00540.1 Prumum lcl NC 024128.1 XP 008225330.1 9878 100 Thecac Thecc1EG001699t1 Pruavi Pav sc0000037.1 g350.1.mk 88.5 97.8 80 98.4 Gosrai Gorai.006G001600.1 Prudul Prudul26A018171P1 99.4 93.9 95.7 Begfuc Begfu2230S02225 99.8 Pruper Prupe.4G060600.1 96.5 Begfuc Begfu528S12716

99.2 88.1 99.3 90.5 Drydru Drydr229S02249

94.1 99.3 Rubocc Bras G22530 Prumum lcl NC 024128.1 XP 008225329.1 9877 89.7 Pruavi Pav sc0000037.1 g340.1.mk 95.9 Roschi RchiOBHm Chr2g0129271

82.9 98.9 93.2 Pruper Prupe.3G121500.1 Fraana FAN iscf00065932.1.g00002.1Fraves FvH4 6g24940.1 95.6 88.9 100 Prudul Prudul26A001386P1 84.1 96.1 91.1 99.4

97.7 90.8 Prumum lcl NC 024129.1 XP 008228969.1 13347 Fraana FAN icon20469667.1.g00001.1 Pruavi Pav sc0001990.1 g150.1.mk

95.3 99.9 Distri Distr3S07917 Fraana FAN iscf00268226.1.g00001.1Fraves FvH4 3g07840.1 100 Mornot L484 004808 Potmic 2132 t 96 Treori lcl JXTC01000038.1 PON96417.1 7691 99.2

98.6 82.5 Roschi RchiOBHm Chr5g0010731 87.8 98.6 Parand lcl JXTB01000797.1 PON32629.1 35971 84.5 100 Rubocc Bras G05239 89.6 100 Fraexc FRAEX38873 v2 000125790.1

85.6 88.6 97.5 95.4 Carpap evm.model.supercontig 209.35 96.2 99.8 Drydru Drydr70S13675 99 97.6 96.7

97 98.3 Citcle Ciclev10017452m 99

100 85.9 81.6 81.3 Citsin orange1.1g047596m

Humlup HL.SW.v1.0.G021605.1 99.1 Citsin orange1.1g047759m Citcle Ciclev10018346m Humlup HL.SW.v1.0.G043236.1 Citsin orange1.1g044066m Alnglu Alngl424419S10201 Mornot L484 019750 Jugreg g36393.t1 Casgla Casgl254S00997 Riccom 28842.m000910 Querob Qrob P0160190.2 Parand lcl JXTB01000417.1 PON41360.1 29032 Casmol augustus masked-scaffold06258-abinit-gene-0.2-mRNA-1 Datglo Datgl497S10564 Treori lcl JXTC01000264.1 PON73801.1Manesc Manes.03G102300.1 24857 Cepfol Cfol v3 03686 Solpen Sopen02g021810.1 Cercan Cerca4S03673 Cicari Ca 00582.1 Sollyc Solyc02g076890.1.1 Medtru MtrunA17 Chr2g0325561 Medtru MtrunA17 Chr2g0325571 Solpen Sopen02g021820.1 Trisub lcl DF973347.1 GAU27073.1 16131 Capann CA02g14250 Tripra Tp57577 TGAC v2 mRNA11878 Solpen Sopen02g021800.1 Daucar DCAR 021453 Helann HanXRQChr04g0115941 Zizjuj lcl NC 029679.1 XP 015873469.1 569 Distri Distr212S06643 Fraexc FRAEX38873 v2 000389830.1 Fraexc FRAEX38873 v2 000250240.1 Gosrai Gorai.010G242000.1 Thecac Thecc1EG029706t1 Gosrai Gorai.009G163100.1 Citsin orange1.1g032674m Citcle Ciclev10017804m

Sollyc Solyc03g006180.2.1 Nicben Niben101Scf03309g07010.1 Solpen Sopen03g002190.1 Nicben Niben101Scf10219g00006.1

Nissch Nissc281327S07795Chafas Chafa1866S07598 Cercan Cerca223S01744 Petaxi Peaxi162Scf00162g00141.1Medtru MtrunA17 Chr2g0283761 Nissch Nissc12S05468

Datglo Datgl199S04931 Casgla Casgl78S26030

Alnglu Alngl45878S10795

Riccom 29900.m001614

Poptri Potri.017G133300.1

Poptri Potri.004G084600.1 Casaus Castanospermum10959-PA Poptri Potri.004G056700.1

Manesc Manes.16G038600.1

Manesc Manes.17G055300.1

Casmol augustus masked-scaffold00680-abinit-gene-0.9-mRNA-1

Tree scale: 0.1 Supplementary Figure 11: Maximum likelihood tree of pp2a.

Cedlib 2066406 GGEA Conifers.p1

Phyhyp 2067844 JRNA Conifers.p1 Parust 2039221 JZVE Conifers.p1

Ararul 2012952 XTZO Conifers.p1

Disarc 2013723 GKCZ Conifers.p1

Chalaw 2069620 AIGO Conifers.p1

Mongot 2013281 LeualbTFDQ 2010154Liverworts.p1 VMXJ Mosses.p1

Gnemon TnS000850087t03

Ginbil Gb 31776 Calfis 2016400 RTMU Liverworts.p1

Scanem 2165887 IRBN Liverworts.p1

Mongot 2012674 TFDQ Liverworts.p1

Calfis 2018808 RTMU Liverworts.p1

Pseama 2079312 AQFM Conifers.p1 Notlon 2012532 AREG Conifers.p1

Abilas 2056645 VSRH Conifers.p1

Larspe 2053447 WVWN Conifers.p1 Selwal 2179759 JKAA Lycophytes.p1 Psewil 2055343 IOVS Conifers.p1 Psemen PME00002977

Picabi MA 2157g0010 Scanem 2164640 IRBN Liverworts.p1 Pinsyl PSY00020668 Phacar 2118998 WCZB Hornworts gametophyte.p1 Pinpon 2071992 JBND Conifers.p1 Pinjef 2082243 MFTM Conifers.p1 Barbar 2133607 OFTV Liverworts.p1 Pinrad 2051123 DZQM Conifers.p1

Pintae PTA00007835 Marpal 2010131 IHWO Liverworts mycorrizal.p1 Marpal 2013609 LFVP Liverworts 2 samples combined.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00001.138

Musacu GSMUA Achr3T00600 001

Anacom Aco013081.1

Setita Seita.2G292900.1

Sorbic Sobic.002G282100.1

Leujul 2021802 IGUH Mosses.p1 85.1 Zeamay Zm00008a009292 84.6

94.1 100

99.8 98.3 Orysat LOC Os09g37060.1 100 100 86.8 97.6 87.9

100 100 97.2 Horvul HORVU5Hr1G084630.1

99.4 Bradis Bradi4g36775.1 100

92.2 99.7 99.9 93.7 Helann HanXRQChr08g0236851

94.8 Pyrbre lcl NW 008988602.1 XP 009340494.1 37148 100 Thecac Thecc1EG036687t1

87.1

100 Gosrai Gorai.009G264300.1

99.7 Carpap evm.model.supercontig 14.235

100 99.9 Pyrcom PCP002696.1 99.8 Citcle Ciclev10029887m

98.9 Maldom MDP0000246977 96.5 99.8 Citsin orange1.1g041109m

100 Manesc Manes.11G099200.1 Maldom MDP0000250405 100 100 Pyrbre lcl NW 008988081.1 XP 009355627.1 8774 Poptri Potri.009G138400.1 100 100 Poptri Potri.004G177900.1 89.2 100 Pyrcom PCP000311.1 99.9 Fraexc FRAEX38873 v2 000056330.1 99.5 Pruper Prupe.8G169200.1 99.6 Daucar DCAR 028942 92.1 94.6 Petaxi Peaxi162Scf00362g00435.1 Prudul Prudul26A004649P1 100 100 Nicben Niben101Scf02908g03007.1

Prumum lcl NC 024131.1 XP 008236064.1 20111 99.9 Capann CA08g19510

100 100 Pruavi Pav sc0000373.1 g800.1.mk 99.8 Sollyc Solyc01g111790.1.1 Potmic 9780 t 100 Solpen Sopen01g053830.1 99.4 100 Fraves FvH4 2g15670.1 Datglo Datgl1128S18571

100 Begfuc Begfu619S38913 99.6 100

Roschi RchiOBHm Chr6g0278971 86.2 100 100 Begfuc Begfu5706S50207 Rubocc Bras G20071 100 Citlan Cla020257

Drydru Drydr380S21190 Cucmel MELO3C020837.2.1

100 100 98.8 Cucsat evm.model.Chr2.1375 99.9 100 100 Momcha lcl NW 019104503.1 XP 022140524.1 11882 94.6 97.2 100 98.7 90.4

89.9 Cucmax CmaCh02G002740.1 Treori lcl JXTC01000088.1 PON89930.1 14218

97.7 100 Cucpep Cp4.1LG05g13460.1

Humlup HL.SW.v1.0.G018489.1Mornot L484 006067 99.9 Parand lcl JXTB01000338.1 PON45053.1 26198 99.8 Cucmos CmoCh02G002710.1

Mimpud Mimpu3929S10261

99.1

94.3 99.8 Chafas Chafa29763S08841 99 100 100

99.1 100 Mimpud Mimpu15901S17920 84.6

96.8

Chafas Chafa38407S22011

100 Cercan Cerca147S00775 Zizjuj lcl NC 029687.1 XP 024932914.1 25456 Casaus Castanospermum16076-PA

Lupang Lup024672.1

Zizjuj lcl NC 029687.1 XP 024932917.1 25459 Nissch Nissc524899S27959

Arahyp arahy.Tifrunner.gnm1.ann1.6AG38Z.1 Jugreg g28960.t1 Distri Distr1012S04224 Aradur Aradu.NF928 Zizjuj lcl NC 029687.1 XP 024932915.1 25457 Araipa Araip.WJD5Q Jugreg g43735.t1 Arahyp arahy.Tifrunner.gnm1.ann1.3BWT9P.1 Lotjap Lj5g3v2246130.1

Cicari Ca 10763.1

Medtru MtrunA17 Chr1g0211361

Zizjuj lcl NC 029687.1 XP 024932916.1 25458

Zizjuj lcl NC 029687.1 XP 015893265.1 25460 Alnglu Alngl9843S12690

Querob Qrob P0610020.2 Vigrad Vradi08g22070.1

Cajcaj Ccajan 08144

Vigung Vigun07g279600.1

Vigang vigan.Vang06g00020.1

Phavul Phvul.007G017700.1

Glymax Glyma.10G283500.1

Tripra Tp57577 TGAC v2 mRNA2496

Trisub lcl DF973178.1 GAU18048.1 7106

Casmol augustus masked-scaffold01457-abinit-gene-0.2-mRNA-1

Tree scale: 0.1 Supplementary Figure 12: Maximum likelihood tree of DnaJ.

Dipcon 2007389 MEKP Leptosporangiate Monilophytes.p1

Hymbiv 2044188 QIAD Leptosporangiate Monilophytes.p1

Pallye 2010100YFGP Liverworts.p3 Pallye 2010102YFGP Liverworts.p1

Racvar 2014284 RDOO Mosses.p2

Racelo 2075575ABCD Mosses.p1 Andrup 2093173 WOGB Mosses.p1

Atrang 2084738 ZTHV Mosses.p1 Sphles 2017458 GOWD Mosses.p1 Dipfol 2069141AWOI Mosses.p1 Sphpal 2007026 RCBT Mosses.p1 Sphrec 2092843 UHLI Mosses.p1 Denobs 2013209Dipdig 2001202XNXF Lycophytes.p1 WAFT Lycophytes.p1 Taklep 2008866 SKQD Mosses.p1 Lycann 2082846 ENQF Lycophytes.p1Pelnee 2112479 JHFI Liverworts.p1

Selsel 2043258 KUXM Lycophytes.p1

Phypat Pp3c12 8390V3.1

Sphfal Sphfalx0011s0055.1 Anocla 2050904Rhyser 2043617VBMM Mosses.p1 JADL Mosses.p1

Phypat Pp3c20 19980V3.1 Necdou 2010029Cliden 2084781 TMAJ Mosses.p1MIRS Mosses.p1 Necdou 2010028 TMAJ Mosses.p1 Loebre 2045721 WSPM Mosses.p1 Anoatt 2058889 QMWB Mosses.p1

Stesub 2069312 LNSF Mosses.p1 Leubra 2001734 ZACW Mosses.p1

Fonant Leujul2071827 2162640 DHWX IGUH Mosses.p1 Mosses.p1 Thudel 2037338 EEMJ Mosses.p1

PseeleCalcor 2011677 2009991 QKQO TAVP Mosses.p1 Mosses.p1 Ortlye 2083361 CMEQ Mosses.p1 Aulhet 2089383 WNGH Mosses.p1

Angeve 2012893 NHCM Eusporangiate Monilophytes.p1 Osmjav 2074720 VIBO Leptosporangiate Monilophytes.p1 Hymbiv 2000008 QIAD Leptosporangiate Monilophytes.p1 Dipcon 2014985 MEKP Leptosporangiate Monilophytes.p1 Pallye 2106831 YFGP Liverworts.p1 Plains 2078948 BGXB Mosses.p1 Metcra 2097445 NRWZ Liverworts.p1 Pelnee 2112392 JHFI Liverworts.p1 Pelepi 2011646 PIUF Liverworts.p1 Pelnee 2112330 JHFI Liverworts.p1 Hedcil 2049290 YWNF Mosses.p1 Pelepi 2001422 PIUF Liverworts.p1 Pelepi 2001420 PIUF Liverworts.p1 Roscap 2042821 XWHK Mosses.p1 Pelepi 2001423 PIUF Liverworts.p1 Pelepi 2001421 PIUF Liverworts.p1 Pelnee 2016219 JHFI Liverworts.p1 Pelepi 2088122 PIUF Liverworts.p1 Ptipul 2136512 HPXA Liverworts.p1 Bryarg 2007767 JMXW Mosses.p1 Odopro 2127963 YBQN Liverworts.p1 Barbar 2132265 OFTV Liverworts.p1 Scanem 2165572 IRBN Liverworts.p1 Phifon 2011524 ORKS Mosses.p2 Mixspe 2154713 NWQC Liverworts.p1 Calfis 2181671 RTMU Liverworts.p1 Racelo 2075559 ABCD Mosses.p1 Baztri 2006518 WZYK Liverworts.p1 BlaspNW c382610 g1 i1 m.184827 Racvar 2115838 RDOO Mosses.p1 Marema 2073475 TFYI Liverworts.p1 Ricnat 2002552 WJLO Liverworts.p1 Scoaqu 2015647 BPSG Mosses.p2 Concon 2043678 ILBQ Liverworts.p1 Marpol 2006153 JPYU Liverworts.p1 Synpri 2014780 GRKU Mosses.p1 Marpol Mapoly0020s0133.1 Marpal scaff20214 FGenesh1.1 Cerpur 2008566 FFPD Mosses.p1 Marpal 2063929 IHWO Liverworts mycorrizal.p1 Marpal 2082153 LFVP Liverworts 2 samples combined.p1 Dicsco 2098873 NGTD Mosses.p1 Marpal 2050963 HMHL Liverworts non mycorrizal.p1 Encbar 2082279 GNQG Cycadales.p1 Leugla 2063142 RGKI Mosses.p1 Amearg 2146965 IAJW Conifers.p1 Leualb 2130070 VMXJ Mosses.p1 Tortax 2008110 EFMS Conifers.p1 Ausspi 2071045 BTTS Conifers.p1 Timaus 2065418 ZQRI Mosses.p1 Widced 2056505 AUDE Conifers.p1 Atrang 2016633 ZTHV Mosses.p1 Disarc 2064636 GKCZ Conifers.p1 Ginbil Gb 09306 Tetpel 2131944 HVBQ Mosses.p1 Ginbil Gb 05958 Ginbil Gb 11172 Dipfol 2071592 AWOI Mosses.p1 Ginbil Gb 36047 Ginbil Gb 01235 Physsp. 2081136 YEPO Mosses.p1 Ginbil 2037620 SGTW Ginkgoales.p1 Ginbil Gb 01234 Phypat Pp3c10 15440V3.1 Encbar 2079014 GNQG Cycadales.p1 Physsp. 2079466 YEPO Mosses.p1 Ginbil Gb 15815 Ginbil Gb 02868 Marpol 2007502 JPYUPhypat Liverworts.p1 Pp3c4 1450V3.1 Sciver 2038129 YFZK Conifers.p1 Athcup 2053769 XIRK Conifers.p1 Marpol Mapoly0826s0001.1 Tornuc 2007589 HQOM Conifers.p1 Marema 2001637 TFYI Liverworts.p1 Amearg 2016976 IAJW Conifers.p1 Marpol Mapoly0060s0100.1 Tortax 2068812 EFMS Conifers.p1 Luncru 2075481 TXVB Liverworts.p1 Taxcus 2072881 ZYAX Conifers.p1 Concon 2044421 ILBQ Liverworts.p1 Ausspi 2075564 BTTS Conifers.p1 Psechi 2077738 YLPM Conifers.p1 Cephar 2004688 NVGZ Conifers 2 samples combined.p1 Cephar 2001145 WYAJ Conifers.p1 Cephar 2001144 WYAJ Conifers.p1 Ausspi 2076280 BTTS Conifers.p1 Taxbac 2005939 WWSS Conifers.p1 Taxbac 2005938 WWSS Conifers.p1 85.6 Psechi 2009945 YLPM Conifers.p1 Taxcus 2001720 ZYAX Conifers.p1 98.2 Taxbac 2007834 WWSS Conifers.p1

93.7 Taicry 2061255 QSNJ Conifers.p1 86.6 Cunlan 2016944 ZQVF Conifers 2 samples combined.p1 Cunlan 2013985 ESYX Conifers branch apex with needles.p1 Cunlan 2000041 OUOI Conifers.p1 Cunlan 2000042 OUOI Conifers.p1

99.8 Vigang vigan.Vang1181s00010.1 96.2 97.7 82.5 Cunlan 2000040 OUOI Conifers.p1

86.7 91.1 Cunlan 2007663 ESYX Conifers branch apex with needles.p1 Vigang vigan.Vang04g10450.1 93.2 80.7 97.7 89.7 99 Metgly 2004082 NRXL Conifers.p1

100 97.1 96.3 Metgly 2004080 NRXL Conifers.p1 Vigang Vigradvigan.Vang03g04040.1 Vradi10g12580.1 96.8 100 90.9 Seqsem 2002700 HBGV Conifers.p1 83.7 99.5 97.8 99.9 Metgly 2004079 NRXL Conifers.p1 99.7 Phavul Phvul.006G207700.1 99.8 92.3 88.5 Metgly 2004081 NRXL Conifers.p1 Vigung Vigun06g224900.1 99.3 86.2 96.3 Glypen 2001968 OXGJ Conifers.p1 99.7 87.9 100 100 Vigang vigan.Vang03g04110.1 92.5 100 98.3 93.5 97.5 98.2 Cryjap 2099037 HOUF Conifers leaf.p1 83.4 99.5 81.4 85.9 97.2 100 100 Vigung Vigun06g224800.1 100 99.8 91.6 Cryjap 2003605 GMHZ Conifers 2 samples combined.p1 85.8 87.9 Phavul Phvul.006G207600.1 97.2 81.7 100 Neopan 2064850 JDQB Conifers.p1 99.8 81.3 Glymax Glyma.08G180300.1 87.2 81 97.2 Piluvi 2059401 ETCJ Conifers.p1 95.8 97.5 94.6 Calgra 2006691 IFLI Conifers March.p1 Glymax Glyma.08G180100.1 98.7 92 99.4

88 97.5 86.3 Calmac 2006840 RMMV Conifers March.p1 92.2 81.2 95.7 99.9 100 Lotjap Lj0g3v0112449.1 93.3 99.1 Auschi 2010654 YYPE Conifers.p1 Lotjap Lj6g3v2218670.1 99 96.5 Disarc 2002225 GKCZ Conifers.p1 86.6 81.2 89.4 85.6 94.4 Lotjap Lj4g3v0338240.1 96.8 81.6 95 89.4 93.280.1 Pappap 2005664 OVIJ Conifers.p1 97.3 100 Medtru MtrunA17 Chr2g0278951 86.5 Piluvi 2004310 ETCJ Conifers.p1

84 96.2 91.5 88.9 92 89.1 95.5 Caldec 2000478 FRPM Conifers.p1 Medtru MtrunA17 Chr2g0278961 99 99.7 100 86.3 Tripra Tp57577 TGAC v2 mRNA14057 81.4 99.2 Chalaw 2002486 AIGO Conifers.p1 99.7 84.7 88.8 Junsco 2006321 XMGP Conifers.p1 88.4 Cajcaj Ccajan 22292 93 87.2 90.5 Micdec 2010212 XQSG Conifers.p1 88.9 99.8 Cajcaj Ccajan 22294 99.2 91.1 Plaori 2006291 BUWV Conifers.p1 81.8 99.8 Plaori 2006290 BUWV Conifers.p1 Cajcaj Ccajan 22293 90.5 95.3 Lupang Lup007969.1 Micdec 2003760 XQSG Conifers.p1 99.7 81.4 Caldec 2002967 FRPM Conifers.p1 Lupang Lup008981.1 80.5 88.6 96.5 Caldec 2002968 FRPM Conifers.p1 99.9 81 Aradur Aradu.KW8EH 98.7 Wolnob 2047512 RSCE Conifers.p1 100 92.7 Arahyp arahy.Tifrunner.gnm1.ann1.GBJ2WV.1 Ararul 2060745 XTZO Conifers.p1 88.2 Nissch Nissc524540S10074 97.5 83.5 Agamac 2003401 ACWS Conifers.p1 98.7 86 Agarob 2009045 MIXZ Conifers.p1 Casaus Castanospermum12172-PA 94.5 85.4 Agamac 2005547 ACWS Conifers.p1 85.9 Vigang vigan.Vang0505s00150.1 100 89.4 93.5 Wolnob 2005063 RSCE Conifers.p1 Vigung Vigun03g133200.1 92.2 86.3 88.6 Wolnob 2005064 RSCE Conifers.p1 Phavul Phvul.002G207300.1 81.3 93 99.9 94 Parust 2002531 JZVE Conifers.p1 Cajcaj Ccajan 22882 99 97.7 98.3 95 92.5 Phyhyp 2061376 JRNA Conifers.p1 Glymax Glyma.05G099600.1 82.1 Lepsp. 2072943 BBDD Conifers.p1 82.6 100 Phyhyp 2059190 JRNA Conifers.p1 Glymax Glyma.05G119200.1 84.7 Mancol 2055417 CDFR Conifers.p1 Glymax Glyma.08G074200.1 99.6 94.3 90.7 Lagfra 2002873 ZQWM Conifers.p1

100 Acmpan 2103106 HILW Conifers.p1 100 85.2 Trisub lcl DF973547.1 GAU34147.1 23205 90.7 Retmin 2009469 VGSX Conifers.p1 Tripra Tp57577 TGAC v2 mRNA10784 99.7 95.4 Nagnag 2008103 UUJS Conifers.p1 Cicari Ca 16682.1 98.5 84 Medtru MtrunA17 Chr4g0050581 92 84 Podcor 2005009 SCEB Conifers.p1 100 96.4 88.7 Daccom 2005589 FMWZ Conifers.p1 Lotjap Lj4g3v0340640.1 85.9 86.9 97 Faltax 2002642 PLYX Conifers 2 samples combined.p1 Lotjap Lj3g3v2385410.1 84.2 97.2 86.3 94.9 95.7 Faltax 2002641 PLYX Conifers 2 samples combined.p1 97.7 90.6 81.5 99.9 Lotjap Lj3g3v2385390.1 99.8 Faltax 2002640 PLYX Conifers 2 samples combined.p1 Lupang Lup014747.1 96.6 100 81 Faltax 2057377 ROWR Conifers.p1 98.7 Nissch Nissc3021S08010 80.6 99.1 99.6 Sunama 2010802 KLGF Conifers.p1 99.9 Nagnag 2007085 UUJS Conifers.p1 92.9 Cercan Cerca23S01932 86.8 96.4 Phyhyp 2062316 JRNA Conifers.p1 Casaus Castanospermum15329-PA Sunama 2010059 KLGF Conifers.p1 98.8 Sunama 2010060 KLGF Conifers.p1 Mimpud Mimpu4320S03530 100 85.3 Mimpud Mimpu3048S02864 Halbid 2007913 OWFC Conifers.p1 99.8 Halbid 2050884 OWFC Conifers.p1 Chafas Chafa5232S10447 90.7

86.5 95.6 Faltax 2016246 PLYX Conifers 2 samples combined.p1 100 99 Mimpud Mimpu5898S25949 100 Faltax 2011436 ROWR Conifers.p1 Lagfra 2084646 ZQWM Conifers.p1 Mimpud Mimpu16713S18246 95.6 85.6 Chafas Chafa7990S04434 99.6 95.8 Parust 2002149 JZVE Conifers.p1 97.5 80.6

Maldom MDP0000220793 93.7 Parust 2002148 JZVE Conifers.p1 92.2 100 96.8 Mancol 2007454 CDFR Conifers.p1 98.3 99.7 92.7 MaldomPyrcom MDP0000198818 PCP022454.1 98 88.1 Halbid 2007914 OWFC Conifers.p1

94.7 99.7 95 95.2 Pruand 2033842 EGLZ Conifers.p2 98.8 100 96.1 Maldom MDP0000407216 99.9 90.3 Acmpan 2005829 HILW Conifers.p1 96.9 100 98.1 83.4 MaldomPyrcom MDP0000118890 PCP000702.1 Acmpan 2008751 HILW Conifers.p1 99.9 Faltax 2005487 PLYX Conifers 2 samples combined.p1 Faltax 2001053 ROWR Conifers.p1 Prudul Prudul26A019235P1 81.3 Faltax 2001054 ROWR Conifers.p1 Nagnag 2110919 UUJS Conifers.p1 Podcor 2049326 SCEB Conifers.p1 Pruper Prupe.1G558200.1 85.4 Retmin 2010781 VGSX Conifers.p1 Rubocc BrasPotmic G25666 32418 t 99.9 95.1 Saxcon 2008993 QCGM Conifers.p1

98.4 Saxcon 2008992 QCGM Conifers.p1 Podrub 2056223 XLGK Conifers.p1 Pruavi Pav sc0001323.1 g710.1.mk Faltax 2002611 QHBI Conifers A.p1 Casgla Casgl43S05250 Faltax 2002609 QHBI Conifers A.p1 Prumum lcl NC 024127.1 XP 008218980.1 3948 99.3 Roschi RchiOBHm Chr7g0226211 Faltax 2002610 QHBI Conifers A.p1 Casgla Casgl43S05249 Faltax 2006674 PLYX Conifers 2 samples combined.p1

100 Faltax 2011679 ROWR Conifers.p1 Alnglu Alngl66059S34279 Faltax 2006675 PLYX Conifers 2 samples combined.p1 Alnglu Alngl66059S05510 Ambtri evm 27.model.AmTr v1.0 scaffold00119.100 98.5 Musacu GSMUA Achr6T30380 001 Querob Qrob P0048480.2 Anacom Aco002834.1 Querob Qrob P0048520.2 Horvul HORVU1Hr1G045870.1 Horvul HORVU5Hr1G057970.1 Bradis Bradi4g28980.1 Bradis Bradi4g28990.3 Citlan Cla006400 Horvul HORVU5Hr1G057890.1 Thecac Thecc1EG007525t1 Horvul HORVU5Hr1G057900.1 Sorbic Sobic.002G184100.1 Cucmel MELO3C018658.2.1Lagsic Lsi03G007760.1 Sorbic Sobic.002G184200.1 Cucsat evm.model.Chr7.527 Setita Seita.2G187900.1 Setita Seita.2G187800.1 Fraexc FRAEX38873 v2 000065290.1 Distri Distr249S01904 Zizjuj lcl NC 029686.1 XP 015890929.1 23012 Mornot L484 016609 Humlup HL.SW.v1.0.G034947.1 Cucpep Cp4.1LG15g02350.1 Parand lcl JXTB01000089.1 PON65297.1 11816 Treori lcl JXTC01000528.1 PON47828.1 32221 Rubocc Bras G10708 Cucmax CmaCh19G002670.1 Fraves FvH4 1g21470.1 Roschi RchiOBHm Chr2g0115291 Potmic 14628 t Cucmos CmoCh19G002870.1 Pyrcom PCP035470.1 Maldom MDP0000214401 Cucpep Cp4.1LG04g06960.1 Maldom MDP0000200426 Drydru Drydr22S02047 Drydru Drydr22S08668 Prumum lcl NC 024126.1 XP 008233493.2 1684 Pruavi Pav sc0006781.1 g070.1.mk Cucmos CmoCh11G014930.1 Pruper Prupe.6G180400.1 Begfuc Begfu7368S40546 Prudul Prudul26A028806P1 Riccom 29877.m000463 Manesc Manes.12G137900.1 Poptri Potri.005G078801.1 Poptri Potri.T080200.1 Poptri Potri.007G088900.1 Begfuc Begfu1689S08599 Helann HanXRQChr08g0224231 Datglo Datgl2066S05072 Datglo Datgl2066S05070 Casmol augustus masked-scaffold29161-abinit-gene-0.1-mRNA-1 Datglo Datgl2066S05071

Distri Distr3574S02672 Jugreg g5676.t1 Jugreg g58103.t1

Riccom 29479.m000068 Jugreg g49063.t1

Manesc Manes.14G167400.1

Alnglu Alngl116861S06959 Alnglu Alngl116861S38561 Casgla Casgl14S24095

Momcha lcl NW 019104507.1 XP 022141929.1 13087 Helann HanXRQChr16g0514071 Querob Qrob P0183250.2 Capann CA12g09540 Helann HanXRQChr16g0514091 Querob Qrob P0631900.2

Daucar DCAR 032174 Daucar DCAR 032175 Ambtri evm 27.model.AmTr v1.0 scaffold00010.199 Chafas Chafa1668S07259 Zizjuj lcl NC 029687.1 XP 015893405.1 25617 Zizjuj lcl NC 029687.1 XP 015893513.1 25730 Gosrai Gorai.007G061600.1Thecac Thecc1EG001165t1 Gosrai Gorai.003G044800.1 Zizjuj lcl NC 029687.1 XP 015893516.1 25727

Casaus Castanospermum03465-PA

Petaxi Peaxi162Scf00295g00043.1

Petaxi Peaxi162Scf00183g00121.1 Nicben Niben101Scf01252g02006.1

Fraexc FRAEX38873 v2 000047010.1

Casmol snap masked-scaffold07608-abinit-gene-0.3-mRNA-1

Tree scale: 0.1 Supplementary Figure 13: Maximum likelihood tree of CCaMK.

Racvar 2007958 RDOO Mosses.p1 Hedcil 2012815 YWNF Mosses.p1 Racelo 2007572ABCD Mosses.p1 Phifon 2011379 ORKS Mosses.p1

Scoaqu 2015875 BPSG Mosses.p1 Dicsco 2011200 NGTD Mosses.p1

Timaus 2012309 ZQRI Mosses.p1 Thudel 2006541 EEMJ Mosses.p1

Stesub 2009164 LNSF Mosses.p1 Necdou 2023845 TMAJ Mosses.p1 Fonant 2074202 DHWX Mosses.p1

Aulhet 2014847 WNGH Mosses.p1

Bryarg 2001954 JMXW Mosses.p1

Plains 2009775 BGXB Mosses.p1 Ortlye 2013487 CMEQ Mosses.p1 Phifon 2006824 ORKS Mosses.p1

Leugla 2003923 RGKI Mosses.p1 Leualb 2008773 VMXJ Mosses.p1

Leugla 2003924 RGKI Mosses.p1 Dicsco 2011201 NGTD Mosses.p1

Cerpur 2006983 FFPD Mosses.p1 Racelo 2007571 ABCD Mosses.p1 Racvar 2018405 RDOO Mosses.p1

Plains 2080273 BGXB Mosses.p1 2080273 Plains Scoaqu 2014956 BPSG Mosses.p1 Ortlye 2084515 CMEQ Mosses.p1 Pseele 2011161 QKQO Mosses.p1 Necdou 2023616 TMAJ Mosses.p1 Rhyser 2048106 JADL Mosses.p1 Anocla 2052700 VBMM Mosses.p1 Leubra 2014486 ZACW Mosses.p2 Leubra 2014485 ZACW Mosses.p2 Thudel 2037531 EEMJ Mosses.p1 Stesub 2011898 LNSF Mosses.p1 Physsp. 2000990 YEPO Mosses.p1 Loebre 2009021 WSPM Mosses.p1 Cliden 2012369 MIRS Mosses.p1 Taklep 2008135 SKQD Mosses.p1 Phypat Pp3c19 20580V3.1 Taklep 2008137 SKQD Mosses.p1 Encstr 2007124 KEFD Mosses.p1 Luncru 2000414 TXVB Liverworts.p1 Marpal 2001291 HMHL Liverworts non mycorrizal.p1 Marpal 2068101 IHWO Liverworts mycorrizal.p1 Physsp. 2003262 YEPO Mosses.p1 Marpal scaff6142 FGenesh5.1 Marpal 2014928 LFVP Liverworts 2 samples combined.p1 Phypat Pp3c21 15330V3.1 Marpal 2001290 HMHL Liverworts non mycorrizal.p1 Dipfol 2002243 AWOI Mosses.p1 Pallye 2009564 YFGP Liverworts.p1 Pallye 2009563 YFGP Liverworts.p1 Dipfol 2002244 AWOI Mosses.p1 Pelepi 2006725 PIUF Liverworts.p1 Buxaph 2013809 HRWG Mosses.p1 Pelnee 2000871 JHFI Liverworts.p1 Pelnee 2000872 JHFI Liverworts.p1 84

Buxaph 2013808 HRWG Mosses.p1 85.3 99.9 Porpin 2018756 UUHD Liverworts.p1 80.3

95.6 Buxaph 2013807 HRWG Mosses.p1 Pornav 2014256 KRUQ Liverworts.p1 100 Fruspp 2019238 CHJJ Liverworts.p1

87 91.9 Radlin 2011506 BNCU Liverworts.p1 Tetpel 2009406 HVBQ Mosses.p1 100 89.1 Schisp. 2019658 LGOW Liverworts.p1 100 Andrup 2004205 WOGB Mosses.p1 100 Calfis 2017526 RTMU Liverworts.p1 90.4 95.8 100 Baztri 2012780 WZYK Liverworts.p1

98 99.9 Scanem 2012821 IRBN Liverworts.p1 99.8 Odopro 2017671 YBQN Liverworts.p1

100 Phacar 2018446 RXRQ Hornworts sporophyte.p2 99.4 Notvin 2013458 TCBC Hornworts.p1 100 99.9 Parhal 2009050 FAJB Hornworts.p1 Parhal 2009049 FAJB Hornworts.p1 100 Phacar 2024694 RXRQ Hornworts sporophyte.p1 Phacar 2002436 WCZB Hornworts gametophyte.p1 98.2 Vigang vigan.Vang0650s00020.1 100 Phacar 2002438 WCZB Hornworts gametophyte.p1 100 Phacar 2002437 WCZB Hornworts gametophyte.p1 Vigrad Vradi0209s00030.1 Selmoe 82473 100 100 Vigung Vigun11g026900.1 90.8 Lycdeu 2081829 PQTO Lycophytes.p1 Phavul Phvul.011G186900.1 Hupluc 2023562 GKAG Lycophytes.p1 96.8 Hupsel 2023213 GTUO Lycophytes.p1 81.5 Cajcaj Ccajan 46131 Hupsel 2010093 YHZW Lycophytes 2 samples combined.p1 Glymax Glyma.08G227200.1 98.7 97.2 100 91.6 99.6 Hupsel 2022482 NYBX Lycophytes A.p1 99.9 99.9 99.5 100 80.9 Glymax Glyma.15G222300.1 Scedis 2014964 EEAQ Eusporangiate Monilophytes.p1 Trisub lcl DF974545.1 GAU49304.1 38362 100 99.4 100 100 100 100 Psinud 2017741 QVMR Eusporangiate Monilophytes.p1 99.6 Tripra Tp57577 TGAC v2 mRNA25879 99.2 Tmepar 2006523 ALVQ Eusporangiate Monilophytes.p1 99.9 97.4 95.3 89.8 89.6 100 Equhye 2129728 JVSZ Eusporangiate Monilophytes.p1 Medtru MtrunA17 Chr8g0355131 99.9 96 89 99.3 100 Osmsp. 2005708 UOMY Leptosporangiate Monilophytes gametophyte.p1 98.6 100 Cicari Ca 20398.1 100 96.3 97.2 100 Osmjav 2078060 VIBO Leptosporangiate Monilophytes.p1 82.7 96.4 Lotjap Lj3 g3v1739 280.1 98.3 100 Dipcon 20 10165 M EKP Leptospor angia te Monilo phytes.p1 98.8 100 99.9 98.8 Dipcon 2010166 MEKP Leptosporangiate Monilophytes.p1 Lupang Lup001774.1 90.6 100 100 Notmon 2063504 YCKE Leptosporangiate Monilophytes.p1 Aradur Aradu.69Z0K 90.8 100 100 99.3 98.6 Adirad 2060298 BMJR Leptosporangiate Monilophytes.p1 96.7 100 91.8100 Wooilv 2073677 YQEC Leptosporangiate Monilophytes.p1 Arahyp arahy.Tifrunner.gnm1.ann1.R5AJY0.1 82.9 Araipa Araip.PZ9H4 99.9 99.6 Linlin 2096686 NOKI Leptosporangiate Monilophytes.p1 100 100 96.9 94.2 100 Linmic 2054839 YIXP Leptosporangiate Monilophytes.p1 Arahyp arahy.Tifrunner.gnm1.ann1.DT2ZPD.1 100 Ginbil Gb 12056 Nissch Nissc17261S33533 99.5 Tetsp. 2070975 CGDN Conifers.p1 99.9 93 89.9 Calmac 2054630 RMMV Conifers March.p1 Casaus Castanospermum16862-PA 100 Amearg 2150463 IAJW Conifers.p1 Mimpud Mimpu11328S00251 100 99.9 Chafas Chafa1194S14649 99.4 Cephar 2111726 NVGZ Conifers 2 samples combined.p1 93.7 100 85.6 Cephar 2060656 GJTI Conifers.p1 Cercan Cerca619S10116 98.4 81.8 96.7 98.9 99.8 Agamac 2069498 ACWS Conifers.p1 Cucmos CmoCh04G026050.1 82.6 Wolnob 2056568 RSCE Conifers.p1 96.3 100 100 Mictet 2009334 MHGD Conifers.p1 Cucpep Cp4.1LG01g21480.1 98.8 100 Mancol 2007022 CDFR Conifers.p1 83.8

Cucmax CmaCh04G024910.1 98.4 99.9 89.2 Retmin 2068679 VGSX Conifers.p1 100 99.1 100 Faltax 2003824 PLYX Conifers 2 samples combined.p1 Lagsic Lsi08G006140.1 90.8 Citlan Cla013661 Faltax 2057157 QHBI Conifers A.p1

82.1 97.8 99.2

87.4 99.9 Ambtri evm 27.model.AmTr v1.0 scaffold00101.38 96.7 97.6 100 100 Aposhe lcl KZ452014.1 PKA51190.1 16157 Momcha lcl NW 019104493.1 XP 022133727.1 5531 85.5 86.5

Cucmel MELO3C019932.2.1 99.8 98.8 100 Phaequ PEQU 26645

99.8

99.3 99.9 99.9 100 Dencat lcl NW 021319817.1 XP 020676624.1 24634 Cucsat evm.model.Chr6.434 92.5

90.9 100 Begfuc Begfu54S12849 85.4 100 99.9 Dencat lcl NW 021319817.1 XP 020676625.1 24635

100 91 97.2 100 99.9 84.3 Musacu GSMUA Achr5T21490 001 82.2 Begfuc Begfu91421S44215 Musacu GSMUA Achr5T21500 001 Datglo Datgl1640S22153 92.8 Anacom Aco012636.1 Orysat LOC Os05g41090.1

99 100 Bradis Bradi2g21790.1 Horvul HORVU1Hr1G068660.3 Mornot L484 020265 Setita Seita.3G197500.1 Sorbic Sobic.010G260600.1 Humlup HL.SW.v1.0.G019297.1 Zeamay Zm00008a018085 Nelnuc NNU 10753-RA Parand lcl JXTB01000137.1 PON59707.1 15766 Helann HanXRQChr09g0258271 Distri Distr391S31865 Daucar DCAR 023134 Treori lcl JXTC01000432.1 PON54469.1 30256 Daucar DCAR 011576 Rhofor TRINITY DN62951 c0 g3 i6.p1 Fraexc FRAEX38873 v2 000337980.2 Fraexc FRAEX38873 v2 000337980.1 Capann CA08g09810 Pyrcom PCP033144.1 Solpen Sopen01g040520.1 Sollyc Solyc01g096820.2.1 Petaxi Peaxi162Scf00647g00529.1 Zizjuj lcl NC 029681.1 XP 024927993.1 7631 Nicben Niben101Scf02891g01008.1 Nicben Niben101Scf17776g00008.1 Nicben Niben101Scf02891g01009.1 Carpap evm.model.supercontig 1289.1 Maldom MDP0000306498 Citsin orange1.1g009980m Zizjuj lcl NC 029681.1 XP 015876262.1 7752 Citcle Ciclev10000859m Carpap evm.model.supercontig 54.31 Thecac Thecc1EG044590t1

Gosrai Gorai.N006600.1 Manesc Manes.10G063500.1 Manesc Maldom MDP0000143220

Potmic 25906 t Prudul Prudul26A023767P1Drydru Drydr32S20242

Pyrbre lcl NW 008988550.1 XP 009339247.1 36009 Pruavi Pav sc0003426.1 g050.1.mk Fraves FvH4 5g27180.1 Pyrbre lcl NW 008988550.1 XP 009339248.1 36010 Rubocc Bras G27363

Jugreg g48181.t1

Casgla Casgl16S00504 Fraana FAN iscf00077997.1.g00001.1 Querob Qrob P0188130.2

Querob Qrob P0188120.2 Alnglu Alngl7889S36097

Riccom 30226.m002047 Roschi RchiOBHm Chr7g0218291 Fraana FAN iscf00302165.1.g00001.1 Poptri Potri.008G011540.1

Poptri Potri.010G247400.1 Prumum lcl NC 024130.1 XP 008231882.2 16155

Casmol maker-scaffold05534-augustus-gene-0.18-mRNA-1

Casmol maker-scaffold05534-augustus-gene-0.18-mRNA-2

Tree scale: 0.1 Supplementary Figure 14: Maximum likelihood tree of CYCLOPS

Polcom 2042496 SZYG Mosses gametophyte.p1

Mixspe 2157287 NWQC Liverworts.p1 Phacar 2141749 RXRQ Hornworts sporophyte.p1

Racelo 2075031ABCD Mosses.p1 Dicsco 2102368 NGTD Mosses.p1 Leualb 2015077 VMXJ Mosses.p1

Leugla 2065124 RGKI Mosses.p1 Scoaqu 2005245 BPSG Mosses.p1Cerpur 2009225 FFPD Mosses.p1

Phacar 2139004 RXRQ Hornworts sporophyte.p1 Physsp. 2016592 YEPOTimaus Mosses.p1 2015750 ZQRI Mosses.p1

Andrup 2014899 WOGBDipfol Mosses.p1 2073705 AWOI Mosses.p1 Atrang 2085278 ZTHV Mosses.p1 Buxaph 2070490 HRWG Mosses.p1 Tetpel 2013208 HVBQ Mosses.p1 Parhal 2057235 FAJB Hornworts.p1 Phypat Pp3c23 22500V3.1 Notvin 2020225 TCBC Hornworts.p1

Pornav 2011093 KRUQ Liverworts.p1 Taklep 2007702 SKQD Mosses.p1 Pornav 2011092 KRUQ Liverworts.p1 Porpin 2014490 UUHD Liverworts.p1 Radlin 2000833 BNCU Liverworts.p1 Marpal 2000586 LFVP Liverworts 2 samples combined.p1 MixspePtipul 2017231 2135876 NWQC HPXA Liverworts.p1 Liverworts.p1

Baztri 2091369 WZYK Liverworts.p1 Marpal 2011348 HMHL LiverwortsScanem 2015799 non mycorrizal.p1 IRBN Liverworts.p1 Pallye 2018977 YFGP Liverworts.p1

Hedcil 2011049 YWNF Mosses.p1 Plains 2081114 BGXB Mosses.p1 Roscap 2010673 XWHK Mosses.p1 Bryarg 2042803 JMXW Mosses.p1 Phifon 2011404 ORKS Mosses.p1 Marpal 2012133 IHWO Liverworts mycorrizal.p1 Ortlye 2000592 CMEQ Mosses.p1 Aulhet 2090541 WNGH Mosses.p1 Pseele 2007014 QKQO Mosses.p1 Rhyser 2011179 JADL Mosses.p1 Anocla 2010668 VBMM Mosses.p1 Leubra 2100051 ZACW Mosses.p1 Leujul 2167700 IGUH Mosses.p1 Calcor 2002155 TAVP Mosses.p1 Marpal scaff2618 FGenesh7.1 Calcor 2002154 TAVP Mosses.p1 Calcor 2002153 TAVP Mosses.p1 Stesub 2009137 LNSF Mosses.p1 Stesub 2009136 LNSF Mosses.p1 Necdou 2184024 TMAJ Mosses.p1 Anoatt 2061729 QMWB Mosses.p1 Luncru 2000384 TXVB Liverworts.p1 Cliden 2008278 MIRS Mosses.p1 Loebre 2002298 WSPM Mosses.p1 Luncru 2000387 TXVB Liverworts.p1 Selapo 2010945 LGDQ Lycophytes.p1 Sellep 2009639 ABIJ Lycophytes.p1

Concon 2046908 ILBQ Liverworts.p1 100 Selsta 2008912 ZZOL Lycophytes.p1 Selmoe predCyclops scaf4

100 Selmoe predCyclops scaf9 95.2 100 99 100 83.7 100 Lycann 2004081 ENQF Lycophytes.p1 89.7

98.5 89.1 100 95.7 99.9 Hupsel 2006383 YHZW Lycophytes 2 samples combined.p1

100 96.6 100 Hupmyr 2010468 CBAE Lycophytes.p1 82 92.5 Hupsqu 2009222 GAON Lycophytes.p1 88.1 95.2 Hupsqu 2012975 GAON Lycophytes.p1

100 Hupluc 2006924 GKAG Lycophytes.p1 Hupsel 2001712 GTUO Lycophytes.p1 Hupsel 2001713 GTUO Lycophytes.p1 Prumum lcl NC 024132.1 XP 008238052.1 21991 Hupsel 2031345 YHZW Lycophytes 2 samples combined.p1 Linmic 2055381 YIXP Leptosporangiate Monilophytes.p1 Prumum lcl NC 024132.1 XP 008238054.1 21990 100 Linlin 2018558 NOKI Leptosporangiate Monilophytes.p1 98.4 Dipcon 2011136 MEKP Leptosporangiate Monilophytes.p1 Prumum lcl NC 024132.1 XP 008238056.1 21992 Osmjav 2077951 VIBO Leptosporangiate Monilophytes.p1 99.9 Osmsp. 2013317 UOMY Leptosporangiate Monilophytes gametophyte.p1 94.1 Prumum lcl NC 024132.1 XP 016651171.1 21988 99.9 Equhye 2007269 JVSZ Eusporangiate Monilophytes.p1 89.6 99.9 Dioedu 2018815 WLIC Cycadales.p1 Prumum lcl NC 024132.1 XP 008238055.1 21989 99.8 98.8 Osmsp. 2012622 UOMY Leptosporangiate Monilophytes gametophyte.p1 100 94.5 Osmjav 2077695 VIBO Leptosporangiate Monilophytes.p1 92.9 100 Psinud 2016627 QVMR Eusporangiate Monilophytes.p1 100 100 84.2 99.7 100 Tmepar 2001888 ALVQ Eusporangiate Monilophytes.p1 100 93.3 96.3 Pruper Prupe.5G020000.1 100 Tmepar 2001887 ALVQ Eusporangiate Monilophytes.p1 Prudul Prudul26A032240P1 Linlin 2005546 NOKI Leptosporangiate Monilophytes.p1 Pruavi Pav sc0001478.1 g270.1.mk 98.5 97.5 99.3 Onosen 2002904 HTFH Leptosporangiate Monilophytes.p1 Pyrbre lcl NW 008988166.1 XP 018505018.1 18074 93.1 100 Dipwic 2087961 UFJN Leptosporangiate Monilophytes.p1 100 96.8 Blespi 2009508 VITX Leptosporangiate Monilophytes.p1 99.5 99.5 100 99.9 Blespi 2007157 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Maldom MDP0000172991 100 97.3 96.8 99.8 Pittri 2010145 UJTT Leptosporangiate Monilophytes.p1 97.4 89.9 100 Pyrcom PCP026193.1 82.8 98.8 95.6 Ptevit 2100386 POPJ Leptosporangiate Monilophytes.p1 89.4 99.7 99.9 Notmon 2002199 YCKE Leptosporangiate Monilophytes.p1 Pyrbre lcl NW 008988166.1 XP 018505017.1 18073 91.8 100 86.1 Adirad 2062549 BMJR Leptosporangiate Monilophytes.p1 Pyrbre lcl NW 008988732.1 XP 009343190.1 39583 93.1 Cycmic CMI00021778 88.4 98.8 Sciver 2005841 YFZK Conifers.p1 Pyrcom PCP041484.1 100 100 99.9 82.7 Mictet 2073857 MHGD Conifers.p1 Maldom MDP0000263508 95 99.9 Halbid 2054883 OWFC Conifers.p1 96.3 86.1 Drydru Drydr202S08474 100 98.9 Cephar 2113043 NVGZ Conifers 2 samples combined.p1 Potmic 29053 t 99.8 Ausspi 2013603 BTTS Conifers.p1 99.4 100 97.6 Psechi 2082599 YLPM Conifers.p1 Fraves FvH4 5g23980.1 99.7 98.5 83.8 99.8 Taicry 2064429 QSNJ Conifers.p1 99.4 100 Auschi 2068955 YYPE Conifers.p1 Roschi RchiOBHmRubocc Chr7g0213421 Bras G15544 100 Chalaw 2069845 AIGO Conifers.p1 99.9 Micdec 2057283 XQSG Conifers.p1 93.2 81.799.6 100 Ambtri evm 27.model.AmTr v1.0 scaffold00048.167 84.2 Aposhe lcl KZ451932.1 PKA61134.1 6084 100 Dencat lcl NW 021319178.1 XP 020703676.1 13417 100 Phaequ PEQU 14765 Parand lcl JXTB01000343.1 PON44789.1Mornot L484 26381 006354 94.8 Humlup HL.SW.v1.0.G034735.1 Musacu GSMUA Achr1T15520 001 99.4 Treori lcl JXTC01000049.1 PON94676.1Mornot L484 0063559460 81.6 Anacom Aco016002.1 95.8 100 Orysat LOC Os06g02520.1 97.2 100 98 100 Horvul HORVU7Hr1G008420.1 Distri Distr526S09389 100 99.1 Bradis Bradi1g50560.3 92.6 98.6 95.6 100 94.8 85.6 Setita Seita.4G012000.1

80 99.1 100 Zeamay Zm00008a024123 89 Alnglu Alngl19262S08206 80.5 Sorbic Sobic.010G013000.1 100 94.1 99.9 89.9 100 100 Alnglu Alngl3972S26264 99.9 Zeamay Zm00008a033907 Jugreg g50324.t1 100 Zizjuj lcl NC 029689.1 XP 015897350.1 29843 100 Rhofor TRINITY DN48500 c0 g3 i1.p1 100 Alnglu Alngl19262S19173Jugreg g50324.t2 98.6 Daucar DCAR 008182 100 Daucar DCAR 004239 Rhofor TRINITY DN72146 c0 g1 i1.p1 Citlan Cla008865 Helann HanXRQChr03g0081161 Lagsic Lsi07G011310.1 Helann HanXRQChr03g0081381 99.9 100 87.1 91.1 88.7 96.9 99.5 99.9 Helann HanXRQChr17g0554671

94.3 90.9 97.7 89.3 91.6 93.3 Helann HanXRQChr09g0247011 99.9 Fraexc FRAEX38873 v2 000109580.2

99.5 97.9 100 Fraexc FRAEX38873 v2 000109580.1 Petaxi Peaxi162Scf02295g00022.1 99.5 Nicben Niben101Scf02346g05007.1 Nicben Niben101Scf11581g02001.1 Cucmel MELO3C013794.2.1 100 Capann CA01g08520 Solpen Sopen08g024410.1 Cucsat evm.model.Chr3.100 Sollyc Solyc08g075760.2.1 95.6 Poptri Potri.003G103100.1 87.7 Poptri Potri.001G130800.4 Manesc Manes.17G003400.1 Riccom 29827.m002598 Cucmax CmaCh16G012170.1 Citsin orange1.1g008933m Citcle Ciclev10000885m Carpap evm.model.supercontig 90.44 Gosrai Gorai.008G220100.1 Thecac Thecc1EG016677t1 Chafas Chafa54149S24099 Cucmos CmoCh16G012610.1 Cercan Cerca9S31619 Casaus Castanospermum15515-PA Medtru MtrunA17 Chr8g0369511 Cucpep Cp4.1LG14g10130.1 Casaus Castanospermum14084-PA Cucpep Cp4.1LG08g09120.1 Cucmos CmoCh06G006070.1 Cucmax CmaCh06G006000.1 BegfucBegfuc Begfu1565S20692Datglo Begfu817S50895 Datgl81S35208

Vigrad Vradi11g07850.1

Cajcaj Ccajan 12408 Vigung Vigun02g102000.1 Cicari Ca 13803.1

Phavul Phvul.002G128600.1 Vigang vigan.Vang0002ss01540.1 Araipa Araip.02MA2 Glymax Glyma.09G213700.1 Aradur Aradu.ZFB7W

Aradur Aradu.H2WL6 Lupang Lup027672.1 Glymax Glyma.01G149500.1 Lotjap Lj2g3v1549600.1

Nissch Nissc2707S07594 Momcha lcl NW 019104523.1 XP 022145367.1 16150

Momcha lcl NW 019104523.1 XP 022145368.1 16151 Medtru MtrunA17 Chr5g0409341

Tripra Tp57577 TGAC v2 mRNA17867

Trisub lcl DF973464.1 GAU31677.1 20735

Arahyp arahy.Tifrunner.gnm1.ann1.0046K4.1

Arahyp arahy.Tifrunner.gnm1.ann1.BJTL8K.1

Arahyp arahy.Tifrunner.gnm1.ann1.DKTU9V.1

Tree scale: 0.1 Supplementary Figure 15: Maximum likelihood tree of SymRK.

Osmsp. 2009606 UOMY Leptosporangiate Monilophytes gametophyte.p1

Faltax 2018563 PLYX Conifers 2 samples combined.p1

Osmjav 2078984 VIBO Leptosporangiate Monilophytes.p1

Dipcon 2108677 MEKP Leptosporangiate Monilophytes.p1

Nagnag 2010568 UUJS Conifers.p1 Retmin 2072494 VGSX Conifers.p1

Ophvul 2008350 QHVS Eusporangiate Monilophytes leaf.p1 Ausspi 2079887 BTTS Conifers.p1

Ararul 2006433 XTZO Conifers.p1

Ararul 2006434 XTZO Conifers.p1

Selsta 2002893 ZZOL Lycophytes.p1

Marpal 2007657 IHWO Liverworts mycorrizal.p1 Marpal 2012405Marpal LFVP 2011505 Liverworts HMHL 2 samplesLiverworts combined.p1 non mycorrizal.p1

Ginbil Gb 30966 Marpal 2012404 LFVP Liverworts 2 samples combined.p1 Selmoe 131152

Marpal scaff5907 FGenesh2.1 Selmoe 31809

Amearg 2025941 IAJW Conifers.p1 Cephar 2007503 GJTI Conifers.p1 Cephar 2113290 NVGZ Conifers 2 samples combined.p1 Cephar 2091883 WYAJ Conifers.p1

Cunlan 2019983 ZQVF Conifers 2 samples combined.p1

Taicry 2012634 QSNJ Conifers.p1

Athcup 2011075 XIRK Conifers.p1

Chalaw 2009831 AIGO Conifers.p1 Concon 2006700 ILBQ Liverworts.p1 Tetsp. 2011543 CGDN Conifers.p1 Piluvi 2007679 ETCJ Conifers.p1

Disarc 2016780 GKCZ Conifers.p1

Pelnee 2015521 JHFI Liverworts.p1 Neopan 2072446 JDQB Conifers.p1

Ambtri evm 27.model.AmTr v1.0 scaffold00046.162

Pelepi 2015132 PIUF Liverworts.p1 Dencat lcl NW 021318823.1 XP 020692125.1 6577 Phacar 2142153 RXRQ Hornworts sporophyte.p1 Scanem 2168092 IRBN Liverworts.p1 Phaequ PEQU 04466 Phacar 2015928 WCZB Hornworts gametophyte.p1 Phaequ PEQU 05618 Dencat lcl NW 021319089.1 XP 020677596.1 11426

Dencat lcl NW 021319089.1 XP 020677592.1 11424 Phacar 2024783 RXRQ Hornworts sporophyte.p1 Dencat lcl NW 021319089.1 XP 020677593.1 11425

Musacu GSMUA Achr9T09200 001

Anacom Aco002116.1

Orysat LOC Os07g38070.1

99.9 Bradis Bradi1g24287.2 100 99.9 Horvul HORVU2Hr1G058820.30

Setita Seita.2G357100.1

100 96.9 100 99.5 Sorbic Sobic.002G343100.1

100

Pyrbre lcl NW 008988233.1 XP 009371365.1 23157 100 Zeamay Zm00008a029124

100 99.3 100 97.7 100 100 100 99.9 98.2 97 95.7 99.2 Monuni 2096287 LRTN Core Eudicots-Asterids.p1 Pyrbre lcl NW 008988155.1 XP 009364823.1 17170 96.9 100

96.8 99.3 Rhofor TRINITY DN55924 c0 g4 i1.p1 97.5 99.9

99.9 100 Helann HanXRQChr09g0262871

100 Helann HanXRQChr11g0324421 Pyrcom PCP044647.1 100

100

99.9 Maldom MDP0000235629 Daucar DCAR 010758 83.2 97.4 100 99.7 100 Daucar DCAR 025861 Pyrcom PCP025047.1 99.6 100 Fraexc FRAEX38873 v2 000294710.1 Pyrbre lcl NW 008988912.1 XP 009345866.1 42030 94.2 99.9 95.9 94.1 97.2 100 100 Fraexc FRAEX38873 v2 000029260.1 92.4 100 93.2 99.3 Maldom MDP0000322681 94.5 100 100 100 Fraexc FRAEX38873 v2 000029260.2 96.5 Prudul Prudul26A002329P1 99.8 99.3 Nicben Niben101Scf00069g12007.1 99.7 Nicben Niben101Scf01477g00020.1 Pruper Prupe.6G209400.1 100 100 Petaxi Peaxi162Scf00703g00117.1 91 Prumum lcl NC 024126.1 XP 008236625.1 1968 85.2 100 Capann CA02g24350

85.3 100 Pruavi Pav sc0004578.1 g110.1.mk 100 Sollyc Solyc02g091590.2.1 96.1 99.8 100 99.5 87.5 100 Solpen Sopen02g036210.1 Fraana FAN iscf00085812.1.g00001.1 100 100 Poptri Potri.007G004700.1 Fraves FvH4 1g19010.1 95.9 100 99.9 80.8 Riccom 28333.m000564

100 Fraana FAN iscf00091613.1.g00002.1Potmic 31778 t Manesc Manes.12G121400.1

100 Citsin orange1.1g002943m 100 99.4 99.1 96.5 100 89.8 Citcle Ciclev10024877m 100 Roschi RchiOBHm Chr2g0110021 98.7 Rubocc Bras G11214 98.8 Carpap evm.model.supercontig 129.17

100 Gosrai Gorai.008G088500.1 Drydru Drydr303S03268 Thecac Thecc1EG000924t1

100 100 97.5 100 91.1 Casmol maker-scaffold05713-augustus-gene-0.12-mRNA-1

100 82.2 94.4 Querob Qrob P0386880.2

95 Treori lcl JXTC01000034.1 PON97099.1 7150 Jugreg g49007.t1

100 100 99 Casgla Casgl291S14102

100 Parand lcl JXTB01000482.1 PON38885.1 30914 Alnglu Alngl603S33230 Humlup HL.SW.v1.0.G001340.1Distri Distr2147S18399 96.4 Cercan Cerca9S31708 Treori lcl JXTC01000034.1 PON97098.1 7149 100 100 98.4 Mimpud Mimpu9946S28982

Mimpud Mimpu26253S21138 96.5 100

98.6

99 100 100 100 Casaus Castanospermum23040-PA 99.7 99.4

80 Cucmel MELO3C022378.2.1 99.2 Nissch Nissc593S10677 92.6 95.1

85.6

99.8 Arahyp arahy.Tifrunner.gnm1.ann1.5W9Q31.1 Cucsat evm.model.Chr6.715Citlan Cla007076 Zizjuj lcl NC 029686.1 XP 024931923.1Lagsic 22595 Lsi09G017890.1 Aradur Aradu.P8MSW Arahyp arahy.Tifrunner.gnm1.ann1.TBZT1P.1

Araipa Araip.C87U1

Casaus Castanospermum23651-PA

Lupang Lup025527.1

Nissch Nissc524545S27149

Araipa Araip.3F2C7

Cucmax CmaCh08G000380.1 Aradur Aradu.Q4WIY

Arahyp arahy.Tifrunner.gnm1.ann1.5KC586.1

Arahyp arahy.Tifrunner.gnm1.ann1.SZ7D6R.1

Cicari Ca 24300.1

Medtru MtrunA17 Chr5g0411631

TripraTp57577 TGAC v2 mRNA38286 Cucmos CmoCh08G000380.1 Tp57577TGAC v2 mRNA38354Tripra

Cucpep Cp4.1LG17g09570.1

Begfuc Begfu848S14144 Datglo Datgl115S18976

Vigrad Vradi11g09090.1

Vigung Vigun02g088500.1

Cajcaj Ccajan 12295

Phavul Phvul.002G116200.1

Lotjap Lj2g3v1467920.1 Vigang vigan.Vang0002ss02210.1 Phavul Phvul.002G143400.1 Momcha lcl NW 019104624.1 XP 022155334.1 25075 Glymax Glyma.09G202300.1 Glymax Glyma.01G020100.1

Momcha lcl NW 019104624.1 XP 022155335.1 25076

Trisub lcl DF973800.1 GAU40327.1 29385

Tree scale: 0.1 Supplementary Figure 16: Maximum likelihood tree of HYP.

Osmsp. 2079476 UOMY Leptosporangiate Monilophytes gametophyte.p1

Anetom 2020976 CQPW Leptosporangiate Monilophytes.p1

Cyaspi 2016643 GANB Leptosporangiate Monilophytes.p1

Dipcon 2102632 MEKP Leptosporangiate Monilophytes.p1

Osmjav 2075543 VIBO Leptosporangiate Monilophytes.p1

Linlin 2002660 NOKI Leptosporangiate Monilophytes.p1

Scedis 2083681 EEAQ Eusporangiate Monilophytes.p1 Ophpet 2012539 WTJG Eusporangiate Monilophytes.p1 Botvir 2014654 BEGM Eusporangiate Monilophytes.p1 Psinud 2011165 QVMR Eusporangiate Monilophytes.p1 Angeve 2008321 NHCM Eusporangiate Monilophytes.p1 Scedis 2008389 EEAQ Eusporangiate Monilophytes.p1

Equhye 2128223 JVSZ Eusporangiate Monilophytes.p1

Equdif 2009925 CAPN Eusporangiate Monilophytes.p1

Marpal 2014546 LFVP Liverworts 2 samples combined.p1 Marpal 2009272 HMHL Liverworts non mycorrizal.p1

Marpal 2014545 LFVP Liverworts 2Marpal samples 2009271 combined.p1 HMHL Liverworts non mycorrizal.p1

Marpal 2010944 IHWO Liverworts mycorrizal.p1

Marpal 2010943 IHWO Liverworts mycorrizal.p1

Marema 2073764 TFYI Liverworts.p1 Concon 2000680 ILBQ Liverworts.p1 Luncru 2010132 TXVB Liverworts.p1 Marpal scaff7062 FGenesh1.1 Luncru 2010131 TXVB Liverworts.p1 Luncru 2010133 TXVB Liverworts.p1

BlaspNW c325655 g2 i1 m.64831 BlaspNW c325655 g2 i3 m.64835 Barbar 2002997BlaspNW OFTV c325655 Liverworts.p1 g2 i4 m.64838 Odopro 2129058 YBQN Liverworts.p1

Thyele 2121838 EWXK Leptosporangiate Monilophytes.p1 Plajap 2138543 UWOD Leptosporangiate Monilophytes.p1 Culmac 2019125 PNZO Leptosporangiate Monilophytes.p1 Culmac 2019126 PNZO Leptosporangiate Monilophytes.p1 Hymbiv 2007839 QIAD Leptosporangiate Monilophytes.p1 Lygjap 2078489 PBUU Leptosporangiate Monilophytes.p1 Cyaspi 2069387 GANB Leptosporangiate Monilophytes.p1 Scanem 2006172 IRBN Liverworts.p1 Plajap 2138960 UWOD Leptosporangiate Monilophytes.p1 Culmac 2151582 PNZO Leptosporangiate Monilophytes.p1 Linlin 2094272 NOKI Leptosporangiate Monilophytes.p1 Pteens 2015551 FLTD Leptosporangiate Monilophytes.p1 Scanem 2006173 IRBN Liverworts.p1 Ptevit 2101230 POPJ Leptosporangiate Monilophytes.p1 Adirad 2060248 BMJR Leptosporangiate Monilophytes.p1 Mixspe 2016790 NWQC Liverworts.p1 Notmon 2002386 YCKE Leptosporangiate Monilophytes.p1 Gagari 2074666 DCDT Leptosporangiate Monilophytes.p1 Parcor 2003914 ZXJO Leptosporangiate Monilophytes.p1 Leuimm 2073335 WGTU Leptosporangiate Monilophytes.p1 Calfis 2179022 RTMU Liverworts.p1 Nepexa 2035984 NWWI Leptosporangiate Monilophytes.p1 Schisp. 2103990 LGOW Liverworts.p1 Gymdry 2000129 HEGQ Leptosporangiate Monilophytes.p1 Polacr 2000734 FQGQ Leptosporangiate Monilophytes.p1 Polacr 2000733 FQGQ Leptosporangiate Monilophytes.p1 Hompyc 2010762 OCZL Leptosporangiate Monilophytes.p1 Pelepi 2090729 PIUF Liverworts.p1 Dipwic 2085957 UFJN Leptosporangiate Monilophytes.p1 Athfil 2004571 URCP Leptosporangiate Monilophytes.p1 Pelnee 2111694 JHFI Liverworts.p1 Blespi 2020299 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Phacar 2019063 RXRQBaztri Hornworts 2090226 sporophyte.p1 WZYK Liverworts.p1 Blespi 2020298 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Phacar 2017189 WCZB Hornworts gametophyte.p1 Theacu 2003657 MROH Leptosporangiate Monilophytes.p1 Pallye 2018646 YFGP Liverworts.p1 Onosen 2000048 HTFH Leptosporangiate Monilophytes.p1 Cysfra 2027554 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Pallye 2018933 YFGP Liverworts.p1 Cysfra 2010706 LHLE Leptosporangiate Monilophytes.p1 Selwil 2049450 KJYC Lycophytes.p1 Selsta 2005439 ZZOL Lycophytes.p2 Selmoe 96710 Psecar 2019988 UPMJ Lycophytes.p1 Parhal 2004099 FAJB Hornworts.p1 Lycdeu 2077072 PQTO Lycophytes.p1 Parhal 2004100 FAJB Hornworts.p1 Phydru 2019755 ZZEI Lycophytes.p1 Notaen 2004664 DXOU Hornworts.p1 Hupmyr 2060931 CBAE Lycophytes.p1 Hupsel 2132400 NYBX Lycophytes A.p1 Phacar 2138076 RXRQ Hornworts sporophyte.p1 Notvin 2013976 TCBC Hornworts.p1 Hupluc 2022351 GKAG Lycophytes.p1 Megfla 2053630 UCRN Hornworts.p1 Lycapp 2006925 ULKT Lycophytes.p1 Psecar 2002381 UPMJ Lycophytes.p1 Denobs 2013140 XNXF Lycophytes.p1 Lycdeu 2081425 PQTO Lycophytes.p1 Taklep 2079108 SKQD Mosses.p1 Lycann 2004374 ENQF Lycophytes.p1 Taklep 2003401 SKQD Mosses.p1 Dipdig 2068253 WAFT Lycophytes.p1

84.7 Dipdig 2006236 WAFT Lycophytes.p1 Psecar 2010152 UPMJ Lycophytes.p1 99.9 Lycdeu 2076817 PQTO Lycophytes.p1 100 Hupsel 2010026 GTUO Lycophytes.p1 98.3 Hupsel 2167002 YHZW Lycophytes 2 samples combined.p1 Hupluc 2009651 GKAG Lycophytes.p1

99.9 100 Hupsel 2025458 NYBX Lycophytes A.p1 94.9 Hupsel 2025457 NYBX Lycophytes A.p1 84.2 98.2 97.4 95.6 86.1 Phydru 2025425 ZZEI Lycophytes.p1

91.3 99.8 99.7 Hupsqu 2009452 GAON Lycophytes.p1 99.4 97.2

91.6 Hupluc 2009654 GKAG Lycophytes.p1 92 Medtru MtrunA17 Chr2g0302241 Hupluc 2009653 GKAG Lycophytes.p1 Hupluc 2009652 GKAG Lycophytes.p1 Medtru MtrunA17 Chr3g0132211 100 100 Hupsel 2011075 YHZW Lycophytes 2 samples combined.p1 87.8 84.8 Medtru MtrunA17 Chr2g0302251 100 Hupsel 2010028 GTUO Lycophytes.p1 Tripra Tp57577 TGAC v2 mRNA14691 100 91.1 Hupsel 2015170 NYBX Lycophytes A.p1 Trisub lcl DF973341.1 GAU26757.1 15815 100 83.8 97.6 Hupsel 2011076 YHZW Lycophytes 2 samples combined.p1 100 100 100 100 97.7 Hupsel 2015171 NYBX Lycophytes A.p1 99.6 98.9 99.1 100 99.4 97.4 90.1 Hupsel 2011074 YHZW Lycophytes 2 samples combined.p1 99.9 Cicari Ca 14800.1 95.6 97.8 99.3 99 Hupsel 2010027 GTUO Lycophytes.p1 Lotjap Lj1g3v1513760.1 98.8 99.6 99.3 95.5 Dioedu 2009179 WLIC Cycadales.p1

97.1 97.7 Lotjap Lj1g3v1513760.2 99.9 100 100 100 100 99.4 97.5 Wolnob 2056730 RSCE Conifers.p1 100 Vigrad Vradi05g05540.1 99.6 84.2 95.1 96.8 100 86.8 Acmpan 2111918 HILW Conifers.p1 Vigang vigan.Vang0669s00010.1 96.2 100 100 98.3 99.7 Lepsp. 2076982 BBDD Conifers.p1 Vigung Vigun09g105800.1 Halbid 2055420 OWFC Conifers.p1 99.6 87.3 98.9 100 Phavul Phvul.009G166200.1 99.1 Parust 2037965 JZVE Conifers.p1 98.3 98.8 Thupli 2040188 VFYZ Conifers.p1 Glymax Glyma.04G196000.1 100 98.8 96.3 Thudol 2011226 NKIN Conifers.p1 Glymax Glyma.06G169800.1 93.1 97.9 100 89.9 99.7 Chalaw 2068273 AIGO Conifers.p1 87.1 94 Cajcaj Ccajan 08494 96 96.2 90.2 88.5 Fokhod 2057155 UEVI Conifers.p1 99.5 Aradur Aradu.5E20L 99.7 Cupdup 2073010 QNGJ Conifers.p1 92.6 Arahyp arahy.Tifrunner.gnm1.ann1.185HYR.1 100 99.9 Micdec 2056839 XQSG Conifers.p1 100 99.8 95.8 Piluvi 2062367 ETCJ Conifers.p1 Arahyp arahy.Tifrunner.gnm1.ann1.6KU1RV.1 99.9 84.9 Auschi 2067697 YYPE Conifers.p1 Araipa Araip.AZ7RZ 99.7 Widced 2054833 AUDE Conifers.p1 Nissch Nissc8731S31816 98 99.8 Disarc 2009968 GKCZ Conifers.p1 Casaus Castanospermum11435-PA 97.2 Neopan 2070553 JDQB Conifers.p1 98 95.4 Calmac 2053321 RMMV Conifers March.p1 Tripra Tp57577 TGAC v2 mRNA38697 96.3 99.1 96.5 95.5 Ambtri evm 27.model.AmTr v1.0 scaffold00013.97 Trisub lcl DF973985.1 GAU43611.1 32669 100 100 Anacom Aco003678.1 Medtru MtrunA17 Chr4g0057931 87.2 100 Musacu GSMUA Achr3T16160 001 100 98.1 Aposhe lcl KZ451921.1 PKA62053.1 5268 Trisub lcl DF974273.1 GAU46987.1 36045 82.9 80.3 99.8 94.3 Aposhe lcl KZ451931.1 PKA61352.1 5952 Tripra Tp57577 TGAC v2 mRNA19904 96.6 99.7 Dencat lcl NW 021319315.1 XP 020684827.1 16533 Medtru MtrunA17Cicari Chr4g0057361 Ca 21208.1 100 93.7 85.7 99.5 96.5 90.8 99.9 Phaequ PEQU 06420 Lotjap Lj4g3v1386910.1 91.9 Orysat LOC Os11g29630.1 Horvul HORVU3Hr1G026350.1 99.6 99.7 Vigang vigan.Vang11g07150.1 96.586.3 Vigrad Vradi07g13410.1 99.7 97.3 100 Bradis Bradi4g19020.1 Setita Seita.8G122300.1 Vigung Vigun03g312500.1 100 100 89.3 Sorbic Sobic.005G116300.1 85.4 99.6 Zeamay Zm00008a015291 Glymax Glyma.17G130600.1 100 Daucar DCAR 026461 97.4 99.9 Glymax Glyma.05G048700.1Cajcaj Ccajan 01780 98.5 Helann HanXRQChr12g0372631 100 95.9 Lupang Lup031428.1 100 Fraexc FRAEX38873 v2 000347340.1

Lupang Lup027516.1 100 Fraexc FRAEX38873 v2 000327400.1 94.8 100 100 98.7 96.3 96.8 Fraexc FRAEX38873 v2 000116530.1 Chafas Chafa341S21262 Petaxi Peaxi162Scf00518g00423.1 90.3 97.2 99.9 81.1 99.9 99.2 94.3 Nicben Niben101Scf02530g00003.1 86.7 Mimpud CercanMimpu14085S29613 Cerca4S25718 100 96.8 100 Nicben Niben101Scf05950g01011.1

93.4 91.9 100 Capann CA07g01710 Casgla Casgl774S02665 89.9 97 Sollyc Solyc05g015480.2.1 Jugreg g14829.t1 100 93.3 100 99.9 Alnglu Alngl172692S18131 95.7 Solpen Sopen05g010810.1 99.3 92.1 98.1 99.4

95.7 99.8 100 98.2 Thecac Thecc1EG008813t1

96.8 100 100 Gosrai Gorai.005G166900.1 100 Querob Qrob P0094130.2 89.9

100 99.9 99.9 Citcle Ciclev10031960m

100 100 Citsin orange1.1g021539m 97.5 99.1 Maldom MDP0000187498 100 Poptri Potri.003G172100.1 Poptri Potri.001G056400.2

Maldom MDP0000212528 100 100 97.4 Poptri Potri.T147601.1 Maldom MDP0000413272 100 Riccom 29929.m004646 82 99.4 Manesc Manes.13G011600.2

99 Pyrcom PCP044002.1 Manesc Manes.13G011600.1 Manesc Manes.12G010800.1 98.8 95.7

91.5 Manesc Manes.12G010800.3

98.6 92.3 100 Manesc Manes.12G010800.2 Prudul Prudul26A026323P1 Casmol augustus masked-scaffold12638-abinit-gene-0.2-mRNA-1 100 99.7 Datglo Datgl55S32306 Pruper Prupe.5G042900.1 87.8 Casgla Casgl10S00028

92.3 Jugreg g3669.t1 Pyrbre lcl NW 008988268.1 XP 009373451.1 25076 87.6 Querob Qrob P0651760.2 Casmol augustus masked-scaffold01258-abinit-gene-0.10-mRNA-1 Potmic 22228 t 99.6 Pyrbre lcl NW 008988268.1 XP 009373450.1 25075 Distri Distr718S10164 Zizjuj lcl NW 015453420.1 XP 015900862.1 33645 Fraves FvH4 5g21420.1 Zizjuj lcl NC 029688.1 XP 015894268.1 26534 Pruavi Pav co4051917.1 g010.1.mk Mornot L484 000867 Pruavi Pav sc0004971.1 g010.1.mk Humlup HL.SW.v1.0.G025966.1 Rubocc Bras G07418 Treori lcl JXTC01001090.1 PON32659.1 35611 Parand lcl JXTB01000243.1 PON50673.1 22208 Prumum lcl NC 024132.1 XP 008238347.1 22232 Drydru Drydr13S06743 Fraana FAN iscf00056820.1.g00001.1Drydru Drydr66S23748 Rubocc Bras G07129 Roschi RchiOBHm Chr4g0430181 Potmic 16381 t Fraana FAN iscf00171292.1.g00001.1 Roschi RchiOBHm Chr7g0208851 Fraana FAN iscf00177226.1.g00001.1 Fraves FvH4 4g23710.1 Mornot L484 001098 Fraana FAN iscf00267105.1.g00002.1 Pruper Prupe.1G225300.1 Prudul Prudul26A017587P1 Pruavi Pav sc0000091.1 g430.1.mk Prumum lcl NC 024127.1 XP 008222166.1 7009 Prumum lcl NC 024127.1 XP 008222165.1 7008 Maldom MDP0000782388 Pyrcom PCP018056.1 Pyrbre lcl NW 008988249.1 XP 009372278.1 24026 Pyrcom PCP033440.1 Maldom MDP0000730072 Maldom MDP0000279990 Fraexc FRAEX38873 v2 000220590.1

Humlup HL.SW.v1.0.G007162.1Distri Distr1427S14489 Citlan Cla002624

Cucsat evm.model.Chr1.940Lagsic Lsi02G005090.1 Parand lcl JXTB01000014.1 PON77295.1 2914 Cucmel MELO3C002365.2.1 Treori lcl JXTC01000273.1 PON72131.1 25255

Cucpep Cp4.1LG09g09660.1

Cucmos CmoCh18G002210.1 Begfuc Begfu2204S25341 Zizjuj lcl NC 029683.1 XP 015882189.1 13933 Cucmax CmaCh18G003150.1 Begfuc Begfu5301S12731

Zizjuj lcl NC 029683.1 XP 024929542.1 13934 Citcle Ciclev10033613m Cepfol Cfol v3 17730 Thecac Thecc1EG014648t1 Daucar DCAR 026228 Daucar DCAR 026216

Gosrai Gorai.008G206500.1 Riccom 30147.m014498

Citsin orange1.1g035915m Poptri Potri.015G097000.1 Poptri Potri.012G098200.2

Manesc Manes.06G120000.1

Helann HanXRQChr09g0273271

Carpap evm.model.supercontig 13.110

Fraexc FRAEX38873 v2Fraexc 000373290.1 FRAEX38873

Momcha lcl NW 019104497.1 XP 022137274.1 9211

Tree scale: 0.1 Supplementary Figure 17: Maximum likelihood tree of HYP3.

Polcom 2011566 SZYG Mosses gametophyte.p1

Physsp. 2019297YEPO Mosses.p1

Hedcil 2013002 YWNFHedcil Mosses.p1 2013002

Timaus 2000820 ZQRI Mosses.p1 Encstr 2013253 KEFD Mosses.p1

Dipfol 2006342AWOI Mosses.p1 Loebre 2010728 WSPM Mosses.p1 Dipfol 2006341AWOI Mosses.p1 Atrang 2016131 ZTHV Mosses.p1

Necdou 2021410 TMAJ Mosses.p1 Cliden 2013083 MIRS Mosses.p1 Leubra 2099232 ZACW Mosses.p1

Phypat Pp3c11 2120V3.1 Anocla 2054640Rhyser VBMM 2011170 Mosses.p1 JADL Mosses.p1

Thudel 2039853 EEMJ Mosses.p1 Aulhet 2014518 WNGH Mosses.p1

Ortlye 2013037 CMEQ Mosses.p1 Hedcil 2052204 YWNF Mosses.p1

Phifon 2010969 ORKS Mosses.p1 Dicsco 2101817 NGTD Mosses.p1

Leualb 2132669 VMXJ Mosses.p1 Racvar 2119477 RDOO Mosses.p1 Scoaqu 2089616 BPSG Mosses.p1

Timaus 2012824 ZQRI Mosses.p1

Bryarg 2042815 JMXW Mosses.p1 Phifon 2009912 ORKS Mosses.p1 Aulhet 2015730 WNGH Mosses.p1 Ortlye 2016901 CMEQ Mosses.p1 Leubra 2016717 ZACW Mosses.p1 Buxaph 2011717 HRWG Mosses.p1 Anoatt 2010811 QMWB Mosses.p1 Anocla 2011936 VBMM Mosses.p1 Rhyser 2010851 JADL Mosses.p1 Timaus 2000817 ZQRI Mosses.p1 Andrup 2096018 WOGB Mosses.p1 Timaus 2000818 ZQRI Mosses.p1 Phypat Pp3c21 7410V3.1 Timaus 2000819 ZQRI Mosses.p1 Phypat Pp3c18 13530V3.1 Racelo 2077283 ABCD Mosses.p1 Dicsco 2100602 NGTD Mosses.p1 Cerpur 2014019 FFPD Mosses.p1 Leugla 2008868 RGKI Mosses.p1 Leualb 2132701 VMXJ Mosses.p1 Sphrec 2011704 UHLI Mosses.p1 Hedcil 2049622 YWNF Mosses.p1 Sphfal Sphfalx0011s0129.1 Plains 2008078 BGXB Mosses.p1 Bryarg 2000449 JMXW Mosses.p1 Sphrec 2093954 UHLI Mosses.p1 Roscap 2010670 XWHK Mosses.p1 Sphfal Sphfalx0001s0367.1 Ortlye 2009208 CMEQ Mosses.p1 Ortlye 2009209 CMEQ Mosses.p1 Aulhet 2090733 WNGH Mosses.p1 Sphrec 2003441 UHLI Mosses.p1 Pseele 2048092 QKQO Mosses.p1 Sphfal Sphfalx0016s0243.1 Leujul 2003644 IGUH Mosses.p1 Leubra 2003700 ZACW Mosses.p1 Taklep 2080505 SKQD Mosses.p1 Fonant 2007195 DHWX Mosses.p1 Sphfal Sphfalx0033s0026.1 Loebre 2007389 WSPM Mosses.p1 Calcor 2000047 TAVP Mosses.p1 Calcor 2000046 TAVP Mosses.p1 Phypat Pp3c26 6484V3.1 Anocla 2005821 VBMM Mosses.p1 Phypat Pp3c26 6480V3.1 Thudel 2007788 EEMJ Mosses.p1 Leualb 2011781Phypat VMXJ Pp3c10 Mosses.p1 12340V3.1 Rhyser 2049437 JADL Mosses.p1 Pseele 2051533 QKQO Mosses.p1 Anoatt 2060052 QMWB Mosses.p1 Necdou 2184602 TMAJ Mosses.p1 Anocla 2005419 VBMM Mosses.p1 Marpol Mapoly0020s0028.1 Atrang 2001708 ZTHV Mosses.p1 Marpal 2009319 HMHL Liverworts non mycorrizal.p2 Andrup 2094765 WOGB Mosses.p1 Marpal 2086537 LFVP Liverworts 2 samples combined.p1 Marpal 2068285 IHWO Liverworts mycorrizal.p1

90.3 Marpal scaff2533 FGenesh8.1 Marpal scaff17685 FGenesh3.1 100 Selmoe 440571

86.2

97.9 Cryacr 2013981 WQML Leptosporangiate Monilophytes.p1

100 84 99.9 Scedis 2008950 EEAQ Eusporangiate Monilophytes.p1

100 100 80.8

86.8 Scedis 2008951 EEAQ Eusporangiate Monilophytes.p1

93.6 95.1 100 99.8 100

99.8 Ophpet 2016714 WTJG Eusporangiate Monilophytes.p1 95.3 100

80 85.7 100 100 95.8 Ophvul 2102862 QHVS Eusporangiate Monilophytes leaf.p1 98.2 94.9 99.9 100 Prumum lcl NC 024132.1 XP 008239588.1 23158 100 97 100 Staeri 2054965 KAWQ Cycadales.p1

99.2 100 Ginbil Gb 31444 99.4 90 Pinpar 2076719 IIOL Conifers.p1 Prumum lcl NC 024132.1 XP 008239344.1 23157 85 100 Pinpin PPI00005651 Pruper Prupe.5G164600.1 100

100 Pinsyl PSY00008381 100 95.5 90.1 100 Pinrad 2054883 DZQM Conifers.p1 Prudul Prudul26A022772P1 87.7 Pruavi Pav sc0006018.1 g100.1.mk 91.4 Pintae PTA00030134 100 98.8 Pinjef 2083162 MFTM Conifers.p1 Pinpon 2016980 JBND Conifers.p1 Pyrcom PCP020401.1 99.9 100 Maldom MDP0000297307 Piceng 2056036 AWQB Conifers.p1 Fraana FAN iscf00228022.1.g00001.1 97.1 100 99.3 Tsuhet 2053216 GAMH Conifers.p1 100 Fraana FAN iscf00004373.1.g00001.1 89.4 98.9 99.2 Abilas 2004250 VSRH Conifers.p1 90 99.9 92.2 Cedlib 2005449 GGEA Conifers.p1 Fraana FAN iscf00037787.1.g00001.1 88 94.2 99.9 99.7 Psemen PME00065226 100 98.6 100 Potmic 3119 t Psemen PME00065229 96.6 Roschi RchiOBHm Chr7g0192411 99.8 93.8 Psewil 2014345 IOVS Conifers.p1 86.5 100

92.5 100 Psemen PME00009093 Rubocc Bras G14496 93.3 100 Ararul 2007919 XTZO Conifers.p1 Drydru Drydr295S10128 80.8 93.3 100 Wolnob 2059835 RSCE Conifers.p1 Fraana FAN iscf00221834.1.g00001.1 98.5 Agamac 2070437 ACWS Conifers.p1 96.9 92.8 Treori lcl JXTC01000036.1 PON96753.1 7458 95.7 Agarob 2013973 MIXZ Conifers.p1 84.9 100 98.8 Parand lcl JXTB01000040.1 PON72304.1 6695 90 Phyhyp 2014170 JRNA Conifers.p1 90.8 96.9 97.7 99.9 Humlup HL.SW.v1.0.G019509.1 97.2 92.2 Pruand 2040010 EGLZ Conifers.p1

100 98.1 Sunama 2094744 KLGF Conifers.p1 93.1 100 Treori lcl JXTC01000036.1 PON96754.1 7459 87.8 Acmpan 2019672 HILW Conifers.p1 81.4 99.1 98 Daccom 2008411 FMWZ Conifers.p1 Parand lcl JXTB01000040.1Mornot PON72305.1 L484 018985 6696 94.6 99 Faltax 2006519 ROWR Conifers.p1 Mornot L484 018984 98.4 99.9 Podcor 2012156 SCEB Conifers.p1 100 98.8 99.8 Podrub 2060455 XLGK Conifers.p1

91.9 95.8 Zizjuj lcl NC 029683.1 XPDistri 024929115.1 Distr1615S15623 14239 93.6 Cephar 2061244 GJTI Conifers.p1 100 86 Cephar 2022433 NVGZ Conifers 2 samples combined.p1 99.9 Cucmel MELO3C031542.2.1 86.8 99.3 Ausspi 2078686 BTTS Conifers.p1 81.9 Cucmel MELO3C002304.2.1 Amearg 2025631 IAJW Conifers.p1

94 100 Cucsat evm.model.Chr1.869 98 97.6 88.6 Tortax 2013190 EFMS Conifers.p1 99.8 90 Lagsic Lsi02G004220.1 86.1 93.8 Citlan Cla005120 99.8 100 Metgly 2012859 NRXL Conifers.p1 93.9 Taicry 2069340 QSNJ Conifers.p1 97.1 96.5 98 Lagsic Lsi02G004200.1 100 91.1 Cunlan 2016900 ESYX Conifers branch apex with needles.p1 94.6 82.4 Cunlan 2052262 OUOI Conifers.p1 100 98.8 98.2 Cucpep Cp4.1LG09g10020.1 98.4 93.8 91.7 100 Cunlan 2102309 ZQVF Conifers 2 samples combined.p1 84.1 86.2 84.6 80.8 83.1 99.6 97.6 91.5 Cryjap 2014927 DSXO Conifers.p1 Cucmos CmoCh18G001570.1 93.7

94.8 99.8 98.7 82.8 Cryjap 2010421 GMHZ Conifers 2 samples combined.p1 91 Cucmax CmaCh18G001950.1 98.7 97.8 94 100 100 86.5 Cryjap 2113171 HOUF Conifers leaf.p1

100 Cryjap 2010420 GMHZ Conifers 2 samples combined.p1

Begfuc Begfu255S02774 100 99.7 85.5 Glypen 2010086 OXGJ Conifers.p1

Datglo Datgl1085S18083 100 Glypen 2010087 OXGJ Conifers.p1 Momcha lcl NW 019104497.1 XPVigrad 022137304.1 Vradi0223s00430.1 9111 Taxdis 2009560 FHST Conifers.p1

98.8

88 Taxdis 2009561 FHST Conifers.p1

Vigang vigan.Vang11g07660.1 94.7 Auschi 2009914 YYPE Conifers.p1

Vigung Vigun03g319400.1 83.2 Piluvi 2064521 ETCJ Conifers.p1 Cajcaj Ccajan 09164 Phavul Phvul.003G205800.1 Widced 2012211 AUDE Conifers.p1 Disarc 2003783 GKCZ Conifers.p1

99.8 Neopan 2072748 JDQB Conifers.p1 Glymax Glyma.17G124700.1 Calmac 2059817 RMMV Conifers March.p1 99.7 Calgra 2145612 IFLI Conifers March.p1 Glymax Glyma.17G124800.1 Thupli 2041968 VFYZ Conifers.p1

Glymax Glyma.05G042100.1 99.3 Fokhod 2062336 UEVI Conifers.p1 Chalaw 2007901 AIGO Conifers.p1 Cicari Ca 21266.1 Cupdup 2013388 QNGJ Conifers.p1 Tetsp. 2072925 CGDN Conifers.p1 Tripra Tp57577 TGAC v2 mRNA38733 Plaori 2008993 BUWV Conifers.p1 Micdec 2058265 XQSG Conifers.p1 Lotjap Lj4g3v1415280.1Araipa Araip.E18N6 Medtru MtrunA17 Chr4g0058371 Lepsp. 2010259 BBDD Conifers.p1 Araipa Araip.VP61Y Trisub lcl DF974933.1 GAU50985.1 40043 Aposhe lcl KZ451970.1 PKA56692.1 10669 Phaequ PEQU 08714 Aradur Aradu.9YL8X Dencat lcl NW 021319394.1 XP 020686573.1 17713 Dencat lcl NW 021319394.1 XP 020686572.1 17714 Araipa Araip.8DE0C Musacu GSMUA Achr4T16180 001 Anacom Aco017322.1 Orysat LOC Os01g68130.1 Bradis Bradi2g58277.3 Araipa Araip.H0XGV Setita Seita.5G422400.1 Sorbic Sobic.003G396900.2 Zeamay Zm00008a034828 Zeamay Zm00008a012980 Zeamay Zm00008a034108 Ambtri evm 27.model.AmTr v1.0 scaffold00049.278 Daucar DCAR 007451 Nissch Nissc522S25037 Helann HanXRQChr05g0156201 Fraexc FRAEX38873 v2 000160420.1 Fraexc FRAEX38873 v2 000018280.1 Sollyc Solyc03g112120.1.1 Solpen Sopen03g031210.1 Sollyc Solyc03g112110.1.1 Capann CA00g00760 Nissch Nissc4595S23899 Petaxi Peaxi162Scf00089g01229.1

Arahyp arahy.Tifrunner.gnm1.ann1.4HF9FM.1

Mimpud Mimpu1375S15195Chafas Chafa2988S02253 Jugreg g10004.t1 Arahyp arahy.Tifrunner.gnm1.ann1.2S9CTF.1 Chafas Chafa220S08081 Cercan Cerca18S16873 Casaus Castanospermum08502-PAMimpud Mimpu11205S05438 Casgla Casgl327S01589

Alnglu Alngl424723S28017

Querob Qrob P0185440.2

Riccom 30147.m013856

Poptri Potri.015G084300.1 Manesc Manes.06G111300.1 Citcle Ciclev10024352m

Gosrai Gorai.003G106900.1 Citsin orange1.1g038722m Thecac Thecc1EG014487t1

Carpap evm.model.supercontig 159.12

Petaxi Peaxi162Scf00089g01230.1 Nicben Niben101Scf09960g00008.1

Nicben Niben101Scf05437g03015.1

Nicben Niben101Scf09960g00009.1

Tree scale: 0.1 Supplementary Figure 18: Maximum likelihood tree of CCD.

Marpal 2009728 LFVP Liverworts 2 samples combined.p1

Marpal 2001982 HMHL Liverworts non mycorrizal.p1

Marpal 2001983 HMHL Liverworts non mycorrizal.p1

Marpal 2006403 IHWO Liverworts mycorrizal.p1

Marpal 2006545 LFVP Liverworts 2 samples combined.p1 Marpal 2006404 IHWO Liverworts mycorrizal.p1

Marpal 2004400 HMHL Liverworts non mycorrizal.p1

Marpal 2006544 LFVP Liverworts 2 samples combined.p1 Marpal 2004399 HMHL Liverworts non mycorrizal.p1

Marpal 2004398 HMHL Liverworts non mycorrizal.p1 Ricnat 2001809 WJLO Liverworts.p1 Marpal 2010674 IHWO Liverworts mycorrizal.p1

Marpol 2039057 JPYU Liverworts.p1

BlaspNW c332681 g2 i3 m.127513 BlaspNW c332681BlaspNW g2 i11 m.127526 c332681 g2 i5 m.127518

Marpal scaff1640 FGenesh6.1 BlaspNW c332681BlaspNW g2 i10 c332681 m.127524 g2 i6 m.127520

Marpal 2010673 IHWO Liverworts mycorrizal.p1 BlaspNW c332681 g2 i4 m.127516

Marpol Mapoly0066s0017.1

Marpol 2039206 JPYU Liverworts.p1Marpal scaff6790 FGenesh3.1 Marema 2005152 TFYI Liverworts.p1 Concon 2002777 ILBQ Liverworts.p1

Concon 2002775 ILBQ Liverworts.p1Marpol Mapoly0056s0019.1 Concon 2002776 ILBQ Liverworts.p1 Luncru 2003899 TXVB Liverworts.p1

Ricnat 2001811 WJLO Liverworts.p1 Marpol Mapoly0012s0198.1 Marpol Mapoly0012s0197.1 Marpal 2001364 LFVP Liverworts 2 samples combined.p1 Marpal 2001363 LFVP Liverworts 2 samples combined.p1 Marpal scaff11689 FGenesh6.1 Marpal 2001365 LFVP Liverworts 2 samples combined.p1 BlaspNW c322404 g1 i4 m.54335 Marpal 2002006 IHWO Liverworts mycorrizal.p1 Scedis 2005934 EEAQ Eusporangiate Monilophytes.p1 Scedis 2005932 EEAQ Eusporangiate Monilophytes.p1 Ophpet 2021908 WTJG Eusporangiate Monilophytes.p1 BlaspNW c322404 g1 i1 m.54325 Ophpet 2005709 WTJG Eusporangiate Monilophytes.p1 Ophvul 2004145 QHVS Eusporangiate Monilophytes leaf.p1 Plajap 2140115 UWOD Leptosporangiate Monilophytes.p1 Phacar 2006352 WCZB Hornworts gametophyte.p1BlaspNW c322404 g1 i5 m.54338 Vitlin 2006342 SKYV Leptosporangiate Monilophytes.p1 Linmic 2057251 YIXP Leptosporangiate Monilophytes.p1 BlaspNW c322404 g1 i2 m.54328 Linlin 2004909 NOKI Leptosporangiate Monilophytes.p1 Phacar 2006351 WCZB Hornworts gametophyte.p1 Gagari 2003225 DCDT Leptosporangiate Monilophytes.p1 BlaspNW c322404 g1 i3 m.54331 Myrruf 2016755 GSXD Leptosporangiate Monilophytes.p1 BlaspNW c332305 g3 i2 m.121336 Onosen 2008957 HTFH Leptosporangiate Monilophytes.p1 Notmon 2002739 YCKE Leptosporangiate Monilophytes.p1 BlaspNW c332305 g3 i1 m.121333 Notmon 2002740 YCKE Leptosporangiate Monilophytes.p1 Notmon 2002738 YCKE Leptosporangiate Monilophytes.p1 Selmoe 132803 Hupmyr 2060736 CBAE Lycophytes.p1 Taklep 2012538 SKQD Mosses.p1 Parhal 2011650 FAJB Hornworts.p1 Taklep 2012539 SKQD Mosses.p1 Cycmic CMI00009988 Notvin 2004786 TCBC Hornworts.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00056.16 Notvin 2004785 TCBC Hornworts.p1 Aposhe lcl KZ454830.1 PKA45714.1 21702 Notaen 2004001 DXOU Hornworts.p1 Phaequ PEQU 23029 Phacar 2007337 WCZB Hornworts gametophyte.p1 Dencat lcl NW 021318470.1 XP 028552320.1 153 Notvin 2004285 TCBC Hornworts.p1 Dencat lcl NW 021318470.1 XP 028552308.1 154 Phacar 2017388 RXRQ Hornworts sporophyte.p1 Dencat lcl NW 021318470.1 XP 028552287.1 152 Megfla 2011891 UCRN Hornworts.p1 Dencat lcl NW 021318470.1 XP 028552256.1 155 Dencat lcl NW 021318470.1 XP 028552230.1 156 Dencat lcl NW 021318470.1 XP 028552330.1 157 Orysat LOC Os08g28410.1 Parhal 2057717 FAJB Hornworts.p1 Horvul HORVU3Hr1G108100.2 Metcra 2097979 NRWZ Liverworts.p1 Bradis Bradi3g34707.2 Bradis Bradi3g34727.3 Metcra 2100434 NRWZ Liverworts.p1 Bradis Bradi3g34720.2 Orysat LOC Os08g28240.1

Pelnee 2113593 JHFI Liverworts.p1 99.9 Horvul HORVU4Hr1G077550.1

88.2 Bradis Bradi3g34688.1 96.7 94.2 98.7 Orysat LOC Os09g15240.1

84.4 Bradis Bradi4g27977.2

100

98.9 100 100 Bradis Bradi4g27988.1 81.8 91.1 Horvul HORVU5Hr1G055740.1

99.8 100 Horvul HORVU1Hr1G000550.2 100 Setita Seita.2G174500.1 Sorbic Sobic.002G168800.3

95.8 99.9 100 Sorbic Sobic.002G168700.3 Zeamay Zm00008a027725

100 Ambtri evm 27.model.AmTr v1.0 scaffold00056.17 Tripra Tp57577 TGAC v2 mRNA37035 97 Ambtri evm 27.model.AmTr v1.0 scaffold00056.18 100 98.2 Trisub lcl DF973143.1 GAU14223.1 3281 100 Musacu GSMUA Achr2T19870 001 100 99.2 99.9 Tripra Tp57577 TGAC v2 mRNA1392 100 Anacom Aco010814.1 100 96.7 99.8 100 99.9 Setita Seita.4G062800.1 Trisub lcl DF973143.1 GAU14225.1 3283 99.9 95.7 100 Sorbic Sobic.010G050300.2 Trisub lcl DF973143.1 GAU14226.1 3284 100 99.1 98.8 100 Zeamay Zm00008a033648 100 100 100 Tripra Tp57577 TGAC v2 mRNA1400 83.7 Ambtri evm 27.model.AmTr v1.0 scaffold00056.15 99.9 89.3 Helann HanXRQChr17g0538661 100 Medtru MtrunA17 Chr3g0140121 99.8 93.5 99.9 100 87.7 99.9 86.1 Manesc Manes.03G057800.1 100 99.9 Poptri Potri.018G042650.1 89.3 97.2 99.8 96.1 100 99.9 Cicari Ca 14620.1 98.8 100 99.7 Poptri Potri.018G043201.1 Lotjap Lj0g3v0073129.1 99.7 100 Manesc Manes.03G058000.1 97.2 96.1 Lotjap Lj1g3v2067530.1 97.9 Manesc Manes.03G057900.2 99.4 99.8 94.3 98.9 Lotjap Lj1g3v2066520.1 100 Manesc Manes.03G057900.1 100 95.8 Lotjap Lj0g3v0073129.3 100 92.4 Datglo Datgl1624S21946 99.1 95 98.7 93.5 Begfuc Begfu4293S34482 Vigrad Vradi05g08800.1 99 100 100 95 81.9 Parand lcl JXTB01000068.1 PON67800.1 9969 Vigang vigan.Vang05g10040.1 92.9 97.9 97.3

92.7 Treori lcl JXTC01000050.1 PON94637.1 9673 94 Vigung Vigun09g192900.1 100 92.5 82.4 88.9 91.9 85.6 94 Treori lcl JXTC01000050.1 PON94636.1 9672 86.8 Phavul Phvul.009G109200.1 100 99.9 84 99.3 Parand lcl JXTB01000068.1 PON67799.1 9968 Glymax Glyma.04G083600.1 89.1 Prumum lcl NC 024127.1 XP 008220103.1 5012 94.8 100 100 95.8 Glymax Glyma.06G085100.1 Prudul Prudul26A019082P1 98.2 Pruper Prupe.1G449200.1 Cajcaj Ccajan 11053 82 100 100 98.8 98.6 Pyrcom PCP015767.1 93.7 Arahyp arahy.Tifrunner.gnm1.ann1.YWII14.2 96.7 93 Pyrbre lcl NW 008988191.1 XP 009368017.1 19953 Araipa Araip.4GU5Y 94.2 100 Pyrbre lcl NW 008988186.1 XP 009367500.1 19608 94.5 100 Maldom MDP0000271304 Arahyp arahy.Tifrunner.gnm1.ann1.I05T7U.1Aradur Aradu.FJ7R7 100 80.8 Maldom MDP0000413903 100 Nissch Nissc523792S35065 Maldom MDP0000316545 89.8 Pruper Prupe.1G449300.1 Nissch Nissc523792S35063 100 96.7 91 Pruavi Pav sc0000800.1 g840.1.mk Nissch Nissc1173S13161 94 100 99 81.4 93.8 97.1 Rubocc Bras G00701 96.2 92 Fraana FAN iscf00037572.1.g00001.1 Casaus Castanospermum04961-PA 98.2 Mimpud Mimpu16191S07480 84.7 99.9 83.2 100 Fraves FvH4 2g35680.1 Cercan Cerca22S18669 100 100 Fraana FAN iscf00163216.1.g00001.1 99.9 90.7 Cercan Cerca6S10562 100 Roschi RchiOBHm Chr6g0306121 91.9 100 Aradur Aradu.BE9S0 100 99.6 Fraves FvH4 5g00520.1 95.4 88.7 100 Fraana FAN iscf00279684.1.g00001.1 Fraana FAN iscf00284939.1.g00001.1 Aradur Aradu.Y26CS 90.5 97.8 Potmic 24475 t Araipa Araip.S2QC7 100 Arahyp arahy.Tifrunner.gnm1.ann1.66FUHL.1 99.2 99.8 Potmic 27162 t

94.3

95.2 94.7 Potmic 31637 t 100 95.1 Helann HanXRQChr17g0538671 99.6 100 100 98.3

100 98.2 98.2 Glymax Glyma.04G083500.1 95.9 Petaxi Peaxi162Scf00227g00019.1 99.5 Arahyp arahy.Tifrunner.gnm1.ann1.I9LXD5.1 100 92.1 Glymax Glyma.06G085000.1Cajcaj Ccajan 11054 89.2 Helann HanXRQChr13g0401841 100

97.2 98.2 99.9 100 99 99.6 Helann HanXRQChr13g0401881 96.6

98 90.6 Helann HanXRQChr13g0401851

94.9

Phavul Phvul.009G109100.1 97.3 97.3 Daucar DCAR 003120 Vigung Vigun09g193000.1

100 99.9

100 95.2 Daucar DCAR 003121 100 100 Cercan Cerca1507S14994 87.7 100 99.2 91.1 Maldom MDP0000131158 92.5 83.7

98.7 83.1 100 Mimpud Mimpu549S25633 98.2 Fraexc FRAEX38873 v2 000370670.1 96.6 99.1 82.2 Fraexc FRAEX38873 v2 000020190.1 Mimpud Mimpu7365S27221 Datglo Datgl1624S21947 Fraexc FRAEX38873 v2 000122630.1 Alnglu Alngl3238S24215 Fraexc FRAEX38873 v2 000122630.2 Jugreg g24500.t1 Capann CA08g04710 Alnglu Alngl3238S24216 Jugreg g24499.t1 Capann CA01g34880 Capann CA11g20400 Solpen Sopen11g028910.1 Nicben Niben101Scf09445g04016.1 Casgla Casgl1077S06946 Solpen Sopen08g020690.1 Casgla Casgl301S14479 Sollyc Solyc08g066720.1.1 Alnglu Alngl6281S05370 Petaxi Peaxi162Scf00323g00925.1 Petaxi Peaxi162Scf00323g00934.1 Querob Qrob P0766810.2 Petaxi Peaxi162Scf00227g00007.1 Datglo Datgl1624S03415 Momcha lcl NW 019104488.1 XP 022139412.1 383 Cucmax CmaCh01G014360.1 Cucmos CmoCh01G014860.1 Cucpep Cp4.1LG02g03700.1 Cucmel MELO3C003462.2.1 Cucsat evm.model.Chr3.4526 Lagsic Lsi04G023320.1 Poptri Potri.018G043000.1 Citlan Cla023114 Citlan Cla023113 Poptri Potri.018G043500.1 Carpap evm.model.supercontig 522.4 Citcle Ciclev10010551m Poptri Potri.018G043100.2 Citsin orange1.1g008275m Thecac Thecc1EG037184t1 Casmol maker-scaffold01303-snap-gene-0.38-mRNA-1 Poptri Potri.006G239301.1 Gosrai Gorai.010G107700.1 Thecac Thecc1EG037185t1 Poptri Potri.006G239200.2Riccom 29794.m003376 Gosrai Gorai.009G050300.1 Casmol maker-scaffold01303-snap-gene-0.42-mRNA-1 Thecac Thecc1EG037186t1 Distri Distr1724S16220 Distri Distr1724S01180 Zizjuj lcl NC 029684.1 XP 015885137.1 17036 Casmol maker-scaffold01303-snap-gene-0.41-mRNA-1 Mornot L484 010699 Poptri Potri.018G042900.1 Treori lcl JXTC01000050.1 PON94639.1 9675 Treori lcl JXTC01000050.1 PON94638.1 9674 Parand lcl JXTB01000068.1 PON67801.1 9970 Mornot L484 008739 Mornot L484 008741 Poptri Potri.018G043400.1 Treori lcl JXTC01000190.1 PON82648.1 21581 Parand lcl JXTB01000793.1 PON32676.1 35933 Poptri Potri.T167700.1 Drydru Drydr146S00824 Casmol maker-scaffold01303-snap-gene-0.40-mRNA-1 Carpap evm.model.supercontig 7.267 Poptri Potri.006G239400.2 Riccom 29794.m003375

Maldom MDP0000431701 Manesc Manes.16G076200.1Maldom MDP0000193584 Casmol augustus masked-scaffold01303-abinit-gene-0.3-mRNA-1 Maldom MDP0000871042

Maldom MDP0000725198 Pyrcom PCP014612.1

Maldom MDP0000186264 Potmic 6870 t

Pyrcom PCP014613.1 Pyrcom PCP014614.1 Maldom MDP0000256445 Pyrcom PCP015766.1

Maldom MDP0000278707

Maldom MDP0000192227

Fraves FvH4 2g35670.1

Pruper Prupe.1G449100.1

Roschi RchiOBHm Chr6g0306131 Pruavi Pav sc0012025.1 g010.1.mk

Fraana FAN iscf00121962.1.g00002.1

Fraana FAN iscf00037572.1.g00002.1 Pyrbre lcl NW 008989585.1 XP 018501816.1 46664

Pyrbre lcl NW 008989585.1 XP 018501817.1 46665

Prumum lcl NC 024127.1 XP 016646977.1 5014

Prumum lcl NC 024127.1 XP 016646976.1 5013

Tree scale: 0.1 Supplementary Figure 19: Maximum likelihood tree of RFCa/RFCb.

Momcha lcl NW 019104492.1 XP 022132979.1 4728

Ambtri evm 27.model.AmTr v1.0 scaffold00011.106

Musacu GSMUA AchrUn randomT23700 001

Cucmax CmaCh07G004800.1

Cucpep Cp4.1LG19g09300.1

Begfuc Begfu14780S46942

Begfuc Begfu5649S50190 Horvul HORVU6Hr1G068810.4 Sorbic Sobic.004G267900.1Zeamay Zm00008a017061 Begfuc Begfu754S40951

Datglo Datgl423S30450

Neopan 2058895 JDQB Conifers.p1 Setita Seita.1G289100.1 Orysat LOC Os02g47605.1 Mancol 2055419 CDFR Conifers.p1 Bradis Bradi3g52746.1 Baztri 2016097 WZYK Liverworts.p1

Baztri 2016098 WZYK Liverworts.p1 Anacom Aco016392.1 Calfis 2005504 RTMU Liverworts.p1 Marpal 2011031 LFVP Liverworts 2 samples combined.p1Scanem 2003922 IRBN Liverworts.p1 Mixspe 2149027 NWQC Liverworts.p1 Marpal 2007952 IHWO Liverworts mycorrizal.p2

Pallye 2104114 YFGP Liverworts.p1

Cucmos CmoCh07G004790.1 Citlan Cla014221 Lagsic Lsi01G006670.1 Cucsat evm.model.Chr6.3232 Cucmel MELO3C007837.2.1 Pelnee 2108736 JHFI Liverworts.p1 Alnglu Alngl22611S20899 Marpal 2076989 LFVP Liverworts 2 samples combined.p1 Casgla Casgl230S11892 Jugreg g36881.t1 Casmol maker-scaffold11144-augustus-gene-0.7-mRNA-1 Querob Qrob P0498440.2 Marpal 2007952 IHWO Liverworts mycorrizal.p1 Querob Qrob P0477110.2 Querob Qrob P0498450.2 Distri Distr99S29781 Zizjuj lcl NC 029686.1 XP 015890007.1 22059 Mornot L484 008535 Treori lcl JXTC01000263.1 PON74019.1 24800 Marpal scaff14619 FGenesh1.1 Parand lcl JXTB01000044.1 PON71428.1 7225 Drydru Drydr282S02822 Rubocc Bras G01064 Concon 2034944 ILBQ Liverworts.p1 Roschi RchiOBHm Chr2g0101071 Potmic 32666 t Luncru 2013331 TXVB Liverworts.p1 Fraana FAN iscf00117590.1.g00001.1 Fraves FvH4 1g12990.1 Phacar 2019918 RXRQPallye Hornworts 2014818 sporophyte.p1 YFGP Liverworts.p1 Fraana FAN iscf00208112.1.g00001.1 Phacar 2118407 WCZB Hornworts gametophyte.p1 Pallye 2018793 YFGP Liverworts.p1 Pruavi Pav sc0000099.1 g560.1.mk Pruper Prupe.7G157200.1 Prumum lcl NC 024133.1 XP 008241892.1 25396 Prudul Prudul26A027560P1 Pyrcom PCP034646.1 Parhal 2055485 FAJB Hornworts.p1 Pyrbre lcl NW 008988239.1 XP 009371639.1 23405 Notvin 2081900 TCBC Hornworts.p1 Pyrbre lcl NW 008988609.1 XP 009340725.1 37351 99.9 Phacar 2138479 RXRQ Hornworts sporophyte.p1 Maldom MDP0000235958 Notvin 2077737 TCBC Hornworts.p1 99.4 95.3 97.2 Pyrcom PCP010091.1 87.3 Pyrbre lcl NW 008988609.1 XP 018499383.1 37350 Carpap evm.model.supercontig 6.141

100 Carpap evm.model.supercontig 15.66

98.4

95.5 Citcle Ciclev10024944m

92.3 100 100 Citsin orange1.1g036742m Thecac Thecc1EG000349t1 100 Gosrai Gorai.003G013700.1 Gosrai Gorai.008G067000.1 84.4 95.1 99.7 100 100 98.2 96.4 100 Daucar DCAR 025953 89 96.7 100 99.5

98.5 Helann HanXRQChr09g0261371 96.4

99.7 84.6 Helann HanXRQChr11g0325481 Vigang vigan.Vang05g00170.1 100 99.8 96.9 94.8 Fraexc FRAEX38873 v2 000245120.1 99.6 96.9 92.2 100 Vigrad Vradi05g15720.1 83.1 Fraexc FRAEX38873 v2 000315990.2

100 Vigung Vigun09g277000.1 Fraexc FRAEX38873 v2 000315990.1

82.8 Phavul Phvul.009G118000.1 92.2 Nicben Niben101Scf02915g05001.1 99.4 95.9 99.4 100 Petaxi Peaxi162Scf00010g01323.1 Glymax Glyma.06G002200.1 100 85.2 89.5 99.8 100 93.8 Petaxi Peaxi162Scf00010g01213.1 100 Cajcaj Ccajan 23777 98 99.8 Trisub lcl DF973533.1 GAU33658.1 22716 96.9 Petaxi Peaxi162Scf00366g00532.1

99.5 99.3 85.7 100 93.2 Nicben Niben101Scf00606g03004.1 98.6 Tripra Tp57577 TGAC v2 mRNA39836 100 99.2 Nicben Niben101Scf00305g05037.1 99.7 94 94.5 Medtru MtrunA17 Chr3g0145801 100 99.9 91.9 Capann CA02g22310 85.8 RFCa 99.9 96.1 Solpen Sopen02g029760.1 98.9 99.8 Cicari Ca 14401.1 99.9 100 97.9 Sollyc Solyc02g085060.1.1 Araipa Araip.LU00V 91.2 92.8 100 Riccom 29634.m002116 Aradur Aradu.5XU8S 100 93.7 88.3 Manesc Manes.01G137000.1 96.3 Nissch Nissc898S32052 97.6 Poptri Potri.005G120901.1 88.8 100 Casaus Castanospermum01041-PA Poptri Potri.007G022900.2 100 Cercan Cerca9S31518 Arahyp arahy.Tifrunner.gnm1.ann1.B93CDZ.1 RFCb 100 Chafas Chafa8999S27973 Chafas Chafa1942S17725 99.9 93.1 98.7 Mimpud Mimpu6482S26514 Cercan Cerca384S03007 100 85.8 95.8 Casaus Castanospermum03747-PA Cucmax CmaCh06G011640.1 99.3 95.5 99.1 Nissch Nissc946S32343 95.3 Cucmax CmaCh00G006580.1 97.2 100 Araipa Araip.XI7DZ 95.1 Cucpep Cp4.1LG08g02250.1 100 Aradur Aradu.UG385 95.9 100 100 98.1 Arahyp arahy.Tifrunner.gnm1.ann1.1IN98U.1 Cucmos CmoCh06G011920.1 100 99.6 98.9 Lotjap Lj2g3v1734490.1 Cucpep Cp4.1LG08g02270.1 97.4 99.8 99 87.2 100 91.3 Cicari Ca 23280.1

Cucsat evm.model.Chr3.987 100 96.2 Medtru MtrunA17 Chr5g0404521 100 Cucmel MELO3C006229.2.1 84.2 Tripra Tp57577 TGAC v2 mRNA2459 Lagsic Lsi05G019210.1 99.3 Tripra Tp57577 TGAC v2 mRNA2396 Citlan Cla021344 94.8

100 95.3 Medtru MtrunA17 Chr5g0404541

99.3 98 Trisub lcl DF973331.1 GAU26229.1 15287 Trisub lcl DF973331.1 GAU26230.1 15288 85.9 91 Begfuc Begfu647S39491 98

95.9 Cajcaj Ccajan 12710 Begfuc Begfu2S29604 89.1 92.7 Momcha lcl NW 019104531.1 XP 022147144.1 17601 100 Glymax Glyma.01G172500.1

Datglo Datgl1467S20861 89.6 100 95.4 Glymax Glyma.11G070700.1 Maldom MDP0000876438 Glymax Glyma.04G105300.1 96.8

84.5 88.5 100 Glymax Glyma.14G175300.1 100 86.4 95.4 99.3 90.9 Pyrcom PCP002165.1 100 Phavul Phvul.002G032800.1 96.8

100 98.5 86 Vigung Vigun02g128800.1 100

97.1 Maldom MDP0000141880 95.7 100 Vigang vigan.Vang07g01020.1

99.9 98.9 99.3 100 100 Maldom MDP0000295361 Vigrad Vradi11g05830.1 Pyrbre lcl NW 008988122.1 XP 009361456.1 14055 99.4 Pyrcom PCP019166.1 100 Selkra 2002882 ZFGK Lycophytes.p1 Selkra 2002883 ZFGK Lycophytes.p1 99

96.9 Selwil 2046362 KJYC Lycophytes.p1

Pyrcom PCP023613.1 100 100

100 Sellep 2039421 ABIJ Lycophytes.p1

98.7 Selsta 2053331 ZZOL Lycophytes.p1 Maldom MDP0000320333 Selmoe 119010 Tmepar 2014914 ALVQ Eusporangiate Monilophytes.p1 Prudul Prudul26A014097P1

94.2

99.9 Tmepar 2014913 ALVQ Eusporangiate Monilophytes.p1 Pruper Prupe.2G108000.1 Pyrbre lcl NW 008988321.1 XP 009376326.1 27720 Taicry 2067055 QSNJ Conifers.p1

100 Potmic 21753 t Athcup 2056700 XIRK Conifers.p1 Taxdis 2008233 FHST Conifers.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00002.196 Musacu GSMUA Achr11T00340 001 Anacom Aco018864.1 Pruavi Pav sc0000503.1 g600.1.mk Bradis Bradi3g34150.1 Rubocc Bras G18562 Horvul HORVU1Hr1G050450.2 Orysat LOC Os10g42400.1 Fraana FAN iscf00138851.1.g00001.1 Prumum lcl NC 024130.1 XP 016649718.1 16467 Setita Seita.9G311300.1 Drydru Drydr597S13351 Zeamay Zm00008a002159 Roschi RchiOBHm Chr1g0341191 Sorbic Sobic.001G288500.1 Poptri Potri.003G093400.2 Thecac Thecc1EG015692t1 Helann HanXRQChr04g0123561 Daucar DCAR 025009 Daucar DCAR 029556 Mornot L484 023856 Fraexc FRAEX38873 v2 000318530.1 Fraexc FRAEX38873 v2 000126990.1 Fraexc FRAEX38873 v2 000316550.1 Fraexc FRAEX38873 v2 000262810.2 Fraexc FRAEX38873 v2 000262810.1

Petaxi Peaxi162Scf00592g00456.1

Capann CA01g26790

Distri Distr50S03080

Humlup HL.SW.v1.0.G037108.1 Jugreg g15171.t2 Jugreg g15171.t1 Alnglu Alngl6428S42216

Casgla Casgl124S07680

Parand lcl JXTB01000168.1 PON56702.1 17922 Treori lcl JXTC01000116.1 PON87508.1 16688 Citcle Ciclev10024044m Citsin orange1.1g042716m

Riccom 28098.m000127

Zizjuj lcl NC 029679.1 XP 024926231.1 2837

Poptri Potri.014G178700.2

Manesc Manes.09G009000.1 Gosrai Gorai.002G232800.1 Thecac Thecc1EG016678t1

Sollyc Solyc01g081080.1.1

Solpen Sopen01g032700.1

Carpap evm.model.supercontig 33.201

Nicben Niben101Scf01502g02024.1

Nicben Niben101Scf01502g02007.1

Nicben Niben101Scf00765g00006.1

Tree scale: 0.1 Supplementary Figure 20: Maximum likelihood tree of KinG1/KinG2.

Polhes 2033762 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1

Polhes 2023425 GYFU Leptosporangiate MonilophytesA type.p1

Polhes 2014417 IXLH Leptosporangiate Monilophytes B type.p1

Cysfra 2017965 LHLE Leptosporangiate Monilophytes.p1 Dipwic 2011724 UFJN Leptosporangiate Monilophytes.p1

Gymdry 2015402 HEGQ Leptosporangiate Monilophytes.p1 Polacr 2012691 FQGQ Leptosporangiate Monilophytes.p1 Blespi 2008660 VITX Leptosporangiate Monilophytes.p1

Linmic 2055338 YIXP Leptosporangiate Monilophytes.p1

Pteens 2018256 FLTDPtevit Leptosporangiate 2004623 POPJ LeptosporangiateMonilophytes.p1 Monilophytes.p1

Cryacr 2004107 WQML Leptosporangiate Monilophytes.p1

Argniv 2074866 XDDT LeptosporangiatePittri 2025974 Monilophytes.p1 UJTT Leptosporangiate Monilophytes.p1 Vitapp 2017045 NDUV Leptosporangiate Monilophytes.p1

Osmsp. 2008743 UOMY Leptosporangiate Monilophytes gametophyte.p1 Vitlin 2013532 SKYV Leptosporangiate Monilophytes.p1 Azocar 2011439 CVEG Leptosporangiate Monilophytes.p1

Anetom 2007648 CQPW Leptosporangiate Monilophytes.p1

Anetom 2007646 CQPW Leptosporangiate Monilophytes.p1

Anetom 2007649 CQPW Leptosporangiate Monilophytes.p1

Scedis 2002396 EEAQ Eusporangiate Monilophytes.p1

Scedis 2002397 EEAQ Eusporangiate Monilophytes.p1

Salcuc Sacu v1.1 s0001.g000488

Azofil Azfi s0013.g013316

Selapo 2008431Sellep 2005341 LGDQ ABIJLycophytes.p1 Lycophytes.p1

Cysfra 2009246 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Cysfra 2008356 XXHP Leptosporangiate Monilophytes Stewart.p1 Cysuta 2001738 HNDZ Leptosporangiate Monilophytes.p1 Ginbil Gb 23644 Ginbil Gb 05131 Neopan 2068631 JDQB Conifers.p1 Cunlan 2098370 ZQVF Conifers 2 samples combined.p1 Acmpan 2017215 HILW Conifers.p1 Selwil 2006402 KJYC Lycophytes.p1 Acmpan 2017214 HILW Conifers.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00117.55 Musacu GSMUA Achr2T21260 001 Selwal 2178769 JKAA Lycophytes.p1 Anacom Aco022209.1 Orysat LOC Os11g26140.1 Selkra 2009000 ZFGK Lycophytes.p1 Horvul HORVU6Hr1G053610.2 Bradis Bradi4g19550.1 Selsel 2008883 KUXM Lycophytes.p1 Setita Seita.8G112800.1 Phacar 2142269 RXRQ Hornworts sporophyte.p2 Zeamay Zm00008a008420 Isoesp. 2076414 PYHZ Lycophytes.p1 Selmoe 131134 Sorbic Sobic.008G005400.1 Sorbic Sobic.005G005000.2

100 Petaxi Peaxi162Scf00215g00010.1 Marpal 2011756 LFVP Liverworts 2 Isotegsamples 2000626 combined.p1 PKOX Lycophytes.p1 97.1 Fraexc FRAEX38873 v2 000074370.1 95.9

85.8 Fraexc FRAEX38873 v2 000356840.1 Marpal 2008460 IHWO Liverworts mycorrizal.p1 87.1 100 Daucar DCAR 023861 Helann HanXRQChr07g0190101

100 Parhal 2056364 FAJB Hornworts.p1 89.5 Petaxi Peaxi162Scf00215g00011.1

100 Nicben Niben101Scf00177g09018.1

99.8 Nicben Niben101Scf07893g00007.1 91.3 Capann CA12g12470

80.1 94.7 Sollyc Solyc04g050940.1.1 Phacar 2007948 RXRQ Hornworts sporophyte.p1 91.8 100 Solpen Sopen04g022060.1 Phacar 2005133 WCZB Hornworts gametophyte.p1 Riccom 29950.m001180 Scedis 2089260 EEAQ EusporangiateCalfis 2171404Marpal Monilophytes.p1 RTMU scaff6817 Liverworts.p1 FGenesh9.1 100 Manesc Manes.08G147300.1 98.6 Poptri Potri.019G030600.1 99.9 Poptri Potri.013G053001.1 95.4 Carpap evm.model.supercontig 51.62 100 Citsin orange1.1g040826m Citcle Ciclev10024299m Thecac Thecc1EG026038t1 Sellep 2001212 ABIJ Lycophytes.p1 100 Gosrai Gorai.004G250200.1

Selwil 2048269 KJYC Lycophytes.p1 100 99.9 Thecac Thecc1EG026039t1 100 99.8 100 Distri Distr1395S14243 Selmoe 126822 99.8 Zizjuj lcl NW 015453473.1 XP 024923356.1 34435

100 Mornot L484 006462 100 99.4 Humlup HL.SW.v1.0.G040720.1 Treori lcl JXTC01000003.1 POO02983.1 1044 99.3 82.6 Parand lcl JXTB01000017.1 PON76579.1 3265 99.9 Rubocc Bras G09167 99.8 94.3 100 98.7 98.1

100 Roschi RchiOBHm Chr3g0448671 100 99.5 Potmic 31934 t Pyrbre lcl NW 008988143.1 XP 018504477.1 16021 93.7 Fraana FAN iscf00215098.1.g00001.1 99.6 90.9 99.7 100 97.5 83.9 99.9 99.1 Fraana FAN iscf00044585.1.g00001.1 85 91 98.8 Fraves FvH4 6g01140.1 100 99 100 Drydru Drydr291S19805 Pyrcom PCP020462.1 Pruavi Pav sc0004456.1 g180.1.mk Maldom MDP0000834158 99.3 Pruper Prupe.6G356000.1 97.2 100 96.2 Pyrcom PCP001341.1 88.9 95.7 Prudul Prudul26A020144P1 93.3 Prudul Prudul26A028126P1 Maldom MDP0000302066

Prumum lcl NC 024127.1Pruper XP 016647035.1 Prupe.1G254900.1 6658 100 100 Pyrcom PCP039552.1 99.9 100 99.9 Pyrbre lcl NW 008988395.1 XP 009379760.1 30870 Pruavi Pav sc0000354.1 g330.1.mk 80.8 Maldom MDP0000189095 98.2 94.7 Pyrcom PCP000235.1 99.3 87.8 94.8 Drydru Drydr13S15502 99.8 98 100 Pyrbre lcl NW 008988509.1 XP 009337946.1 34834 82.6 99.9 93.3 Fraves FvH4 4g34610.1 96.3 95.8 99.9 Casmol augustus masked-scaffold05717-abinit-gene-0.0-mRNA-1 92.3 99.6 Jugreg g33197.t1 Fraves FvH4 4g34600.1 95.9

Fraana FAN iscf00166001.1.g00001.1 100 87.5 Jugreg g33190.t1 99.9 KinG2 94.4 100 Fraana FAN iscf00208275.1.g00001.1 Datglo Datgl726S34093 95.3 100 Begfuc Begfu4039S33776 91.389.9 96.7 Potmic 24027 t 99.8 99.9 Momcha lcl NW 019104572.1 XP 022152108.1 22178 Roschi RchiOBHm Chr4g0443971 100 100 Cucmos Cm oCh11G00971 0.1 Rubocc Bras G00335 87.1 Cucmel MELO3C029613.2.1 97.4 100 Citlan Cla002534 Humlup HL.SW.v1.0.G044113.1 99.5 96.1 99.9 99.9 Lagsic Lsi06G007280.1 Humlup HL.SW.v1.0.G044114.1 99.5 99.5 100 Cercan Cerca40S23847 96.3 Parand lcl JXTB01000141.1 PON59326.1 16077 100 Chafas Chafa95193S28798 100 Treori lcl JXTC01000021.1 PON98935.1 5173 Mimpud Mimpu5476S25599 Mornot L484 027791 Mimpud Mimpu11749S00369 KinG1 95.6 Distri Distr416S02901 94.7 Casaus Castanospermum01118-PA 88.3 98.8 100 99.4 96.2 99.5 Casaus Castanospermum07228-PA

Zizjuj lcl NC 029688.1 BegfucXP 024933691.1 Begfu369S03713 26964 100 Nissch Nissc5449S28722 83.299.9 96.5 100 Araipa Araip.Y9Y5W Vigrad Vradi0073s00120.1 Arahyp arahy.Tifrunner.gnm1.ann1.RWX2HP.2 94.1 100 98.5 Arahyp arahy.Tifrunner.gnm1.ann1.UE9VED.1 Vigang vigan.Vang0033ss00600.1 99.9 100 Vigung Vigun03g237300.1 97.4 96 91.8 93.9 Aradur Aradu.V3IQ0 100 100 Cicari Ca 07236.1 Phavul Phvul.003G052300.2 97 97 98.8 99.5 98.5 Medtru MtrunA17 Chr7g0275121 Glymax Glyma.08G287900.1 88.7 100 99.5 99.8 84.6 99.8 Trisub lcl DF973139.1 GAU13598.1 2656 Glymax Glyma.18G137600.1 100 80.8 Tripra Tp57577 TGAC v2 mRNA15540 Cajcaj Ccajan 01063 100 Araipa Araip.904Y1 100 Tripra Tp57577 TGAC v2 mRNA29301 99.1 93.2 100 Cajcaj Ccajan 10823 98.4 95.2 94.1 94.6

99.9 Glymax Glyma.03G253600.1

Aradur Aradu.FJ5VY 80.2 99.9 85.5 97.1 Glymax Glyma.19G251100.1 Phavul Phvul.006G108300.1 Arahyp arahy.Tifrunner.gnm1.ann1.I2ULHV.1 100 99.4 100 Vigung Vigun06g119200.1

100 96.8 Nissch Nissc2652S19636 99.8 91 Vigrad Vradi0083s01260.1 92.4 99.9 94.1 94.7 Lotjap Lj0g3v0063059.1 100 99.8 99.1 Vigang vigan.Vang03g10050.1

100 100 97.6

Arahyp arahy.Tifrunner.gnm1.ann1.HSMU8H.1 100 100 Auschi 2070029 YYPE Conifers.p1 Chafas Chafa1819S31451 99.5 97.8 100 99.8 Calmac 2057224 RMMV Conifers March.p1

100

94.9

93.3 Mimpud Mimpu1914S08036 96 Neopan 2003736 JDQB Conifers.p1 Cercan Cerca76S04573 100 96.6 100 97 Ambtri evm 27.model.AmTr v1.0 scaffold00006.307

Casgla Casgl46S02051 99.8 100 Musacu GSMUA Achr8T23540 001 Jugreg g5414.t1 99.7

99.9 Alnglu Alngl95484S37956 Aposhe lcl KZ451911.1 PKA63100.1 4298 Phaequ PEQU 09382 Dencat lcl NW 021320070.1 XP 020703063.1 28448 Dencat lcl NW 021320070.1 XP 028556808.1 28449 Querob Qrob P0352890.2 Anacom Aco015287.1 Bradis Bradi5g12775.1 Gosrai Gorai.005G183100.1 Orysat LOC Os04g39180.1 Setita Seita.7G128900.1 ThecacRiccom Thecc1EG010245t1 29631.m000999 Zeamay Zm00008a007144 Sorbic Sobic.006G111400.2 Carpap evm.model.supercontig 140.42 Manesc Manes.12G029800.1Capann CA11g02680 Thecac Thecc1EG016859t1 Citsin orange1.1g040363m Gosrai Gorai.006G029200.1 Capann CA11g02080 Tripra Tp57577 TGAC v2 mRNA4068 Casmol snap masked-scaffold00263-abinit-gene-0.24-mRNA-1 Citcle Ciclev10018188m Citsin orange1.1g042871m Riccom 29822.m003359 Sollyc Solyc05g005660.1.1 Manesc Manes.17G122900.1 Helann HanXRQChr17g0547871 Solpen Sopen05g001660.1 Daucar DCAR 011214 Daucar DCAR 015038 Petaxi Peaxi162Scf00129g01041.1 Solpen Sopen02g031730.1 Capann CA02g29430 Daucar DCAR 024142 Casgla Casgl1S06336 Jugreg g27933.t2 Querob Qrob P0433530.2 Casmol maker-scaffold11236-snap-gene-0.11-mRNA-1 Cercan Cerca7S29788 Nicben Niben101Scf03534g00008.1 Pyrcom PCP002379.1 Chafas Chafa95461S29743 Casaus Castanospermum11491-PA Glymax Glyma.19G010700.1 Tripra Tp57577 TGAC v2 mRNA2364 Petaxi Peaxi162Scf00338g00013.1 Medtru MtrunA17 Chr6g0451071 TripraTp57577 TGAC v2 mRNA2387 Datglo Datgl540S10979 Helann HanXRQChr08g0208831 Distri Distr42S24212

Maldom MDP0000224607 Maldom MDP0000196795 Pyrcom PCP030411.1 Fraexc FRAEX38873 v2 000028380.1 Maldom MDP0000162515 Potmic 1317 t Maldom MDP0000197725

Prudul Prudul26A032019P1Pruper Prupe.3G282300.1

Fraves FvH4 3g27000.1 Rubocc Bras G09750

Mornot L484 008415

Drydru Drydr226S18348

Pyrbre lcl NW 008988296.1 XP 018507097.1 26581 Pruavi Pav sc0000009.1 g750.1.mk

Roschi RchiOBHm Chr2g0170941 Fraana FAN iscf00076375.1.g00001.1

Humlup HL.SW.v1.0.G026438.1

Prumum lcl NC 024129.1 XP 016649025.1 14970

Treori lcl JXTC01000465.1 PON52030.1 30968 Zizjuj lcl NC 029682.1 XP 024928980.1 10821

Zizjuj lcl NC 029682.1 XP 024928981.1 10822 Parand lcl JXTB01000882.1 PON32006.1 36507 Zizjuj lcl NC 029682.1 XP 024928982.1 10820

Tree scale: 0.1 Supplementary Figure 21: Maximum likelihood tree of VAPYRIN/VAPYRIN-like.

Dencat lcl NW 021320054.1 020680598.1 XP 28113

Polhes 2000057 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1

Ambtri evm 27.model.AmTr v1.0 scaffold00004.96

Aposhe lcl KZ454794.1 PKA45816.1 21534 Cysfra 2129609 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Aposhe lcl KZ451969.1 PKA56999.1 10230

Polhes 2001056 GYFU LeptosporangiateCephar Monilophytes 2019092 NVGZ A type.p1 Conifers 2 samples combined.p1

Faltax 2005086 PLYX Conifers 2 samples combined.p1

Polamo 2012954 YLJA Leptosporangiate Monilophytes.p1 Musacu GSMUAAchr8T20280 001

Disarc 2012351 GKCZ Conifers.p1 Auschi 2071080 YYPE Conifers.p1 Cysfra 2089779 XXHP Leptosporangiate Monilophytes Stewart.p1 Horvul HORVU4Hr1G002180.1

Nepexa 2129222Polgly 2080017 NWWI CJNTLeptosporangiate Leptosporangiate Monilophytes.p1 Monilophytes.p1 Micdec 2009407Fokhod XQSG 2060530 Conifers.p1 UEVI Conifers.p1 Sorbic Sobic.001G149400.1 Piluvi 2064370 ETCJ Conifers.p1 Zeamay Zm00008a004787 Zeamay Zm00008a019719

Orysat LOC Os03g45290.1 Taxdis 2063267 FHST Conifers.p1 Taicry 2066441 QSNJ Conifers.p1 Psechi 2082750 YLPM Conifers.p1 Setita Seita.9G151600.1 Ausspi 2078762 BTTS Conifers.p1 Gagari 2076238 DCDT Leptosporangiate Monilophytes.p1 Cephar 2011946 GJTI Conifers.p1 AnacomAco008773.1 Notmon 2011551 YCKE Leptosporangiate Monilophytes.p1 Podcor 2010464 SCEB Conifers.p1

Myrruf 2013541 GSXD Leptosporangiate Monilophytes.p1 Pruand 2010717 EGLZ Conifers.p1 Gagari 2009160 DCDT Leptosporangiate Monilophytes.p1 Adirad 2015494 BMJR Leptosporangiate Monilophytes.p1 Osmsp. 2013284 UOMY LeptosporangiateCryacr 2008213 Monilophytes WQML Leptosporangiate gametophyte.p1 Monilophytes.p1 Davfej 2039224 OQWW Leptosporangiate Monilophytes.p1 Anetom 2097813 CQPW Leptosporangiate Monilophytes.p1

Osmjav 2076565 VIBO Leptosporangiate Monilophytes.p1

Phaequ PEQU 18240 Aposhe lcl KZ451888.1 PKA66067.1 1413 Aposhe lcl KZ452015.1 PKA50910.1 16342 Dencat lcl NW 021318735.1 XP 028549247.1 5521 Phaequ PEQU 00058 Dencat lcl NW 021319658.1 XP 020677073.1 22231 Phaequ PEQU 09027 Lotjap Lj1g3v3975850.1 Cajcaj Ccajan 05182 Glymax Glyma.16G038200.1 Glymax Glyma.19G114600.1 Phavul Phvul.001G113900.1 Vigung Vigun01g090500.1 Vigrad Vradi0007s00890.1 Vigang vigan.Vang0490s00190.1 Nissch Nissc3099S01973 Arahyp arahy.Tifrunner.gnm1.ann1.P89NTP.1 Araipa Araip.BY5SK Arahyp arahy.Tifrunner.gnm1.ann1.RRY6M7.1 Aradur Aradu.J5EZU Lupang Lup000011.1 Chafas Chafa95466S05308 Mimpud Mimpu4695S10722 Nissch Nissc25250S01565 Lupang Lup001531.1 Cicari Ca 04609.1 Medtru MtrunA17 Chr6g0461061 Calfis 2179330 RTMU Liverworts.p1 Trisub lcl DF973364.1 GAU27947.1 17005 Pornav 2113439 KRUQ Liverworts.p1 Tripra Tp57577 TGAC v2 mRNA30897 Lotjap Lj0g3v0049599.1 Radlin 2086613 BNCU Liverworts.p1 Glymax Glyma.05G088400.1 Cajcaj Ccajan 46635 Phavul Phvul.004G051200.1 Vigung Vigun04g077700.1 Vigrad Vradi01g08090.1 Marpol Mapoly0059s0031.1 Vigang vigan.Vang02g12510.1 Selsel 2009362 KUXM Lycophytes.p1 Casaus Castanospermum10080-PA Marpol Mapoly0060s0009.1 Casaus Castanospermum10306-PA Marpal scaff11970 FGenesh4.1 100 Phydru 2012709 ZZEI Lycophytes.p1 Cercan Cerca37S02975 99.9 Distri Distr90S03983 Notvin 2020647 TCBC Hornworts.p1 Phacar 2119369 WCZB Hornworts gametophyte.p1 98.5 Zizjuj lcl NW 015454130.1 XP 024925139.1 39370 Megfla 2008617 UCRN Hornworts.p1 Mornot L484 000326 Phacar 2022549 RXRQ Hornworts sporophyte.p1 Mornot L484 000080 Parhal 2011634 FAJB Hornworts.p1 Mornot L484 000695 Treori lcl JXTC01000825.1 PON36556.1 34916 Parand lcl JXTB01000643.1 PON34778.1 34171

100 Drydru Drydr46S04331 99.2 91.2 97.9 100 Rubocc Bras G21509 100 Roschi RchiOBHm Chr3g0496481 100

100

100 Potmic 207 t 96.6 94.5 82.5

96.3 100 Fraana FAN iscf00016554.1.g00001.1

92 100 100 94.7 82.6 Fraana FAN iscf00104169.1.g00001.1

80.5 99.9 Fraves FvH4 1g28430.1 83 99.9 100 100 91.1 86.7 99.6 100 86.2 100 Fraana FAN iscf00320314.1.g00001.1

87.1 100 99.9 92.5 Pruavi Pav sc0000595.1 g020.1.mk Outgroup 99.4 100 Prumum lcl NW 007362749.1 XP 008245689.1 29062 99.9 99.1 99.9 100 Prudul Prudul26A020481P1 97.3 96.5 100 97.3 100 99.7 100 98 Pruper Prupe.7G009400.1 100 95.4 88.4 99.9 Maldom MDP0000665380 99.6 100 100

100 98.2 Pyrbre lcl NW 008988064.1 XP 009353186.1 6428 100 100 99.9 100 99.7 Pyrcom PCP008499.1 89.3 98.6 Pyrcom PCP024567.1 100 100 100 89.1 Pyrbre lcl NW 008988174.1 XP 009366487.1 18751 100 88.2 Solpen Sopen09g029110.1 100 Pyrcom PCP011426.1 100 93.7 99.9 Maldom MDP0000299546 Sollyc Solyc09g074280.1.1 99.8 96 Maldom MDP0000141327 Solpen Sopen09g029120.1 82.1 100 Maldom MDP0000303416 99.9 Sollyc Solyc09g074290.1.1 100 97.297.7 100 Maldom MDP0000160886 100 99.8 Querob Qrob P0120360.2 Capann CA00g67430 100 99.9 99.1 Casgla Casgl16S00526 Nicben Niben101Scf05301g01003.1Capann CA00g67420 100 100 100 Alnglu Alngl4792S30622 Nicben Niben101Scf01985g04012.1 99.8 Alnglu Alngl4792S04638 92.3 100 Alnglu Alngl17976S18492 Nicben Niben101Scf09808g02001.1 100 Datglo Datgl2886S16749 92.5 87.5 99.9 Petaxi Peaxi162Scf00006g00369.1 90.9 88 100 99.3 100 Begfuc Begfu70929S13527 89.3 100 Petaxi Peaxi162Scf00006g00365.1 92 Citlan Cla002905 Fraexc FRAEX38873 v2 000104520.1 100 VAPYRIN Lagsic Lsi03G015790.1 100 99.6 Cucmel MELO3C009784.2.1 Daucar DCAR 018375 97.6 98 100 83.1 100 Cucsat evm.model.Chr3.3751 Daucar DCAR 018376 86.5 Cucmax CmaCh14G005290.1 100 Daucar DCAR 012440 100 Cucmos CmoCh14G005320.1 100 Daucar DCAR 002779 94 Cucpep Cp4.1LG03g08490.1 99.9 100 Helann HanXRQChr01g0002881 100 Poptri Potri.013G062000.1 Manesc Manes.08G154600.1 Helann HanXRQChr10g0283061 94.1 99.9 99.6 Riccom 30072.m000965 Gosrai Gorai.004G214200.1 97.3 99.7 Citsin orange1.1g037006m 100 100 Thecac Thecc1EG004499t1 Citcle Ciclev10019618m 93.5 Carpap evm.model.supercontig 9.143 90.2 Carpap evm.model.supercontig 161.13 Citcle Ciclev10019999m 85.6 100 Thecac Thecc1EG025861t1 98.6 Cepfol Cfol v3 22516 100 88.4 Gosrai Gorai.007G257200.1 99.6 99.2 Gosrai Gorai.013G195100.1 Manesc Manes.05G070400.1 100 100 98.6 Gosrai Gorai.004G251600.1 Riccom 29647.m002055 97.8 100 Gosrai Gorai.008G034200.1 100 VAPYRIN-like 99.9 100 Poptri Potri.002G213200.1 Nicben Niben101Scf05841g01025.1

100 99.3 100 Alnglu Alngl35802S09714 100 100 Nicben Niben101Scf03634g04003.1 100 Casgla Casgl106S00094 97.5 85.8 Petaxi Peaxi162Scf00575g00001.1 96.5 100 Jugreg g44871.t1 100 Nicben Niben101Scf07438g03002.1 100 100 100 100 Capann CA10g18250 98.8 100 100 Querob Qrob P0291090.2 100 100 90 100 Solpen Sopen10g032010.1 99.4 99.8 99.5 100 Sollyc Solyc10g081500.1.1 96.9 97.5 94.8 Pyrcom PCP024281.1 90.8 100 100 Fraexc FRAEX38873 v2 000318370.1 100 98.4 100 Fraexc FRAEX38873 v2 000320880.1 Casmol augustus masked-scaffold00514-abinit-gene-0.6-mRNA-1 100 Daucar DCAR 013480 Maldom MDP0000164956 100 99.9 100 94.4 100 Daucar DCAR 020658 Maldom MDP0000252045 100 100 Pyrbre lcl NW 008989005.1 XP 009347110.1 43170 Helann HanXRQChr07g0197151 Maldom MDP0000832931 100 100 Helann HanXRQChr11g0348641 87.9 100 95.2 100 Helann HanXRQChr13g0398991 Prudul Prudul26A009152P1 98.9 99.8 100 99.9 100 100 100 Helann HanXRQChr13g0398581 Pruper Prupe.8G249900.1 100 100 99.2 96.2 100 100 Atrang 2017210 ZTHV Mosses.p1 100

94 93.3 97.4 Phypat Pp3c10 23790V3.1 87.8 100

99.8

99.8 Ortlye 2016476 CMEQ Mosses.p1 Potmic 18304 t 96.4 Fraves FvH4 2g24420.1 94.4 91.6

95.7 Pruavi Pav sc0000848.1 g090.1.mk 99 Phifon 2011315 ORKS Mosses.p1

100

100

Prumum lcl NC 024131.1 XP 008234958.1 19059 100 84.5 Taklep 2007287 SKQD Mosses.p1

100 Rubocc Bras G09630 100 Taklep 2007286 SKQD Mosses.p1 100 98.2 Drydru Drydr327S03387 100 100 99.9 Sphpal 2036738 RCBT Mosses.p1 99.9 100 90.8 Sphfal Sphfalx0093s0059.1 Sphrec 2020794 UHLI Mosses.p1

93.5 100 Angeve 2013519 NHCM Eusporangiate Monilophytes.p1 Mornot L484 020426 96.7 Psinud 2000109 QVMR Eusporangiate Monilophytes.p1 Psinud 2000110 QVMR Eusporangiate Monilophytes.p1 Humlup HL.SW.v1.0.G029130.1 100 Treori lcl JXTC01000241.1 PON78466.1 23791 Osmsp. 2080824 UOMY Leptosporangiate Monilophytes gametophyte.p1 Distri Distr957S11047 Osmjav 2078330 VIBO Leptosporangiate Monilophytes.p1 80.2 Parand lcl JXTB01000081.1 PON66259.1 11126 99.9 99.5 Lygjap 2000330 PBUU Leptosporangiate Monilophytes.p1 Anetom 2008299 CQPW Leptosporangiate Monilophytes.p1 87 Cucmel MELO3C015881.2.1 99 Culmac 2151963 PNZO Leptosporangiate Monilophytes.p1 Citlan Cla014720 100 99.9 Dipwic 2015016 UFJN Leptosporangiate Monilophytes.p1 Lagsic Lsi02G023330.1 93.9 91 90.1 Zizjuj lcl NC 029687.1 XPCucsat 015891603.1 evm.model.Chr7.1625 23784 100 98.2 93 Ptevit 2018627 POPJ Leptosporangiate Monilophytes.p1 90.3 100 Pittri 2089993 UJTT Leptosporangiate Monilophytes.p1

98.8 98.6 100 Cycmic CMI00025831 81.8 Staeri 2055018 KAWQ Cycadales.p1 100 Cucmax CmaCh08G003770.1 99.9 Ginbil Gb 00093 Cucpep Cp4.1LG17g06750.1 100 Ginbil Gb 00092

100 Wolnob 2058571 RSCE Conifers.p1 Cucmos CmoCh08G003720.1 100 Agamac 2068223 ACWS Conifers.p1 Datglo Datgl6308S11957 Phyhyp 2010680 JRNA Conifers.p1 93.5 81.7 Begfuc Begfu9285S14931 Parust 2007725 JZVE Conifers.p1 Begfuc Begfu573S12978 Lagfra 2089065 ZQWM Conifers.p1 Mancol 2007925 CDFR Conifers.p1 96.8 Begfuc Begfu3698S03699 Pruand 2009248 EGLZ Conifers.p1 Mictet 2075476 MHGD Conifers.p1 95.7 Begfuc Begfu11328S07126 Acmpan 2003887 HILW Conifers.p1 Acmpan 2003886 HILW Conifers.p1 Podrub 2010285 XLGK Conifers.p1 Begfuc Begfu58469S13013 90.9 Retmin 2073148 VGSX Conifers.p1 Begfuc Begfu16611S08487 Nagnag 2007327 UUJS Conifers.p1 Momcha lcl NW 019104553.1 XP 022150256.1 20464BegfucDatglo Begfu5075S04765 Datgl123S01580 Sciver 2010992 YFZK Conifers.p1 Taxbac 2011211 WWSS Conifers.p1 Ausspi 2010622 BTTS Conifers.p1 Cephar 2112894 NVGZ Conifers 2 samples combined.p1 Begfuc Begfu91577S06399 Cephar 2089635 WYAJ Conifers.p1 Cephar 2061825 GJTI Conifers.p1 Vigrad Vradi08g09860.1 Cunlan 2007623 ESYX Conifers branch apex with needles.p1 Cunlan 2010084 ZQVF Conifers 2 samples combined.p1 Cunlan 2052814 OUOI Conifers.p1 Vigang vigan.Vang06g18120.1 Taicry 2069042 QSNJ Conifers.p1 Vigung Vigun07g114900.1 Athcup 2065116 XIRK Conifers.p1 Metgly 2066318 NRXL Conifers.p1 Taxdis 2013665 FHST Conifers.p1 Cryjap 2113451 HOUF Conifers leaf.p1 Cryjap 2147831 GMHZ Conifers 2 samples combined.p1 Cicari Ca 09929.1 Cryjap 2004652 DSXO Conifers.p1 Phavul Phvul.007G167500.1 Chalaw 2071679AIGO Conifers.p1 Thudol 2005638 NKIN Conifers.p1 Thupli 2041922 VFYZ Conifers.p1 Tetsp. 2072274 CGDN Conifers.p1 Plaori 2010881 BUWV Conifers.p1 Caldec 2009681 FRPM Conifers.p1 Caldec 2009682 FRPM Conifers.p1 Piluvi 2010340 ETCJ Conifers.p1 Piluvi 2010341 ETCJ Conifers.p1 Glymax Glyma.02G151200.1 Auschi 2071697 YYPE Conifers.p1

Aradur Aradu.7VM84 Lotjap Lj5g3v1681470.1 Aradur Aradu.P5BCJ

Medtru MtrunA17 Chr1g0196261 Lupang Lup024633.1 Tripra Tp57577 TGAC v2 mRNA17541 Araipa Araip.CJ9D7

Nissch Nissc8077S11319 Aradur Aradu.2DM5J Trisub lcl DF973433.1 GAU30684.1 19742

Chafas Chafa1332S06652 Cercan Cerca12S00492

Mimpud Mimpu15348S07329

Arahyp arahy.Tifrunner.gnm1.ann1.TWB4J4.1

Arahyp arahy.Tifrunner.gnm1.ann1.KRYP2Z.1 Casaus Castanospermum14330-PA Casaus Castanospermum15786-PA

Arahyp arahy.Tifrunner.gnm1.ann1.9V8R16.1

Disarc 2010781 GKCZ Conifers.p1 Disarc 2010782 GKCZ Conifers.p1 Pappap 2011748 OVIJ Conifers.p1

Neopan 2010346 JDQB Conifers.p1 Arahyp arahy.Tifrunner.gnm1.ann1.6Q5HDN.1

Aposhe lcl KZ451918.1 PKA62290.1 5041 Aposhe lcl KZ452307.1 PKA48605.1 18694 Aposhe lcl KZ451935.1 PKA60902.1 6657

Calmac 2059808 RMMV Conifers March.p1

Ambtri evm 27.model.AmTr v1.0 scaffold00197.12

Dencat lcl NW 021318604.1 XP 020688526.1 2759 Dencat lcl NW 021319579.1 XP 020702101.1 21282

Tree scale: 0.1 Supplementary Figure 22: Maximum likelihood tree of LIN/LIN-like.

Sarsan 2042440 SERM Core Eudicots-Asterids.p1Monuni 2016131 LRTN Core Eudicots-Asterids.p1

Monuni 2005151 LRTN Core Eudicots-Asterids.p1 Sarsan 2043369 SERM Core Eudicots-Asterids.p1

Cephar 2014415 NVGZ Conifers 2 samples combined.p1 Monuni 2009359 LRTN Core Eudicots-Asterids.p1 Dencat lcl NW 021319682.1 XP 020689090.1Sarsan 2007089 22701 SERM Core Eudicots-Asterids.p1

Cunlan 2100132 ZQVF Conifers 2 samples combined.p1 Davfej 2224986 OQWW Leptosporangiate Monilophytes.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00041.177 Ambtri evm 27.model.AmTr v1.0 scaffold00041.174

Adirad 2015409 BMJR Leptosporangiate Monilophytes.p1 Osmjav 2010906 VIBO Leptosporangiate Monilophytes.p1

Fraexc FRAEX38873 v2 000310180.3 Fraexc FRAEX38873 v2 000310180.2 Notmon 2009961 YCKE Leptosporangiate Monilophytes.p1 Fraexc FRAEX38873 v2 000310180.4

Rhofor TRINITY DN10998 c0 g1 i1.p1 Aposhe lcl KZ451886.1 PKA66456.1 1122

Helann HanXRQChr12g0367211

Amearg 2023808 IAJW Conifers.p1

Daucar DCAR 013871

Phaequ PEQU 17419

Selsta 2053323 ZZOL Lycophytes.p1 Selsta 2052617 ZZOL Lycophytes.p1

Psemen PME00108938 Sellep 2010613 ABIJ Lycophytes.p1

Baztri 2006998 WZYK Liverworts.p1 Baztri 2007000 WZYK Liverworts.p1

OdoproCalfis 2016929 2017531 YBQN RTMU Liverworts.p1 Liverworts.p1 Schisp. 2102497 LGOW Liverworts.p1

Fraexc FRAEX38873 v2 000310180.1 Petaxi Peaxi162Scf00066g00042.1 Nicben Niben101Scf02597g01005.1 Capann CA04g12340 Solpen Sopen04g025800.1 Sollyc Solyc04g057940.2.1 Schisp. 2103353 LGOW Liverworts.p1 Poptri Potri.005G240100.2 Poptri Potri.002G021600.2 Riccom 30170.m014192 Selmoe 418457 Manesc Manes.05G146700.2 Manesc Manes.05G146700.1 Citcle Ciclev10024300m Citsin orange1.1g000744m Pallye 2108509 YFGP Liverworts.p1 Carpap evm.model.supercontig 26.52 Thecac Thecc1EG021979t1 Marpal 2012106 LFVP Liverworts 2 samples combined.p2 Gosrai Gorai.002G254900.1 Pelnee 2112836 JHFI Liverworts.p1 Casmol maker-scaffold00770-augustus-gene-0.38-mRNA-1 Selmoe 413195 Querob Qrob P0666670.2 Pelepi 2015107 PIUF Liverworts.p1 Jugreg g1960.t1 Marpal 2008533 IHWO Liverworts mycorrizal.p1 Casgla Casgl36S16522 Pelnee 2008106 JHFI Liverworts.p1 Alnglu Alngl11730S14460 Marpal 2011575 HMHL Liverworts non mycorrizal.p2 Alnglu Alngl11730S14454 Pelnee 2008105 JHFI Liverworts.p1 Mimpud Mimpu2183S08467 Marpal 2012106 LFVP Liverworts 2 samples combined.p1 Chafas Chafa1912S17660 Marpal 2011575 HMHL Liverworts non mycorrizal.p1 Casaus Castanospermum25803-PA Lupang Lup001700.1 Nissch Nissc1944S06591 Marpal scaff1987 FGenesh5.1 Arahyp arahy.Tifrunner.gnm1.ann1.F7688A.4 Marpal 2083086 LFVP Liverworts 2 samples combined.p1 Araipa Araip.7A4AR Arahyp arahy.Tifrunner.gnm1.ann1.Z5I6I4.4 Marpal 2008533 IHWO Liverworts mycorrizal.p2 Aradur Aradu.C7AWI Cajcaj Ccajan 22455 Glymax Glyma.10G194500.1 Glymax Glyma.12G174500.1 Phavul Phvul.007G136300.1 Vigung Vigun07g186600.1 Vigang vigan.Vang06g09070.1 Vigrad Vradi08g15740.1 Lotjap Lj5g3v1697440.2 Luncru 2012489 TXVB Liverworts.p1 Lotjap Lj5g3v1697430.1 Pornav 2016028Marpol KRUQ Mapoly0094s0019.1 Liverworts.p2 Lotjap Lj5g3v1697440.1 Marpal 2014908 LFVP Liverworts 2 samples combined.p1 Cicari Ca 29590.1 Marpal 2066411 PelneeIHWO Liverworts2008105 JHFI mycorrizal.p1 Liverworts.p2 Cicari Ca 09968.1 Medtru MtrunA17 Chr1g0196911 Tripra Tp57577 TGAC v2 mRNA13848 Marpal 2063150 IHWO LiverwortsMarpal scaff8652 mycorrizal.p1 FGenesh2.1 100 Trisub lcl DF973165.1 GAU16937.1 5995 100 Datglo Datgl423S09828 100 Begfuc Begfu10983S15953 86.9 Momcha lcl NW 019104488.1 XP 022135985.1 1283 Momcha lcl NW 019104488.1 XP 022136008.1 1290

100 Momcha lcl NW 019104488.1 XP 022135992.1 1282 90.2

100 100 Momcha lcl NW 019104488.1 XP 022135949.1 1285 86.8 Momcha lcl NW 019104488.1 XP 022135967.1 1287 100 100

100 Momcha lcl NW 019104488.1 XP 022135959.1 1286 100 100 100 100 99.4 Momcha lcl NW 019104488.1 XP 022135976.1 1288 100

95.9 100 100 100 99.9 Momcha lcl NW 019104488.1 XP 022136000.1 1289 100 100 100 99.9 100 100 100 100 97.5 100 86.8 100 Momcha lcl NW 019104488.1 XP 022135943.1 1284 97.4 99.1 100 100 Cucmos CmoCh09G000970.1 100 98.1 100 Cucmax CmaCh09G001010.1

100 Cucpep Cp4.1LG17g09150.1 97 95.1 100 99.9 100 100 Cucpep Cp4.1LG06g00600.1

100 98.1 Cucmel MELO3C003747.2.1 Cucsat evm.model.Chr3.4263 Vigrad Vradi07g28420.1 100 100 Vigang vigan.Vang10g01980.1 Cucsat evm.model.Chr3.4263.1 Citlan Cla020848 Vigung Vigun03g022400.1 99.7 99.9 Lagsic Lsi04G017500.1 Phavul Phvul.002G311800.1 100 Lagsic Lsi04G017560.1 83.8 Glymax Glyma.05G229600.1 100 Mornot L484 016060 100 Glymax Glyma.08G037000.1 100 100 90.8 Treori lcl JXTC01000055.1 PON93899.1 10290 100 100 Parand lcl JXTB01000048.1 PON70719.1 7745 Tripra Tp57577 TGAC v2 mRNA24264 100 LIN 100 100 100 Cajcaj Ccajan 15678 100 Distri Distr142S05277 100 Trisub lcl DF973116.1 GAU11683.1 741 100 Zizjuj lcl NW 015453919.1 XP 024924817.1 38433 100 96 99.9 99.6 90.3 Zizjuj lcl NC 029684.1 XP 024930397.1 16769 96.2 Medtru MtrunA17 Chr8g0390311 100 99.6 100 Zizjuj lcl NC 029684.1 XP 024930396.1 16768 90.8 100 85 Drydru Drydr276S09581 Cicari Ca 15737.1 100 Maldom MDP0000745911 Lotjap Lj4g3v3061490.2 100 100 100 91.8 100 Pyrbre lcl NW 008988050.1 XP 009334977.1 3305 100 99.8 100 Lotjap Lj4g3v3061490.1 100 100 100 82.9 Pyrcom PCP025802.1 Lotjap Lj4g3v3061490.3 100 100 93 Pruavi Pav sc0001364.1 g030.1.mk 100 97.8 92.6 92.6 Aradur Aradu.D4WQD 100 100 Pruper Prupe.1G364600.1 Arahyp arahy.Tifrunner.gnm1.ann1.LGD3I1.3 100 100 98.5 99.8 Prudul Prudul26A030302P1 81.2 Arahyp arahy.Tifrunner.gnm1.ann1.AAED67.1 100 10099.9 Prumum lcl NC 024127.1 XP 008221253.1 6177 100 100 100 97.7 Prumum lcl NC 024127.1 XP 008221252.1 6176 Araipa Araip.1Q1XN 99.6 100 100 Prumum lcl NC 024127.1 XP 016648064.1 6175 Nissch Nissc181589S16735 100 Rubocc Bras G02236 Casaus Castanospermum08249-PA 100 96 Roschi RchiOBHm Chr6g0302931 98.8 Arahyp arahy.Tifrunner.gnm1.ann1.3QR2KS.2 Roschi RchiOBHm Chr6g0302941 100 100 91.6 Aradur Aradu.8BK6A 100 Potmic 9479 t 97.3 100 100 87.2 Fraana FAN iscf00044624.1.g00001.1 Arahyp arahy.Tifrunner.gnm1.ann1.VBA0Y3.3 100 100 Araipa Araip.D8XCD 100 100 99.9 90.6 Fraana FAN iscf00054331.1.g00001.1 Fraana FAN iscf00027504.1.g00001.1 Nissch Nissc26490S07435 100 100 100 Fraana FAN iscf00080767.1.g00001.1 Lupang Lup004513.1 100 89.5 Fraana FAN iscf00085426.1.g00001.1 100 Fraana FAN iscf00141564.1.g00001.1 Casaus Castanospermum23258-PA 99.8 100 95.3 99.9 100 93.2 Fraves FvH4 2g38380.1 Mimpud Mimpu144815S01118 100 99.6 98.1 100 Fraana FAN iscf00200393.1.g00001.1 Chafas Chafa2196S18537 100 100 LIN-like Encbar 2000462 GNQG Cycadales.p1 Cercan Cerca117S12893 99.7 99.4 96.7 Staeri 2010850 KAWQ Cycadales.p1 Cercan Cerca570S26907 100 97.9 90.2 Ginbil Gb 32192 Pyrcom PCP029108.1 100 100 Ginbil Gb 02502 100 99.9 100 80 Abilas 2054444 VSRH Conifers.p1 99.9 100 100 Maldom MDP0000230799 93 Abilas 2053983 VSRH Conifers.p1 100 99.9 98.7 Psemen PME00108782 Pyrbre lcl NW 008988062.1Maldom XP 018502155.1 MDP0000164019 5884 100 97.8 Pyrcom PCP021470.1 100 100 94.8 Pintae PTA00026958 98.4 96 100 100 100 87.4 Pinjef 2003903 MFTM Conifers.p1 Pruper Prupe.7G226000.1 100 Pinjef 2003904 MFTM Conifers.p1 Cephar 2021515 NVGZ Conifers 2 samples combined.p1 Prudul Prudul26A014351P1 100 Amearg 2026279 IAJW Conifers.p1

100 9094.9 Phyhyp 2066245 JRNA Conifers.p1 100 98.2 99.8 99.8 100 Cunlan 2016142 ZQVF Conifers 2 samples combined.p1 Pruavi Pav sc0000212.1 g350.1.mk 98.9 100 Potmic 13537 t 100 97.7 Metgly 2064821 NRXL Conifers.p1 Fraves FvH4 1g05520.1 100 Prumum lcl NC 024133.1 XP 008242573.1 26181 100 99.9 Cunlan 2021376 ZQVF Conifers 2 samples combined.p1 99 100 100 Fraana FAN iscf00038820.1.g00001.1 100 Cunlan 2016771 ESYX Conifers branch apex with needles.p1

100 100 89 100 Staeri 2011225 KAWQ Cycadales.p1 Rubocc Bras G07730 100 100 Ginbil Gb 38779 96.5 100 Roschi RchiOBHm Chr2g0091211 100 100 Ararul 2061599 XTZO Conifers.p1 Drydru Drydr728S24172 95.5 100 100 100 100 Wolnob 2054186 RSCE Conifers.p1 99.6 Sunama 2092324 KLGF Conifers.p1 94.1 Mornot L484 002741 99.4 Phyhyp 2014652 JRNA Conifers.p1 100 98.5 Mancol 2061867 CDFR Conifers.p1

99.9 100 Lagfra 2092614 ZQWM Conifers.p1 99.8 100 100 100 100 Mancol 2060578 CDFR Conifers.p1

99.4 Parand lcl JXTB01000244.1 PON50525.1Distri 22242Distr290S21200 100 Mictet 2013834 MHGD Conifers.p1 Treori lcl JXTC01000011.1 POO00898.1 Citlan3530 Cla004095 Acmpan 2017905 HILW Conifers.p1 Lagsic Lsi06G008510.1 Faltax 2080409 PLYX Conifers 2 samples combined.p1

94.4 100 99.4 Faltax 2016966 PLYX Conifers 2 samples combined.p1 99.9 Zizjuj lcl NC 029690.1 XP 024922363.1 30880 Daccom 2009590 FMWZ Conifers.p1 100 100 Podrub 2055289 XLGK Conifers.p1

Zizjuj lcl NC 029690.1 XP 015898519.1 31141 97.3 Cucmel MELO3C024693.2.1 Podcor 2011430 SCEB Conifers.p1 Nagnag 2116034 UUJS Conifers.p1 Cucsat evm.model.Chr1.3324 Cephar 2017604 NVGZ Conifers 2 samples combined.p1 Cephar 2010232 GJTI Conifers.p1 100 Cucmos CmoCh11G006310.1 Amearg 2148153 IAJW Conifers.p1 Cucpep Cp4.1LG04g10200.1 Taxbac 2009497 WWSS Conifers.p1 Taxcus 2009237 ZYAX Conifers.p1 Cucmax CmaCh11G006230.1 Taicry 2012895 QSNJ Conifers.p1 Cucmax CmaCh11G006220.1 Metgly 2064529 NRXL Conifers.p1 Fokhod 2061705 UEVI Conifers.p1 Begfuc Begfu91872S06543 Tetsp. 2011650 CGDN Conifers.p1 Begfuc Begfu1677S01451 Micdec 2052297 XQSG Conifers.p1 Datglo Datgl1324S20065Jugreg g37759.t1 Caldec 2061897 FRPM Conifers.p1 Casgla Casgl55S02277 Cupdup 2070619 QNGJ Conifers.p1 Auschi 2070125 YYPE Conifers.p1 Disarc 2013618 GKCZ Conifers.p1 Alnglu Alngl40820S26566 Widced 2012408 AUDE Conifers.p1 Piluvi 2011219 ETCJ Conifers.p1

91.5 Calgra 2141576 IFLI Conifers March.p1 Calmac 2060208 RMMV Conifers March.p1 100 99.9 Neopan 2002948 JDQB Conifers.p1 Cryjap 2075972 DSXO Conifers.p1 Cryjap 2019272 GMHZ Conifers 2 samples combined.p1

Manesc Manes.16G113200.2 100 Cryjap 2107169 HOUF Conifers leaf.p1 Cryjap 2006297 DSXO Conifers.p1 Manesc Manes.16G113200.3Riccom 29912.m005488 Athcup 2059111 XIRK Conifers.p1 Momcha lcl NW 019104521.1 XP 022145063.1 15835 Metgly 2061320 NRXL Conifers.p1 Chalaw 2066344 AIGO Conifers.p1 Fokhod 2058164 UEVI Conifers.p1 Manesc Manes.16G113200.1 Piluvi 2059337 ETCJ Conifers.p1 Auschi 2067235 YYPE Conifers.p1 Disarc 2076142 GKCZ Conifers.p1 Poptri Potri.018G083600.3 Widced 2059187AUDE Conifers.p1 Taicry 2012895 QSNJ Conifers.p2 Cunlan 2003553 ZQVF Conifers 2 samples combined.p1 Cunlan 2002462 ESYX Conifers branch apex with needles.p1 Taxcus 2073670 ZYAX Conifers.p1 Psechi 2003267YLPM Conifers.p1 Psechi 2003266YLPM Conifers.p1 Citcle Ciclev10007255m Ambtri evm v1.027.model.AmTr scaffold00109.97 Citsin orange1.1g001349m

Cepfol Cfol v3 21887 Thecac Thecc1EG037843t1 Gosrai Gorai.009G026500.1

Capann CA07g06710 Solpen Sopen07g008980.2 Solpen Sopen07g008980.1 Sollyc Solyc07g020870.1.1

Daucar DCAR 028695 Carpap evm.model.supercontig 23.66 Daucar DCAR 010478

Nelnuc NNU 26127-RA

Bradis Bradi2g07750.2

Phaequ PEQU 14111 Anacom Aco010789.1

Nicben Niben101Scf06148g00002.1 Setita Seita.5G008400.1

Orysat LOC Os01g12930.1 Nicben Niben101Scf03164g03009.1Petaxi Peaxi162Scf00231g00433.1 Zeamay Zm00008a010663

Helann HanXRQChr10g0318721 Sorbic Sobic.003G008100.1 Helann HanXRQChr09g0239381Horvul HORVU3Hr1G052520.1 Fraexc FRAEX38873 v2 000032140.1

Musacu GSMUA Achr10T22180 001

Aposhe lcl KZ451950.1 PKA59058.1 8273

Dencat lcl NW 021319790.1 XP 020673672.1 24162

Tree scale: 0.1 Supplementary Figure 23: Maximum likelihood tree of CASTOR.

Necdou 2020431TMAJ Mosses.p1

Leubra 2010440 ZACW Mosses.p1 Pseele 2005887 QKQO Mosses.p1

Aulhet 2011593 WNGH Mosses.p1

Ortlye 2001289 CMEQ Mosses.p1 Leujul 2003727 IGUH Mosses.p1 Racvar 2008242 RDOO Mosses.p1 Ortlye 2001288 CMEQ Mosses.p1 Leujul 2003728 IGUH Mosses.p1 Hedcil 2051821 YWNF Mosses.p1 Racvar 2008243 RDOO Mosses.p1Phifon 2059497 ORKS Mosses.p1

Synpri 2021658 GRKU Mosses.p1 Cerpur 2001085 FFPD Mosses.p1

Leualb 2014292Leugla VMXJ 2008348 Mosses.p1 RGKI Mosses.p1 Scoaqu 2019398Dicsco BPSG2102620 Mosses.p1 NGTD Mosses.p1 Scoaqu 2019399 BPSG Mosses.p1

Timaus 2011279 ZQRI Mosses.p1 Physsp. 2019726Timaus YEPO 2011280Mosses.p1 ZQRI Mosses.p1

Encstr 2008087 KEFD Mosses.p1 Encstr 2008088 KEFD Mosses.p1

Andrup 2009098 WOGB Mosses.p1 Tetpel 2017766Dipfol 2010327 HVBQ AWOI Mosses.p1 Mosses.p1 Andrup 2009099 WOGB Mosses.p1 Phypat Pp3c24 1450V3.1 Sphles 2013151 GOWD Mosses.p1 Odopro 2008590 YBQN Liverworts.p1 Phypat Pp3c10 22510V3.1 Odopro 2008589Taklep YBQN 2009340 Liverworts.p1 SKQD Mosses.p1 Scanem 2168202 IRBN Liverworts.p1

MixspeCalfis 2161170 2181442 NWQC RTMU Liverworts.p1 Liverworts.p1Sphfal Sphfalx0019s0067.1 Marpal 2010988 LFVP Liverworts 2 samples combined.p1Schisp. 2015499 LGOW Liverworts.p1 Schisp. 2015497 LGOW Liverworts.p1 Schisp. 2015500 LGOW Liverworts.p1 Metcra 2008139 NRWZ Liverworts.p1

Anoatt 2061774 QMWB Mosses.p1 Calcor 2005799 TAVP Mosses.p1 92.7 Calcor 2005798 TAVP Mosses.p1 Anocla 2008504 VBMM Mosses.p1 Rhyser 2004217 JADL Mosses.p1 Metcra 2008137 NRWZ Liverworts.p1 Rhyser 2004216 JADL Mosses.p1 Selmoe 84001 Selkra 2041869 ZFGK Lycophytes.p1 Selmoe 60947 Psecar 2002257 UPMJ Lycophytes.p1 100 Psecar 2002258 UPMJ Lycophytes.p1 Hupluc 2024190 GKAG Lycophytes.p1

89.2 Hupsel 2025580 NYBX Lycophytes A.p1 Dipdig 2006633 WAFT Lycophytes.p1 Denobs 2009794 XNXF Lycophytes.p1 100 100 Marpal 2065256 IHWO LiverwortsPelnee mycorrizal.p12005396 JHFI Liverworts.p1 Scedis 2000705 EEAQ Eusporangiate Monilophytes.p1 Scedis 2000706 EEAQ Eusporangiate Monilophytes.p1

85.9 86.6 Thyele 2123530 EWXK Leptosporangiate Monilophytes.p1 Pelnee 2005397 JHFI Liverworts.p1 Osmsp. 2005519 UOMY Leptosporangiate Monilophytes gametophyte.p1 Osmjav 2003466 VIBO Leptosporangiate Monilophytes.p1 Osmsp. 2005520 UOMY Leptosporangiate Monilophytes gametophyte.p1 Pelepi 2016395 PIUF Liverworts.p1 100 Dipcon 2014955 MEKP Leptosporangiate Monilophytes.p1 Lygjap 2079166 PBUU Leptosporangiate Monilophytes.p1 100 Osmjav 2078495 VIBO Leptosporangiate Monilophytes.p1 Osmsp. 2004626 UOMY Leptosporangiate Monilophytes gametophyte.p1 Salcuc Sacu v1.1 s0034.g011200 Culmac 2026224 PNZO Leptosporangiate Monilophytes.p1 Marpal scaff3376 FGenesh14.1 Cryacr 2011041 WQML Leptosporangiate Monilophytes.p1 81.3 Adirad 2007308 BMJR Leptosporangiate Monilophytes.p1 Ptevit 2010464 POPJ Leptosporangiate Monilophytes.p1 Blespi 2099876 VITX Leptosporangiate Monilophytes.p1 Dipwic 2090077 UFJN Leptosporangiate Monilophytes.p1 Luncru 2013251 TXVB Liverworts.p1 Leuimm 2001274 WGTU Leptosporangiate Monilophytes.p1 Leuimm 2001272 WGTU Leptosporangiate Monilophytes.p1 Phacar 2019311 RXRQ Hornworts sporophyte.p1Marpol Mapoly0024s0089.1 Cysfra 2015855 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 MegflaBlaspNW 2009914 c331267 UCRN Hornworts.p1g3 i2 m.107637 Cysfra 2090763 XXHP Leptosporangiate Monilophytes Stewart.p1 Phacar 2019312 RXRQ Hornworts sporophyte.p1Marpol Mapoly0173s0003.1 Cysfra 2013343 LHLE Leptosporangiate Monilophytes.p1 Phacar 2006408 WCZB MegflaHornworts 2009916 gametophyte.p1 UCRN Hornworts.p1 100 Cysree 2010835 RICC Leptosporangiate Monilophytes.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00066.172 Megfla 2009915 UCRN Hornworts.p1 Aposhe lcl KZ451939.1 PKA60201.1 6853 Phacar 2025169 RXRQ Hornworts sporophyte.p1 Phaequ PEQU 08590 Dencat lcl NW 021319083.1 XP 020699560.1 10183 Dencat lcl NW 021319083.1 XP 028550902.1 10185 Dencat lcl NW 021319083.1 XP 028550904.1 10187 Dencat lcl NW 021319083.1 XP 020699559.1 10184 Dencat lcl NW 021319083.1 XP 028550903.1 10186

100 Phacar 2011662 WCZB Hornworts gametophyte.p1 99.6 Musacu GSMUA Achr7T23790 001 Anacom Aco011381.1 100 Phacar 2011663 WCZBParhal Hornworts 2003947 gametophyte.p1 FAJB Hornworts.p1 Orysat LOC Os03g62650.1

Parhal 2009689 FAJB Hornworts.p1 92.3 Horvul HORVU5Hr1G120340.12 Bradis Bradi1g02000.4 Parhal 2009688 FAJB Hornworts.p1 100 100 Setita Seita.9G015600.1 99 Sorbic Sobic.001G016700.1 Zeamay Zm00008a019037 98.7 100

100 Helann HanXRQChr01g0023321 Notvin 2010166 TCBC Hornworts.p1 99.6 100 Daucar DCAR 028970 Megfla 2010566 UCRN Hornworts.p1 Fraexc FRAEX38873 v2 000119370.1 Fraexc FRAEX38873 v2 000226470.2 94 Fraexc FRAEX38873 v2 000226470.1 Fraexc FRAEX38873 v2 000119360.2 Sphpal 2005585 RCBT Mosses.p1 99.9 Sphfal Sphfalx0154s0016.1 Fraexc FRAEX38873 v2 000119360.3 Taklep 2010141 SKQD Mosses.p1 Fraexc FRAEX38873 v2 000119360.1 Capann CA00g86490 Petaxi Peaxi162Scf00883g00321.1 Nicben Niben101Scf05468g02013.1

100 Nicben Niben101Scf05468g02018.1 Nicben Niben101Scf03392g01011.1 Nicben Niben101Ctg12814g00002.1 Sollyc Solyc03g059160.1.1 Solpen Sopen03g013350.2 Solpen Sopen03g013350.1 Capann CA03g13650 100 Capann CA05g20300

100 Capann CA00g96410 Sollyc Solyc03g059150.2.1

100 Solpen Sopen03g013340.1 Riccom 29957.m001428 Fraana FAN iscf00279710.1.g00001.1 Manesc Manes.02G213500.1

Fraana FAN iscf00028836.1.g00001.1 94.5 Poptri Potri.013G128100.1 Fraana FAN iscf00215276.1.g00001.1 Poptri Potri.019G097000.1 Fraana FAN iscf00030548.1.g00001.1 Poptri Potri.019G113433.1 Citcle Ciclev10018782m Fraana FAN iscf00047156.1.g00001.1 94.7 Carpap evm.model.supercontig 9.383

99.2 Cepfol Cfol v3 30246

80.5 Thecac Thecc1EG019847t1 Fraana FAN iscf00112479.1.g00001.1Fraves FvH4 6g26000.1 88.5 98.9 Gosrai Gorai.005G009000.1 Fraana FAN icon19424105.1.g00001.1 99.1 99.6 98.7 95.7 91.6 Mornot L484 020382 100 96.9 98.9 Humlup HL.SW.v1.0.G020131.1

99.8 Parand lcl JXTB01000011.1 PON77952.1 2306 Roschi RchiOBHm Chr7g0218571 82.8 Potmic 12086 t 100 87.6 Treori lcl JXTC01000400.1 PON57130.1 29448 Roschi RchiOBHm Chr7g0220721 100 100 99.7 100 98.1 91.7 96.3 Distri Distr74S27651 100 96.2 99.2 87.5 Zizjuj lcl NC 029679.1 XP 015870059.1 4114 100 86.5 Rubocc Bras G27571 99.2 100 Zizjuj lcl NC 029679.1 XP 015870075.1 4116 100 100 100 91.8 100 96 89.7 86.787.6 100 85.3 Drydru Drydr34S20655 100 93.1 Zizjuj lcl NC 029679.1 XP 015870066.1 4117 89.2 86.5 Pyrcom PCP036180.1 99.7 99.1 Zizjuj lcl NC 029679.1 XP 015870051.1 4115 100 100 83.7 Maldom MDP0000379735 99.7 98.7 Zizjuj lcl NC 029679.1 XP 015870098.1 4118 100 92 91.1 99.9 Maldom MDP0000151400 97.7 100 Rubocc Bras G04111 99.4 100 99.8 100 100 98.8 100 Roschi RchiOBHm Chr4g0405621 Maldom MDP0000295929 97.8 85.3 98.7 99.3 82 Potmic 13174 t 89.2 100 99.7 96.7 Pyrcom PCP010379.1 100 88.4 100 Pyrbre lcl NW 008988079.1 XP 009355444.2 8465 84.1 100 Fraana FAN iscf00185237.1.g00001.1 99.2 99.997.499.9 95.7 Fraana FAN iscf00008774.1.g00001.1 100 100 82 100 Pruavi Pav sc0001196.1 g880.1.mk 99.9 100 99.3 Fraana FAN iscf00317365.1.g00001.1 Prumum lcl NC 024127.1 XP 008218766.1 3769 100 CASTOR Fraana FAN iscf00369244.1.g00001.1 99.7 99.6 100 99.8 95.9 99.797.3 Prudul Prudul26A018806P1 83.1 88.192.5 Fraves FvH4 4g10120.1 98.2 96.4 96.9 91 Fraana FAN icon19961561.1.g00001.1 Pruper Prupe.1G577700.1 99.7 99.8 98.9 99.3 Pruavi Pav sc0000065.1 g520.1.mk 99.9 99.5 94.8 Treori lcl JXTC01000170.1 PON83935.1 20233 98.799.1 99.9 Pruper Prupe.1G102500.1 99.1 94.8 96.9 Parand lcl JXTB01000271.1 PON48776.1 23481 99.8 100 100 Prudul Prudul26A013668P1 99.9 Humlup HL.SW.v1.0.G019005.1 92.5 Prudul Prudul26A007096P1 Mornot L484 018454 98.787.7 93 Prumum lcl NC 024127.1 XP 008223608.1 8328 99.8 93.1 95.5 100 100 89.5 94.7 100 Prumum lcl NC 024127.1 XP 008223609.1 8329 96.2 100 Zizjuj lcl NC 029680.1 XP 024926356.1 7274 100 Drydru Drydr411S21715 94 98.2 81.9 94 Maldom MDP0000119506 Zizjuj lcl NC 029680.1 XPDistri 024926357.1 Distr27S20547 7273 80.7 100 99.299.1 89.2 100 100 Maldom MDP0000687888 100 99.1 100 94.1 Pyrcom PCP015836.1 Tripra Tp57577 TGAC v2 mRNA34119 90.3 95.7 99 99.9 99.8 Pyrbre lcl NW 008988113.1 XP 009360012.1 12839 100 98.8 100 88.7 88.3 100 99.8 Trisub lcl DF973288.1 GAU24400.1 13458 100 94.7 99.9 88.9 Pyrbre lcl NW 008988113.1 XP 009360013.1 12838 82.7 94 93.5 Medtru MtrunA17Cicari Chr2g0277131 Ca 02780.1 95 94.5 98.5 85.1 Casgla Casgl15S09157 98.9 99 96.5 99.9 100 98.5 100 98.8 100 93.3 Alnglu Alngl10396S13200 84.8 100 89 88.3 86.5 99.3 100 Alnglu Alngl10396S13196 87.1 100 90.9 94.9 Tripra Tp57577 TGAC v2 mRNA2184 96.8 84 98 100 85.2 88.9 94.6 95.3 Casmol maker-scaffold13033-snap-gene-0.6-mRNA-1 90.1 100 100 99.4 100 Lotjap Lj6g3v2275010.2 99.9 92 Trisub lcl DF973288.1 GAU24399.1 13457 94.7 98.9 98.9 Casmol maker-scaffold08388-snap-gene-0.13-mRNA-1 99.9 Lotjap Lj6g3v2275020.1 96.993.6 100 Jugreg g50723.t1 100 92.9 99.3 100 100 98.291 98.2 98.8 Lotjap Lj6g3v2275010.1 99.9 86.4 96.1 Jugreg g50723.t2 97.8 98.7

96 97.7 Jugreg g50723.t3 Vigrad Vradi10g13330.1 100 100

93.2 100 Begfuc Begfu7312S40424 100 87.2 Datglo Datgl3865S29648 Vigang vigan.Vang0958s00050.1 99.493.9 100 Vigung Vigun06g235400.1 99.9 Momcha lcl NW 019104570.1 XP 022151987.1 21900

100 100 100 97.6 Momcha lcl NW 019104570.1 XP 022151986.1 21899 Phavul Phvul.006G218700.1 90.7 Momcha lcl NW 019104570.1 XP 022151988.1 21898 Glymax Glyma.16G003300.1 99.8 Citlan Cla022948

100 Glymax Glyma.12G167300.1Cajcaj Ccajan 17266 89.8 Lagsic Lsi04G007020.1

99.6 Lupang Lup014919.1 98.4 Cucsat evm.model.Chr5.2091 Araipa Araip.TN563 Cucmel MELO3C011849.2.1 Aradur Aradu.0FI0R Cucmax CmaCh04G018480.1 Araipa Araip.V5LSC Cucpep Cp4.1LG01g16310.1 Cucmos CmoCh04G019430.1 Cercan Cerca418S24048 Cercan Cerca521S26257 Chafas Chafa96088S30744 Nissch Nissc2435S18814 Casaus Castanospermum16718-PA Lupang Lup029273.1 Arahyp arahy.Tifrunner.gnm1.ann1.ARQ4UL.2 Nissch Nissc1394S14527 Arahyp arahy.Tifrunner.gnm1.ann1.8IGA7D.1Mimpud Mimpu7200S27069 Arahyp arahy.Tifrunner.gnm1.ann1.XB6ANN.1 Casaus Castanospermum16457-PAChafas Chafa1019S13516 Aradur Aradu.97UJ3 CercanAratha Cerca38S23201 AT5G49960.1 Arahyp arahy.Tifrunner.gnm1.ann1.LGEW2E.1 Araipa Araip.LQZ8D Aralyr AL8G23930.t1 Arahyp arahy.Tifrunner.gnm1.ann1.PUPF9M.2 Arahal Araha.7363s0009.1 Lotjap Lj1g3v5061360.1 Lotjap Lj1g3v5061350.1 Medtru MtrunA17 Chr7g0276651 Capgra Cagra.2776s0020.1 Cajcaj Ccajan 11017 Caprub Carub.0008s0986.1 Glymax Glyma.19G263500.1 BoestrBrarap Bostr.15774s0130.1 Brara.B01595.1 Phavul Phvul.009G263100.1 Vigung Vigun09g000400.1 Vigang vigan.Vang0966s00020.2 Vigrad Vradi05g00040.1 Ginbil Gb 17779 Parust 2040238 JZVE Conifers.p1 Retmin 2013020 VGSX Conifers.p1 Mictet 2007904 MHGD Conifers.p1 Mictet 2007905 MHGD Conifers.p1 Ginbil Gb 31318 Citcle Ciclev10000208m Cephar 2012402 GJTI Conifers.p1 Cephar 2005739 WYAJ Conifers.p1 Tarhas lcl NW 010960764.1 XP 010527696.1Citsin orange1.1g002475m 4452 Cephar 2005741 WYAJ Conifers.p1 Cephar 2000310 NVGZ Conifers 2 samples combined.p1 Tarhas lcl NW 010960764.1 XP 010527699.1 4454 Piluvi 2003548 ETCJ Conifers.p1 Tarhas lcl NW 010960764.1 XP 010527695.1Manesc Manes.07G023400.2Riccom 4451 29765.m000755 Calmac 2002501 RMMV Conifers March.p1 Manesc Manes.07G023400.1 Calmac 2002500 RMMV Conifers March.p1 Tarhas lcl NW 010960764.1 XP 010527694.1 4450 Cunlan 2003848 ZQVF Conifers 2 samples combined.p1 Poptri Potri.004G223400.1Cepfol Cfol v3 29949 Cunlan 2000427 ESYX Conifers branch apex with needles.p1 Tarhas lcl NW 010960764.1 XP 010527698.1 4453 Taicry 2003353 QSNJ Conifers.p1 Poptri Potri.003G008800.1 Taicry 2003354 QSNJ Conifers.p1 Tarhas lcl NW 010960764.1 XP 010527697.1 4449 Taicry 2003355 QSNJ Conifers.p1 Ginbil Gb 08564 Cycmic CMI00010981 Staeri 2057018 KAWQ Cycadales.p1 Encbar 2015334 GNQG Cycadales.p1 Carpap evm.TU.contig 47972.1 Taxbac 2008636 WWSS Conifers.p1 Thecac Thecc1EG006180t2 Cephar 2020961 NVGZ Conifers 2 samples combined.p1 Citlan Cla022930 Cephar 2012134 GJTI Conifers.p1 Gosrai Gorai.005G265200.1 Cunlan 2017385 ZQVF Conifers 2 samples combined.p1 Athcup 2003216 XIRK Conifers.p1 Metgly 2010720 NRXL Conifers.p1 Tetsp. 2072050 CGDN Conifers.p1 Lagsic Lsi04G007160.1 Auschi 2006321 YYPE Conifers.p1 Auschi 2006322 YYPE Conifers.p1 Carpap evm.model.supercontigCucsatCucsat evm.model.Chr5.2066.1 evm.model.Chr5.2066 113.52 Neopan 2010546 JDQB Conifers.p1 Cucmel MELO3C011822.2.1 Disarc 2075671 GKCZ Conifers.p1 Wolnob 2009869 RSCE Conifers.p1 Agamac 2012543 ACWS Conifers.p1 Halbid 2013195 OWFC Conifers.p1 Sunama 2009173 KLGF Conifers.p1 Parust 2002217 JZVE Conifers.p1 Lagfra 2008468 ZQWM Conifers.p1 Mancol 2009814 CDFR Conifers.p1 Phyhyp 2014230 JRNA Conifers.p1 Saxcon 2014320 QCGM Conifers.p1 Acmpan 2019156 HILW Conifers.p1 Podcor 2009007 SCEB Conifers.p1 Cucmax CmaCh04G018620.1 Jugreg g18013.t1 Retmin 2012900 VGSX Conifers.p1 Daccom 2005810 FMWZ Conifers.p1 Faltax 2003096 PLYX Conifers 2 samples combined.p1 Faltax 2003095 PLYX Conifers 2 samples combined.p1 Faltax 2009183 QHBI ConifersA.p1 Faltax 2009184 QHBI ConifersA.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00017.65 Zosmar Zosma3g00720.1 Cucmos CmoCh04G019600.1BegfucDatglo Begfu724S40364 Datgl754S34464 Nelnuc NNU 04782-RA Cucpep Cp4.1LG01g16410.1Alnglu Alngl351S25184

Casgla Casgl1999S11039

Capann CA10g09510 Capann CA10g09500 Solpen Sopen10g013890.2 Solpen Sopen10g013890.1 Sollyc Solyc10g044890.1.1

Diacar Dca18390.1

Daucar DCAR 006675

Betvul Bv6 144160 zztn.t2 Anacom Aco011208.1 Bradis Bradi2g56274.2 Betvul Bv6 144160 zztn.t1 Phaequ PEQU 30614 Setita Seita.5G395500.1 Momcha lcl NW 019104570.1 XP 022151837.1 21876 Petaxi Peaxi162Scf00002g02319.1 Zeamay Zm00008a013201

Nicben Niben101Scf01993g08008.1Petaxi Peaxi162Scf00002g02318.1 Sorbic Sobic.003G370200.1 Helann HanXRQChr06g0181371 Orysat LOC Os01g64980.1

Fraexc FRAEX38873 v2 000386390.1 Fraexc FRAEX38873 v2 000067210.1 Fraexc FRAEX38873 v2 000075830.1 Horvul HORVU3Hr1G082670.10

Musacu GSMUA Achr7T23140 001

Casmol maker-scaffold02501-augustus-gene-0.34-mRNA-1 Casmol maker-scaffold02501-augustus-gene-0.35-mRNA-1

Aposhe lcl KZ451982.1 PKA54947.1 13132

Dencat lcl NW 021318566.1 XP 020689159.1 1731 Dencat lcl NW 021318566.1 XP 020689155.1 1730 Dencat lcl NW 021318566.1 XP 020689158.1 1732 Dencat lcl NW 021318566.1 XP 020689156.1 1729

Tree scale: 0.1 Supplementary Figure 24: Maximum likelihood tree of EXO70.

Marpal 2008636 LFVP Liverworts 2 samples combined.p1

Marpal 2068192 IHWO Liverworts mycorrizal.p1

Metcra 2100803 NRWZ Liverworts.p1

Marema 2002123 TFYI Liverworts.p1

Pelepi 2006592 PIUF Liverworts.p1 Marema 2002124 TFYI Liverworts.p1

Concon 2005448 ILBQ Liverworts.p1

Ricnat 2001559 WJLO Liverworts.p1

Luncru 2075420 TXVB Liverworts.p1

Marpal scaff2064 FGenesh4.1 BlaspNW c242431 g1 i1 m.16664

Taklep 2009456 SKQD Mosses.p1 BlaspNW c242431 g1 i2 m.16666

Taklep 2009457 SKQD Mosses.p1 Necdou 2006885 TMAJ Mosses.p1

Marpol Mapoly0113s0036.1 Necdou 2006886 TMAJ Mosses.p1

Anocla 2052155 VBMM Mosses.p1 Loebre 2009070 WSPM Mosses.p1

Leubra 2008762 ZACW Mosses.p1

Pseele 2050499 QKQO Mosses.p1 Leujul 2167804 IGUH Mosses.p1 Aulhet 2010470 WNGH Mosses.p1

Ortlye 2085581 CMEQ Mosses.p1

Phifon 2058158 ORKS Mosses.p1

Cerpur 2058562 FFPD Mosses.p1 Dicsco 2009306 NGTD Mosses.p1

Leualb 2132425 VMXJ Mosses.p1 Racvar 2014381 RDOO Mosses.p1

Racvar 2014382 RDOO Mosses.p1

Scoaqu 2018074 BPSG Mosses.p1

Scoaqu 2018075 BPSG Mosses.p1

Timaus 2014752 ZQRI Mosses.p1

Pelnee 2113527 JHFI Liverworts.p1 Radlin 2018390 BNCU Liverworts.p1

Calfis 2007004 RTMU Liverworts.p1

Mixspe 2158840 NWQC Liverworts.p1

Odopro 2017350 YBQN Liverworts.p1

Scanem 2165939 IRBN Liverworts.p1 Timaus 2014753 ZQRI Mosses.p1 Fruspp 2138493 CHJJ Liverworts.p1 Frusp. 2008520 TGKW Liverworts.p1

Porpin 2015586 UUHD Liverworts.p1

Pornav 2004248 KRUQ Liverworts.p1

Pornav 2004247 KRUQ Liverworts.p1 Physsp. 2017842 YEPO Mosses.p1 Phacar 2140644 RXRQ Hornworts sporophyte.p1 Parhal 2057575 FAJB Hornworts.p1

Phacar 2119966 WCZB Hornworts gametophyte.p1

Phacar 2142129 RXRQ Hornworts sporophyte.p1

Megfla 2053966 UCRN Hornworts.p1

Notaen 2006320 DXOU Hornworts.p1

Dipfol 2073454 AWOI Mosses.p1 Notvin 2011773 TCBC Hornworts.p1 Phypat Pp3c11 17530V3.1 Notvin 2011774 TCBC Hornworts.p1 Lycapp 2087818 ULKT Lycophytes.p1

Isoesp. 2002515 PYHZ Lycophytes.p1 Sphrec 2013911 UHLI Mosses.p1 Isoesp. 2002514 PYHZ Lycophytes.p1 Sphpal 2034815 RCBT Mosses.p1 Isoesp. 2002513 PYHZ Lycophytes.p1

Sphfal Sphfalx0014s0208.1 Osmsp. 2079015 UOMY Leptosporangiate Monilophytes gametophyte.p1

Ginbil Gb 38868

Thudel 2008786 EEMJ Mosses.p1 Ginbil Gb 10202 Chalaw 2071231 AIGO Conifers.p1 Stesub 2069183 LNSF Mosses.p1 Cryjap 2010252 GMHZ Conifers 2 samples combined.p1 Sphfal Sphfalx0182s0003.1 Taxdis 2000507 FHST Conifers.p1 Calcor 2020996 TAVP Mosses.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00065.130 Anoatt 2061711 QMWB Mosses.p1 Aposhe lcl KZ451890.1 PKA65640.1 1538

Phaequ PEQU 15748 Necdou 2016866 TMAJ Mosses.p1 Dencat lcl NW 021319222.1 XP 020678883.2 14934

Pseele 2051031 QKQO Mosses.p1 Phaequ PEQU 35339

Musacu GSMUA AchrUn randomT27140 001

Leujul 2016513 IGUH Mosses.p1 Anacom Aco012222.1 Leubra 2099530 ZACW Mosses.p1 Bradis Bradi3g40510.1

Fonant 2009434 DHWX Mosses.p1 Horvul HORVU7Hr1G052100.1

Orysat LOC Os08g40840.1 Fonant 2009433 DHWX Mosses.p1 Setita Seita.6G212800.1

Ortlye 2085632 CMEQ Mosses.p1 Zeamay Zm00008a003285 Sorbic Sobic.007G202700.1 Leualb 2129092 VMXJ Mosses.p1 Drydru Drydr146S15888

Cerpur 2013316 FFPD Mosses.p1 Rubocc Bras G00491

Synpri 2018439 GRKU Mosses.p1 Roschi RchiOBHm Chr6g0309751 Racvar 2118146 RDOO Mosses.p1 Potmic 1332 t

Fraana FAN iscf00206928.1.g00001.1 Timaus 2018718 ZQRI Mosses.p1 Fraves FvH4 2g32950.1

Fraana FAN iscf00161328.1.g00001.1 Physsp. 2018578 YEPO Mosses.p1 Pruavi Pav sc0002445.1 g060.1.mk

Necdou 2005514 TMAJ Mosses.p1 Prumum lcl NC 024127.1 XP 008220534.1 5286 Phypat Pp3c1 6940V3.1 Prudul Prudul26A008816P1 Necdou 2005513 TMAJ Mosses.p1 Pruper Prupe.1G422000.1 Anocla 2012034 VBMM Mosses.p1 Maldom MDP0000252438 Loebre 2010422 WSPM Mosses.p1 Pyrcom PCP036639.1 100 Pyrbre lcl NW 008988041.1 XP 009360847.1 1407 Leujul 2010232 IGUH Mosses.p1 Maldom MDP0000299180 Leubra 2100115 ZACW Mosses.p1 99.9 Maldom MDP0000312450 Pseele 2047625 QKQO Mosses.p1 96.9 Pyrbre lcl NW 008988296.1 XP 009375167.1 26653

Ortlye 2005348 CMEQ Mosses.p1 Pyrcom PCP012979.1

Hedcil 2052228 YWNF Mosses.p1 95.3 Mornot L484 004009

Racvar 2017308 RDOO Mosses.p1 Treori lcl JXTC01000077.1 PON91133.1 13166

Scoaqu 2010382 BPSG Mosses.p1 Parand lcl JXTB01000036.1 PON72965.1 6115

Distri Distr232S19140

Zizjuj lcl NW 015454151.1 XP 015868852.1 39423 Atrang 2085437 ZTHV Mosses.p1 Zizjuj lcl NW 015453409.1 XP 015900502.1 33212 Phypat Pp3c7 25390V3.1 100 Cerpur 2001750 FFPD Mosses.p1 Datglo Datgl77S34711

Cerpur 2001751 FFPD Mosses.p1 Begfuc Begfu5619S04944

Dicsco 2008797 NGTD Mosses.p1 Begfuc Begfu6728S39821

Momcha lcl NW 019104491.1 XP 022131421.1 4374 Leualb 2128423 VMXJ Mosses.p1 100

Racvar 2005747 RDOO Mosses.p1 Cucmos CmoCh05G001360.1 Cucmax CmaCh05G001320.1 Scoaqu 2022955 BPSG Mosses.p1 Lagsic Lsi08G015340.1 Plains 2080334 BGXB Mosses.p1 Citlan Cla022634 Roscap 2049264 XWHK Mosses.p1 Cucmel MELO3C010799.2.1

Ortlye 2085810 CMEQ Mosses.p1 Cucsat evm.model.Chr2.1841

Aulhet 2090745 WNGH Mosses.p1 Poptri Potri.014G015500.1

Hedcil 2052289 YWNF Mosses.p1 Manesc Manes.05G182300.1 100 Riccom 30170.m013607 Phifon 2059541 ORKS Mosses.p1 99.2 Citsin orange1.1g005534m

Citcle Ciclev10003655m Andrup 2011341Phypat WOGB Pp3c26 Mosses.p1 13820V3.1 Carpap evm.model.supercontig 142.35

Thecac Thecc1EG034688t1 86.6 Sphfal Sphfalx0032s0143.1 Sphrec 2003960 UHLI Mosses.p1 Gosrai Gorai.009G220500.1

Sphpal 2025245 RCBT Mosses.p1 Helann HanXRQChr04g0102781

Daucar DCAR 009877 Sphfal Sphfalx0009s0094.1 Sphrec 2020772 UHLI Mosses.p1 Fraexc FRAEX38873 v2 000218640.1 Sphles 2014471 GOWD Mosses.p1 Petaxi Peaxi162Scf00081g02225.1

Nicben Niben101Scf02723g00006.1 100 90.1 Nicben Niben101Scf00080g04007.1 100 Capann CA04g17680 98.8 100 Solpen Sopen04g031370.1 100 91.8 98.8 96.7 Sollyc Solyc04g077760.1.1 100 99.1 99.7 90.1 100 100 100 Casmol augustus masked-scaffold03950-abinit-gene-0.8-mRNA-1

90 Jugreg g59616.t1

100 100 100 100 Alnglu Alngl29306S23209 81.5 90.5 87.1 100 99.7 Casgla Casgl4S17182 97 97.3 100 100 100 100 99.3 99.9 Cercan Cerca163S15630 100 100 100 100 100 100 98.4 100 100 100 99.9 Mimpud Mimpu3578S22847 99.6 100 100 100 98.3 100 Chafas Chafa2421S19202 82.5 100 100 100 Nissch Nissc1009S04850 84.5 100 100 96.5 99.6 100 Casaus Castanospermum27764-PA 99.9 100

100 Lotjap Lj0g3v0083399.1 100 93.2 100 99.2 99.6 97.3 100 100 100 Cicari Ca 09348.1 99.9 100 Pyrbre lcl NW 008988065.1 XP 009353306.1 6633 99.9 100 Medtru MtrunA17 Chr1g0152401 100 92.6 100 100 99.8 Pyrbre lcl NW 008988065.1 XP 009353342.1 6677 81.2 97.5 Trisub lcl DF973351.1 GAU27347.1 16405 93.4 100 100 99.9 100 Tripra Tp57577 TGAC v2 mRNA13550 100 86.2 100 Nissch Nissc2463S07208

98.2 Pyrcom PCP019270.1 97.2 Aradur Aradu.0VP21 Pyrbre lcl NW 008988144.1 XP 009363625.1 16104 Maldom MDP0000917699 99 94.4 99.3 99.2 99.9 Arahyp arahy.Tifrunner.gnm1.ann1.3URM83.1 Pyrbre lcl NW 008988191.1 XP 009367998.1 20070 98 100 98.4 100 100 Araipa Araip.Q56KQ 97.496.4 100 100

100 Arahyp arahy.Tifrunner.gnm1.ann1.8JVH3I.1

100 100

100 Glymax Glyma.17G234500.1 Pyrcom PCP003812.1 99.5 100 97.1 100 100 Maldom MDP0000247480 99.9 89.3 Glymax Glyma.U030600.1 Prudul Prudul26A005962P1 87.9 100 95.6100 Cajcaj Ccajan 03260 100 100 Phavul Phvul.001G028400.1 Prumum lcl NC 024127.1Pruper XP 008219950.1 Prupe.1G459300.1 4898 92.2 100 91.7 Vigung Vigun08g031100.1 100 Pruavi Pav sc0003562.1 g410.1.mk 100 100 100 95.2 Vigrad Vradi06g14580.1 100 99.8 99.2 Vigang vigan.Vang01g18420.1 Potmic 9652 t 80.3 99.6 99.9 Equhye 2132219 JVSZ Eusporangiate Monilophytes.p1 Fraves FvH4 2g36720.1 Equdif 2011070 CAPN Eusporangiate Monilophytes.p1 Roschi RchiOBHm Chr6g0305081 100 100 98.2 91.9 100 98.9 100 98.9 Scedis 2017560 EEAQ Eusporangiate Monilophytes.p1 Rubocc Bras G00779 98.3 100 98.8 Psinud 2000531 QVMR Eusporangiate Monilophytes.p1 100 98.8

Drydru Drydr146S00862 100 Zizjuj lcl NW 015453790.1 XP 015867261.1 37762 Osmsp. 2003297 UOMY Leptosporangiate Monilophytes gametophyte.p1 98.2 100 97.7 100 Osmsp. 2003296 UOMY Leptosporangiate Monilophytes gametophyte.p1 Zizjuj lcl NW 015453790.1 XP 015867262.1 37763 99.8 100 Osmsp. 2010765 UOMY Leptosporangiate Monilophytes gametophyte.p1 Zizjuj lcl NW 015454292.1 XP 015869251.1 39824 99.6 Salcuc Sacu v1.1 s0009.g004325

Distri Distr598S03323 100 Azofil Azfi s0049.g030799 Parand lcl JXTB01000036.1 PON73048.1 6198 94.8 100 100 100 Adirad 2015344 BMJR Leptosporangiate Monilophytes.p1 Treori lcl JXTC01000001.1 POO03845.1 149 100 100 Myrruf 2001382 GSXD Leptosporangiate Monilophytes.p1 100 Humlup HL.SW.v1.0.G015027.1 Cryacr 2006023 WQML Leptosporangiate Monilophytes.p1 90.1 95.8 EXO70 Cryacr 2006022 WQML Leptosporangiate Monilophytes.p1 Mornot L484 019845 100 99.6 100 Cucpep Cp4.1LG11g05410.1 100 Pteens 2003457 FLTD Leptosporangiate Monilophytes.p1

97.7 100 100 99.5 100 84.3 Ptevit 2022020 POPJ Leptosporangiate Monilophytes.p1 Cucmos CmoCh05G006500.1 99.5 98.7 100 100 Cysfra 2013890 XXHP Leptosporangiate Monilophytes Stewart.p1 Cucmax CmaCh05G006230.1 100 96.7 89.6 99.7 95.2 99.9 100 100 Cysfra 2027706 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Cucpep Cp4.1LG07g01830.1 100 97 95.2 100 Cysfra 2012413 LHLE Leptosporangiate Monilophytes.p1 Cucmos CmoCh12G002500.1 90.3 99.6 95.2 91.3 Cysree 2003759 RICC Leptosporangiate Monilophytes.p1 Cucmax CmaCh12G002980.1 100 99.7 100 Dipwic 2090657 UFJN Leptosporangiate Monilophytes.p1 Citlan Cla022251 81.5 94.3 99.1 100 Blespi 2015716 VITX Leptosporangiate Monilophytes.p1 Lagsic Lsi08G011200.1 100 100 98.1 Athfil 2065989 URCP Leptosporangiate Monilophytes.p1 Cucsat evm.model.Chr2.2258 94.4 100 99.7 98.688.5 Wooilv 2012677 YQEC Leptosporangiate Monilophytes.p1 Cucmel MELO3C011181.2.1 100 92.8 Leuimm 2006493 WGTU Leptosporangiate Monilophytes.p1 100 Momcha lcl NW 019104491.1 XP 022131810.1 4001 99.5 100 Polacr 2075026 FQGQ Leptosporangiate Monilophytes.p1 100 100 Begfuc Begfu1527S47038 100 94.6 100 93.5 99 100 97.5 Bolrep 2002671 JBLI Leptosporangiate Monilophytes.p1 Begfuc Begfu55500S12885 100 87.1 100 Bolrep 2002670 JBLI Leptosporangiate Monilophytes.p1 100 99.1 86.9 87.9 Datglo Datgl338S08439 91.1 99.1100 Phlpse 2014324 ZQYU Leptosporangiate Monilophytes.p1 Casgla Casgl196S24425 100 Phlpse 2014325 ZQYU Leptosporangiate Monilophytes.p1 Casgla Casgl23S04286 89 89.4 Polhes 2024436 GYFU Leptosporangiate Monilophytes A type.p1 Alnglu Alngl7774S05963 98.6 100 Polhes 2028276 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 99.2100 Alnglu Alngl119035S07014 100 99.9 100 Polgly 2081519 CJNT Leptosporangiate Monilophytes.p1 Jugreg g17803.t1 100 96.4 Staeri 2012234 KAWQ Cycadales.p1

Jugreg g24578.t1 99.8 Ginbil Gb 17993 99.898.8100 86.897 98.9 85.2 100 Abilas 2058952 VSRH Conifers.p1 Querob Qrob P0544580.2 100 87.7 100 Tsuhet 2056747 GAMH Conifers.p1 99.3 Larspe 2055650 WVWN Conifers.p1 Vigang vigan.Vang01g12770.1 Casmol augustus masked-scaffold03409-abinit-gene-0.1-mRNA-1 Psewil 2009347 IOVS Conifers.p1 Vigrad Vradi06g12200.1 99 99.9 100 100 99.1 Psemen PME00074949 Vigung Vigun08g065000.1 99 99.898 91.8 Psemen PME00074947 Phavul Phvul.001G060100.2 92.1 100 Piceng 2009836 AWQB Conifers.p1 Glymax Glyma.14G135100.1 97 100 100 100 88.8 100 Picabi MA 10430208g0010 96.9 92.2 Glymax Glyma.17G197600.1 100 100 100 Pinrad 2055857 DZQM Conifers.p1 Cajcaj Ccajan 04811 100 10099.7 100 81.9 99.5 Pinpon 2012608 JBND Conifers.p1 100 100100 100 100 99.7 Pinjef 2016521 MFTM Conifers.p1 Tripra Tp57577 TGAC v2 mRNA12449 100 100 100 96.4 98.3 100 Pinpin PPI00076398 Trisub lcl DF973149.1 GAU15210.1 4268 100 99.6 100 Pinsyl PSY00016285 Medtru MtrunA17Cicari Chr1g0147911 Ca 09793.1 100 99.1 96.6 100 Welmir 2062326 TOXE Gnetales.p1 100 Lotjap Lj3g3v2863540.1 100 100 89 Gnemon TnS000976221t02 97.1

Lupang Lup019335.1 95.5 100 100 Ararul 2012601 XTZO Conifers.p1 98.7 100 Wolnob 2002277 RSCE Conifers.p1 Nissch Nissc524246S25610 90 99.8 99.3 91.6 99.7 100 98.1 Halbid 2006741 OWFC Conifers.p1 88.9 100 Casaus Castanospermum06218-PA 100 97.8 Sunama 2012270 KLGF Conifers.p1 Mimpud Mimpu5137S11004 99.8 99.9 Cercan Cerca6S10518 100 100 Pruand 2010618 EGLZ Conifers.p1 100 100 Parust 2042517 JZVE Conifers.p1 Arahal Araha.10571s0002.1 96.2 Aralyr AL7G20500.t1 100 Mancol 2065059 CDFR Conifers.p1

Aratha AT4G31540.1 100 Lagfra 2092467 ZQWM Conifers.p1

99.3 Saxcon 2012155 QCGM Conifers.p1

100 Caprub Carub.0007s0903.1 100 100 Podcor 2055477 SCEB Conifers.p1 90.1 Capgra Cagra.3807s0025.1 Podrub 2060168 XLGK Conifers.p1 100 100 100 Boestr Bostr.7867s1008.1 97.1 98.9 Retmin 2073735 VGSX Conifers.p1 Brarap Brara.A00618.1 99.3 Nagnag 2117480 UUJS Conifers.p1 100 100 Braolecap Bol017986 100 97.3 Daccom 2059575 FMWZ Conifers.p1 Braolecap Bol017447 100 100 Dacbal 2001966 IZGN Conifers.p1 100 100 Brarap Brara.H01344.1 100 100 100 Faltax 2059709 QHBI Conifers A.p1 97.3 96.893.8 92.8 100 Eutsal Thhalv10024589m 100 Faltax 2084458 PLYX Conifers 2 samples combined.p1 97.2 100 100 100 100 Faltax 2013310 ROWR Conifers.p1

100 100

100 100 100 Psechi 2007859 YLPM Conifers.p1

100 99.9 100 Tornuc 2017834 HQOM Conifers.p1

Tarhas lcl NW 010966177.1 XP 010548545.1 23342 Cephar 2020196 NVGZ Conifers 2 samples combined.p1 Thecac Thecc1EG036831t1 99.6 Carpap evm.model.supercontig 23.26 Cephar 2062230 GJTI Conifers.p1 Tarhas lcl NW 010971389.1 XP 010526266.1 39960 100 94.2 Gosrai Gorai.010G245500.1 Cunlan 2020885 ZQVF Conifers 2 samples combined.p1 100 Manesc Manes.16G134900.1 97.8 99.9 Cunlan 2089198 ESYX Conifers branch apex with needles.p1 100

91.4 100 100 100 Taicry 2069313 QSNJ Conifers.p1 Manesc Manes.16G134900.2 100 Riccom 29848.m004463

97.3 Cryjap 2147613 GMHZ Conifers 2 samples combined.p1

98.7

Poptri Potri.018G008400.1 99.1 Cryjap 2113190 HOUF Conifers leaf.p1

99.1

87.5 100 97.5 92.9 100 Poptri Potri.006G272900.2 99.8 Glypen 2048228 OXGJ Conifers.p1

100

99.9 Taxdis 2065501 FHST Conifers.p1 Citsin orange1.1g042046m 99.3 100 98 100 Citcle Ciclev10007643m 100 98.8 100 100 Piluvi 2065221 ETCJ Conifers.p1

100 99.9 Pappap 2012701 OVIJ Conifers.p1 Spiole Sp 191250 sucp.t1 99.7 100 100 Disarc 2016450 GKCZ Conifers.p1 Chequi AUR62015976-RA 100 94.4 99.9 100 100 Calmac 2058684 RMMV Conifers March.p1 Betvul Bv3 055440Diacar Dca18750.1 cwjs.t1 100 93.2 Fokhod 2010043 UEVI Conifers.p1 94.7 100 Chalaw 2071595 AIGO Conifers.p1

Solpen Sopen12g032220.2 Thupli 2042194 VFYZ Conifers.p1

97.3 Solpen Sopen12g032220.1 94.6 Thudol 2013456 NKIN Conifers.p1

Sollyc Solyc12g096370.1.1Capann CA12g19140 Cupdup 2002813 QNGJ Conifers.p1 Tetsp. 2011348 CGDN Conifers.p1

Micdec 2058059 XQSG Conifers.p1

Plaori 2013071 BUWV Conifers.p1

Nicben Niben101Scf01721g08009.1 100 Ambtri evm 27.model.AmTr v1.0 scaffold00019.401

Zosmar Zosma169g00420.1 Nicben Niben101Scf05004g04016.1 Solpen Sopen08g022750.1 Petaxi Peaxi162Scf00459g00084.1 Zosmar Zosma19g00630.1 Sollyc Solyc08g069100.1.1Capann CA01g09840 Zosmar Zosma597g00030.1

Spipol Spipo5G0003600

Spipol Spipo12G0058700

Spipol Spipo28G0021900

Petaxi Peaxi162Scf00213g00071.1 99.5 Aposhe lcl KZ452013.1 PKA51377.1 15652

Aposhe lcl KZ451889.1 PKA65789.1 1447

93.8 100

99.9 Dencat lcl NW 021318618.1 XP 028547835.1 3087 100 97.4 Phaequ PEQU 30355

Musacu GSMUA Achr5T04880 001 Fraexc FRAEX38873 v2 000059630.1 100 Daucar DCAR 003072 Musacu GSMUA Achr3T05660 001 Fraexc FRAEX38873Helann HanXRQChr13g0412501 v2 000167670.1 Pyrcom PCP001153.1 Musacu GSMUA Achr4T02260 001 Helann HanXRQChr03g0082511 Anacom Aco021318.1

Orysat LOC Os06g48330.1

Horvul HORVU7Hr1G098020.1 Maldom MDP0000278159 Bradis Bradi1g33940.1

Pyrcom PCP005085.1 Setita Seita.4G244700.1

Sorbic Sobic.010G248100.1

Maldom MDP0000915255 Zeamay Zm00008a020463 Orysat LOC Os02g05620.1 Pruper Prupe.3G018000.1 Bradis Bradi3g03860.1

Horvul HORVU6Hr1G021690.1 Utrgib Utricularia gibba unitig 0 6620296 6622314 unitig 0.g2190.t1 1 CDS 875799521 11465 Pyrbre lcl NW 008988405.1 XP 009333976.1 31289 Prudul Prudul26A016989P1 Setita Seita.1G088800.1

Zeamay Zm00008a020941 Fraves FvH4 6g37240.1 Pyrbre lcl NW 008989276.1 XP 009349638.1 45470 Zeamay Zm00008a018781 Rubocc Bras G14344 Sorbic Sobic.004G041100.1 Utrgib Utricularia gibba unitig 747 2187014 2189026 unitig 747.g21905.t1 -1 CDS 875840765 22250 Nelnuc NNU 19865-RA

Pruavi Pav sc0000293.1 g230.1.mk Betvul Bv7 177700 dygi.t1 Drydru Drydr490S04613 Spiole Sp 034570 jrza.t1

Roschi RchiOBHm Chr2g0150001 Chequi AUR62025638-RA Chequi AUR62001363-RA

Prumum lcl NC 024129.1 XP 008227936.1 12414 Daucar DCAR 006249 Helann HanXRQChr15g0497441

Fraexc FRAEX38873 v2 000154640.1

Petaxi Peaxi162Scf00213g00124.1

Mornot L484 004977 Nicben Niben101Scf27226g00001.1 Nicben Niben101Scf04195g00010.1

Capann CA12g14960 Distri Distr2035S30914 Solpen Sopen12g024240.1 Humlup HL.SW.v1.0.G005206.1 Sollyc Solyc12g055770.1.1

Citlan Cla015495 Manesc Manes.16G045500.1 Humlup HL.SW.v1.0.G014321.1 Treori lcl JXTC01000175.1 PON83649.1 20610 Riccom 29578.m000206 Poptri Potri.010G250500.1 Treori lcl JXTC01000175.1 PON83648.1 20609 Poptri Potri.008G008700.1 Cepfol Cfol v3 33994

Citsin orange1.1g005829m Parand lcl JXTB01000032.1 PON73693.1 5581 Cucmel MELO3C024293.2.1 Citcle Ciclev10025071m Lagsic Lsi02G028430.1 Gosrai Gorai.009G118500.1 Thecac Thecc1EG028038t1 Parand lcl JXTB01000032.1 PON73694.1 5582 Cucsat evm.model.Chr7.2157 Tarhas lcl NW 010966500.1 XP 010550815.1 25269 Eutsal Thhalv10012259m

Eutsal Thhalv10012056m

Braolecap Bol031587

Brarap Brara.E01623.1

ArathaAT1G51640.1

ArahalAraha.2389s0017.1

AralyrAL1G59550.t1

Boestr Bostr.26675s0034.1

Capgra Cagra.2346s0019.1

Caprub Carub.0001s4050.1

Querob Qrob P0736800.2

Casmol snap masked-scaffold02453-abinit-gene-0.12-mRNA-1

Jugreg g34817.t1

Alnglu Alngl68390S05602 Alnglu Cucmos CmoCh17G006210.1 Cucpep Cp4.1LG12g09610.1

Cucmax CmaCh17G006390.1 Zizjuj lcl NC 029688.1 XP 015894013.1 26258

Datglo Datgl534S10840 Begfuc Begfu1101S06986

Cajcaj Ccajan 00057

Vigung Vigun08g126500.1 Phavul Phvul.008G255500.1

Glymax Glyma.07G004000.1 Araipa Araip.L66A6 Aradur Aradu.X53KQ Glymax Glyma.08G222500.1 Lotjap Lj3g3v2043280.1

Lupang Lup020339.1

Cajcaj Ccajan 26245 Lupang Lup002518.1

Nissch Nissc1056S00144 Cercan Cerca5S04069

Medtru MtrunA17 Chr2g0300651

Medtru MtrunA17 Chr4g0002391 Casgla Casgl124S23950

Chafas Chafa2067S07876 Momcha lcl NW 019104489.1 XP 022148480.1 2273

Mimpud Mimpu3183S02923

Tripra Tp57577 TGAC v2 mRNA16254 Momcha lcl NW 019104489.1 XP 022148489.1 2274

Momcha lcl NW 019104489.1 XP 022148496.1 2272

Casaus Castanospermum12770-PA

Casaus Castanospermum23074-PA

Arahyp arahy.Tifrunner.gnm1.ann1.RFL709.1

Arahyp arahy.Tifrunner.gnm1.ann1.V20YGC.1

Tree scale: 0.1 Supplementary Figure 25: Maximum likelihood tree of FatM.

Arahyp arahy.Tifrunner.gnm1.ann1.C2SFPD.1

AraipaAraip.1PE3B

Arahyp arahy.Tifrunner.gnm1.ann1.BCJ5R8.1

Arahyp arahy.Tifrunner.gnm1.ann1.H8W5PF.2

Arahyp arahy.Tifrunner.gnm1.ann1.ZKU6BD.1

Arahyp arahy.Tifrunner.gnm1.ann1.I8ZEWE.1

Arahyp arahy.Tifrunner.gnm1.ann1.TA3H6N.1

AradurAradu.Q1LBD

AradurAradu.0EA4R

AraipaAraip.4509F

AradurAradu.Q57RH

AraipaAraip.RRH7G

Arahyp arahy.Tifrunner.gnm1.ann1.LCII34.2

Arahyp arahy.Tifrunner.gnm1.ann1.5L01PW.1

AraipaAraip.J6FGQ

Arahyp arahy.Tifrunner.gnm1.ann1.0VM2VP.1

Arahyp arahy.Tifrunner.gnm1.ann1.3BV5AA.2

AradurAradu.ZL5SD

AraipaAraip.MR3NT

Lupang Lup014150.1

Ginbil Gb 35712

Arahyp arahy.Tifrunner.gnm1.ann1.L4EP3N.1 Arahyp arahy.Tifrunner.gnm1.ann1.4E7QKU.1

Mictet 2073193 MHGD Conifers.p1

Vigang vigan.Vang09g03850.1

Tripra Tp57577 TGAC v2 mRNA27674

Vigrad Vradi02g13400.1 Trisub lcl DF973192.1 GAU19061.1 8119

Vigung Vigun09g062800.1

Phavul Phvul.009G200200.1

Glymax Glyma.06G211300.1

Medtru MtrunA17 Chr4g0062811

Araipa Araip.SBA9Y Aradur Aradu.ZG6C0 Glymax Glyma.04G151600.1 Vigung Vigun03g349800.1

Phavul Phvul.003G176200.1 Vigang vigan.Vang11g08220.1

Vigrad Vradi07g18220.1

Tripra Tp57577 TGAC v2 mRNA10706 Cicari Ca 21614.1

Ginbil Gb 30766

Trisub lcl DF974100.1 GAU45121.1 34179 Nissch Nissc792S30976

Neopan 2066534 JDQB Conifers.p1

Cajcaj Ccajan 35537

Glymax Glyma.17G120400.1 Arahyp arahy.Tifrunner.gnm1.ann1.L8EKIA.1 Glymax Glyma.05G012300.1

Gnemon 2015138 GTHK Gnetales.p1

Ephsin 2033694 VDAO Gnetales.p1 Arahyp arahy.Tifrunner.gnm1.ann1.KT8BMX.1 Brarap Brara.H02869.1 Micdec 2051547 XQSG Conifers.p1 Mimpud Mimpu2012S08207 Gnemon TnS000049721t01

Mimpud Mimpu3189S22103 Fokhod 2058710 UEVI Conifers.p1

Welmir 2062354 TOXE Gnetales.p1

Braolecap Bol041218

Braolecap Bol021081 Brarap Brara.F00531.1 Medtru MtrunA17 Chr2g0306391

AradurAradu.8Y7VD

Cryjap 2020253 GMHZ Conifers 2 samples combined.p1 Cajcaj Ccajan 01838 Cryjap 2007944 HOUF Conifers leaf.p1 Fraana FAN iscf00006042.1.g00001.1

Lotjap Lj0g3v0119999.1

Mimpud Mimpu3444S22544 Glypen 2010940 OXGJ Conifers.p1

Mimpud Mimpu27942S09200 Athcup 2057808 XIRK Conifers.p1 Lupang Lup018530.1

AraipaAraip.21S3V

Lupang Lup013308.1

Lupang Lup026282.1

Braolecap Bol006555Brarap Brara.I05304.1 Amearg 2146966 IAJW Conifers.p1

Cicari Ca 26404.1

Nissch Nissc5054S09340

Cunlan 2019119 ZQVF Conifers 2 samples combined.p1

Pyrbre lcl NW 008988236.1 XP 009371429.1 23227 Chafas Chafa4210S22587

Pyrbre lcl NW 008988278.1 XP 009374053.1 25627

Lupang Lup028944.1

Casaus Castanospermum09663-PA Eutsal Thhalv10007761m

Caprub Carub.0001s0787.1

Capgra Cagra.4395s0041.1 Fraana FAN iscf00265386.1.g00001.1 Maldom MDP0000298759

Maldom MDP0000294705

Casaus Castanospermum13976-PA Fraana FAN iscf00113535.1.g00001.1 Tarhas lcl NW 010964923.1 XP 010533200.1 9513 Fraana FAN iscf00161568.1.g00001.1 Aratha AT1G08510.1

Tarhas lcl NW 010964923.1 XP 010533201.1 9514 Arahal Araha.0425s0002.1 Maldom MDP0000951278Pyrcom PCP012452.1 Pyrcom PCP000563.1

Fraana FAN iscf00076100.1.g00001.1 Boestr Bostr.25219s0093.1 Tarhas lcl NW 010967707.1 XP 010557578.1 31511

Fraves FvH4 1g04250.1 Prumum lcl NC 024133.1 XP 016651836.1 26277

Prumum lcl NC 024133.1 XP 008242684.1 26279 Calgra 2141597 IFLI Conifers March.p1

Pintae PTA00056007

Aralyr AL1G18940.t1 Prumum lcl NC 024133.1 XP 008242683.1 26278

Disarc 2006730 GKCZ Conifers.p1

Pintae PTA00053986

Ginbil Gb 14789

Ginbil Gb 07469 Calgra 2142299 IFLI Conifers March.p1

Zizjuj lcl NW 015453530.1 XP 015902462.1 35272 Roschi RchiOBHm Chr2g0089811

Zizjuj lcl NC 029690.1 XP 024922332.1 30761 Ginbil 2002544 SGTW Ginkgoales.p1 Pappap 2012178 OVIJ Conifers.p1 Humlup HL.SW.v1.0.G040965.1

Treori lcl JXTC01000507.1 PON49102.1 31855 Auschi 2007347 YYPE Conifers.p1

Zizjuj lcl NC 029690.1 XP 015898199.1 30762 Pruavi Pav sc0002156.1 g180.1.mk Humlup HL.SW.v1.0.G045836.1 Potmic 4774 t Parand lcl JXTB01000034.1 PON73368.1 5872

Tetsp. 2006831 CGDN Conifers.p1

Prudul Prudul26A003172P1 Pruper Prupe.7G234600.1 Metgly 2061658 NRXL Conifers.p1

Ginbil Gb 22117

Mornot L484 025596

Cercan Cerca68S28466

Ginbil Gb 22110 Piluvi 2010355 ETCJ Conifers.p1 Plaori 2005570 BUWV Conifers.p1

Ginbil Gb 22116

Junsco 2008289 XMGP Conifers.p1

Rubocc Bras G07649 Auschi 2007346 YYPE Conifers.p1 Neopan 2004112 JDQB Conifers.p1

Ginbil Gb 11733 Distri Distr2S17677 Psemen PME00119499 Auschi 2007348 YYPE Conifers.p1

Plaori 2005571 BUWV Conifers.p1 Ginbil 2002545 SGTW Ginkgoales.p1 Disarc 2006583 GKCZ Conifers.p1 Thudol 2049731 NKIN Conifers.p1 Metgly 2009925 NRXL Conifers.p1 Micdec 2000419 XQSG Conifers.p1

Ginbil Gb 35711

Ginbil 2002543 SGTW Ginkgoales.p1 Thupli 2006962 VFYZ Conifers.p1 Fraana FAN iscf00079170.1.g00002.1 Drydru Drydr443S12164

Seqgig 2007707 QFAE Conifers Glaucum.p1

Pintae PTA00083195 Taxdis 2000941 FHST Conifers.p1 Cryjap 2019641 GMHZ Conifers 2 samples combined.p1

Cryjap 2011880 HOUF Conifers leaf.p1

Ginbil Gb 22115 Tsuhet 2057255 GAMH Conifers.p1 Cunlan 2011799 ZQVF Conifers 2 samples combined.p1

Picabi MA 10197220g0010 Metgly 2009828 NRXL Conifers.p1 Chalaw 2006775 AIGO Conifers.p1

Picabi MA 8456588g0010

Psemen PME00119500

Psemen PME00119498 Psewil 2054704 IOVS Conifers.p1

Ginbil Gb 35710

Pinpin PPI00061380 Ginbil Gb 21293 Pinpin PPI00011175

Gosrai Gorai.004G279300.1 Pinrad 2013263 DZQM Conifers.p1

Citcle Ciclev10008435m Cunlan 2009490 OUOI Conifers.p1 Citsin orange1.1g014795m Pinpin PPI00058040 Pinjef 2013856 MFTM Conifers.p1

Pinpon 2011741 JBND Conifers.p1 Gosrai Gorai.001G003300.1 Keteve 2014421 JUWL Conifers.p1

Picsit PSI00002044 Abilas 2058201 VSRH Conifers.p1 Keteve 2014420 JUWL Conifers.p1 Gosrai Gorai.010G068500.1 Pinpin PPI00071766 Notlon 2010149 AREG Conifers.p1

Psewil 2010237 IOVS Conifers.p1

Halbid 2005639 OWFC Conifers.p1

Psemen PME00012023 Picabi MA 191613g0010 Halbid 2005637 OWFC Conifers.p1

Taxdis 2061482 FHST Conifers.p1

Pseama 2014986 AQFM Conifers.p1 Pruand 2003366 EGLZ Conifers.p1 Gosrai Gorai.013G231200.1 Larspe 2054347 WVWN Conifers.p1 Pruand 2003365 EGLZ Conifers.p1 Lagfra 2012903 ZQWM Conifers.p1

Pinpar 2079320 IIOL Conifers.p1 Sunama 2094080 KLGF Conifers.p1

Cedlib 2015269 GGEA Conifers.p1

Pinpin PPI00076041 Pinpin PPI00064042 Pinsyl PSY00003113 Pinsyl PSY00002257 Begfuc Begfu3358S31609 Phyhyp 2005146 JRNA Conifers.p1 Pintae PTA00053751 Phyhyp 2005145 JRNA Conifers.p1 Utrgib Utricularia gibba unitig 46 2040871 2042322 unitig 46.g18394.t1 1 CDS 875822049 13047 Poptri Potri.T082100.2 Parust 2006644 JZVE Conifers.p1 Mancol 2002668 CDFR Conifers.p1 Lepsp. 2006014 BBDD Conifers.p1 Mancol 2002669 CDFR Conifers.p1 Piceng 2002694 AWQB Conifers.p1 Catagr 2000568 NPRL Conifers.p1

Piceng 2002693 AWQB Conifers.p1 Pinrad 2055130 DZQM Conifers.p1 Catagr 2000567 NPRL Conifers.p1 Lepsp. 2006013 BBDD Conifers.p1 Mancol 2002667 CDFR Conifers.p1 Utrgib Utricularia gibba unitig 37 1954312 1956137 unitig 37.g12648.t1 1 CDS 875819929 13330 Pinpon 2072780 JBND Conifers.p1

Pinjef 2008138 MFTM Conifers.p1

Mictet 2009847 MHGD Conifers.p1

Agarob 2014066 MIXZ Conifers.p1 Poptri Potri.018G072700.1 Ararul 2001752 XTZO Conifers.p1 Mictet 2009846 MHGD Conifers.p1 Agamac 2070448 ACWS Conifers.p1 Ararul 2001751 XTZO Conifers.p1

Wolnob 2058576 RSCE Conifers.p1

Poptri Potri.006G157200.2Poptri Potri.006G155800.1

Saxcon 2013319 QCGM Conifers.p1

Nagnag 2009305 UUJS Conifers.p1

Acmpan 2000042 HILW Conifers.p1 Retmin 2009464 VGSX Conifers.p1 Podcor 2007591 SCEB Conifers.p1 Utrgib Utricularia gibba unitig 746 136601 138266 unitig 746.g26582.t1 1 CDS 875838717 14011 Acmpan 2000041 HILW Conifers.p1

Sciver 2009071 YFZK Conifers.p1 Podrub 2006284 XLGK Conifers.p1

Daccom 2009885 FMWZ Conifers.p1 Podrub 2006285 XLGK Conifers.p1 Manesc Manes.S047300.2 Daccom 2009884 FMWZ Conifers.p1 Podrub 2006283 XLGK Conifers.p1 Manesc Manes.S047300.1 Manesc Manes.16G064400.1

Cucmel MELO3C025309.2.1 Begfuc Begfu1718S01535 Cucsat evm.model.Chr1.1925 Cucsat evm.model.Chr1.1925.1 Dacbal 2010632 IZGN Conifers.p1 Begfuc Begfu29361S10537 Dacbal 2010631 IZGN Conifers.p1 Momcha lcl NW 019104521.1 XP 022144975.1 15779 Faltax 2008819 ROWR Conifers.p1 Faltax 2002937 PLYX Conifers 2 samples combined.p1 Thecac Thecc1EG037945t1 Momcha lcl NW 019104521.1 XP 022144977.1 15781 Faltax 2059517 QHBI Conifers A.p1

Cucpep Cp4.1LG18g04540.1 Faltax 2002936 PLYX Conifers 2 samples combined.p1 Momcha lcl NW 019104521.1 XP 022144974.1 15778 Cucmos CmoCh10G006340.1 Staeri 2008874 KAWQ Cycadales.p1 Riccom 29848.m004677 Faltax 2008820 ROWR Conifers.p1 Momcha lcl NW 019104521.1 XP 022144976.1 15780 Faltax 2002938 PLYX Conifers 2 samples combined.p1

Cycmic 2004440 XZUY Cycadales.p1

Helann HanXRQChr10g0311341 Encbar 2011212 GNQG Cycadales.p1 Helann HanXRQChr10g0311311 Lagsic Lsi06G009060.1

Cucmax CmaCh10G005940.1 Begfuc Begfu1592S08346

Cycmic CMI00011127

Begfuc Begfu4878S12494 Ginbil 2039495 SGTW Ginkgoales.p1

Ginbil Gb 39975

Helann HanXRQChr10g0311351 Begfuc Begfu1592S08362 Cucpep Cp4.1LG04g09870.1

Citlan Cla012316 Begfuc Begfu11835S17189 Jugreg g17361.t1 Cucmax CmaCh11G005900.1 Alnglu Alngl849S36802

Cepfol Cfol v3 35435

Casmol maker-scaffold02723-augustus-gene-0.15-mRNA-1 Ginbil Gb 17546 Begfuc Begfu2889S10495

Begfuc Begfu1533S08147

Jugreg g27440.t1

Petaxi Peaxi162Scf00199g00111.1 Utrgib Utricularia gibba unitig 748 502573 504232 unitig 748.g7153.t1 -1 CDS 875841411 4327 Cucmos CmoCh11G005920.1 Petaxi Peaxi162Scf00199g00018.1 Casgla Casgl8S26038

Querob Qrob P0475380.2

Helann HanXRQChr10g0311301 Cucpep Cp4.1LG07g09930.1

Petaxi Peaxi162Scf00361g00312.1

Cucpep Cp4.1LG11g11030.1

Helann HanXRQChr10g0311291

Nicben Niben101Scf08341g04007.1 Cucsat evm.model.Chr2.135 Cucsat evm.model.Chr2.135.2 Nicben Niben101Scf01586g00004.1 Cucmel MELO3C004540.2.1Cucsat evm.model.Chr2.135.1

Pyrcom PCP005950.1 Petaxi Peaxi162Scf00546g00419.1 Lagsic Lsi11G002820.1

Momcha lcl NW 019104649.1 XP 022156309.1 25950 Cucmos CmoCh05G013360.1 Capann CA09g15720Sollyc Solyc12g006930.1.1 Solpen Sopen12g002890.1 Datglo Datgl297S27508

Cucmax CmaCh05G013240.1 Cephar 2009765 NVGZ Conifers 2 samples combined.p1

Cephar 2009764 NVGZ Conifers 2 samples combined.p1 Datglo Datgl310S07970 Cucmax CmaCh08G006280.1 Cephar 2017398 WYAJ Conifers.p1

Cephar 2009766 NVGZ Conifers 2 samples combined.p1 Fraves FvH4 6g30870.1 Cucmos CmoCh12G012620.1 Lagsic Lsi11G002810.1 Tortax 2011977 EFMS Conifers.p1 Cephar 2061866 GJTI Conifers.p1 Amearg 2151213 IAJW Conifers.p1 Citlan Cla016747 Tornuc 2016472 HQOM Conifers.p1 Cucmax CmaCh12G012340.1 Taxbac 2007285 WWSS Conifers.p1 Cucpep Cp4.1LG17g08850.1 Potmic 16008 t Taxcus 2003610 ZYAX Conifers.p1

Taxcus 2003609 ZYAX Conifers.p1

Cucmos CmoCh08G006130.1 Helann HanXRQChr05g0138201

Psechi 2011356 YLPM Conifers.p1 Helann HanXRQChr03g0062101 Momcha lcl NW 019104860.1 XP 022158833.1 28166 Ausspi 2006384 BTTS Conifers.p1

Psechi 2011357 YLPM Conifers.p1

Ausspi 2006383 BTTS Conifers.p1

Taicry 2008621 QSNJ Conifers.p1 Rubocc Bras G21724 Cunlan 2007490 ESYX Conifers branch apex with needles.p1 Taicry 2008620 QSNJAthcup Conifers.p1 2009758 XIRK Conifers.p1

Metgly 2064931 NRXL Conifers.p1 Seqgig 2062396 QFAE Conifers Glaucum.p1 Rubocc Bras G21726 Helann HanXRQChr09g0240511 Fraexc FRAEX38873 v2 000019430.1 Cunlan 2101838 ZQVF Conifers 2 samples combined.p1

Fraexc FRAEX38873 v2 000019430.2 Cunlan 2053077 OUOI Conifers.p1 Glypen 2003982 OXGJ Conifers.p1 Daucar DCAR 018326 Glypen 2003981 OXGJ Conifers.p1 Cucsat evm.model.Chr7.2074 Taxdis 2004678 FHST Conifers.p1

Taxdis 2004676 FHST Conifers.p1 Helann HanXRQChr06g0180041 Taxdis 2004679 FHST Conifers.p1

Taxdis 2004677 FHST Conifers.p1

Cryjap 2006627 HOUF Conifers leaf.p1 Fraexc FRAEX38873 v2 000295410.1 Cryjap 2011201 GMHZ Conifers 2 samples combined.p1

Cryjap 2009965 DSXO Conifers.p1 Cucsat evm.model.Chr7.2075 Cryjap 2011199 GMHZ Conifers 2 samples combined.p1

Cryjap 2009964 DSXO Conifers.p1 Citlan Cla015415 Cryjap 2011200 GMHZ Conifers 2 samples combined.p1

Cryjap 2006628 HOUF Conifers leaf.p1 Cupdup 2075176 QNGJ Conifers.p1

Cryjap 2006626 HOUF Conifers leaf.p1 Junsco 2008272 XMGP Conifers.p1 Chalaw 2002804 AIGO Conifers.p1 Fokhod 2001112 UEVI Conifers.p1 Tetsp. 2009152 CGDN Conifers.p1 Thudol 2051704Thupli NKIN 2003113 Conifers.p1 VFYZ Conifers.p1 Caldec 2061548 FRPM Conifers.p1

Micdec 2057484 XQSG Conifers.p1

Daucar DCAR 028741 Piluvi 2010736 ETCJ Conifers.p1

Momcha lcl NW 019104510.1 XP 022142884.1 13816 Prudul Prudul26A004485P1 Plaori 2054554 BUWV Conifers.p1 Piluvi 2010735 ETCJ Conifers.p1 Prudul Prudul26A008636P1

Drydru Drydr70S23989 Pruper Prupe.3G074700.1

Diacar Dca55992.1 Auschi 2009243 YYPE Conifers.p1 Pruavi Pav sc0000716.1 g170.1.mk Drydru Drydr338S10695 Auschi 2009242 YYPE Conifers.p1 Calgra 2145348 IFLI Conifers March.p1 Widced 2061912 AUDE Conifers.p1 Diacar Dca40104.1 Pappap 2011836 OVIJ Conifers.p1 Calmac 2059291 RMMV Conifers March.p1 Diacar Dca15431.1Diacar Dca56981.1

Neopan 2005511 JDQB Conifers.p1 Pruper Prupe.3G074600.1 Daucar DCAR 010439 Disarc 2013265 GKCZ Conifers.p1 Diacar Dca61033.1 Neopan 2005510 JDQB Conifers.p1

Daucar DCAR 012090

Chequi AUR62033409-RA Zizjuj lcl NC 029679.1 XP 024927141.1 4075 Distri Distr63S26526 Alnglu Alngl48384S04666

Chequi AUR62011036-RA

Spiole Sp 034010 dyjj.t1

Diacar Dca34259.1

Diacar Dca59835.1 Casmol maker-scaffold01207-augustus-gene-0.37-mRNA-1 Alnglu Alngl18533S18787 Casmol maker-scaffold01207-augustus-gene-0.37-mRNA-2

Jugreg g45103.t1Casgla Casgl31S15265 Betvul Bv8 195640 njig.t1

Chequi AUR62009817-RA Spiole Sp 047730 jjfa.t1 Querob Qrob P0629360.2 Zizjuj lcl NC 029679.1 XP 015869294.1 4072 Chequi AUR62038129-RA

Betvul Bv7 176720 zsid.t1 Zizjuj lcl NC 029679.1 XP 024929110.1 4073 Alnglu Alngl242S21523

Humlup HL.SW.v1.0.G035302.1

Datglo Datgl178S04160 Zizjuj lcl NC 029679.1 XP 015869379.1 4071

Humlup HL.SW.v1.0.G035301.1 Distri Distr63S26514

Selmoe 13356

Datglo Datgl1163S18999

Manesc Manes.14G147400.1

Manesc Manes.11G051700.1

Manesc Manes.11G051800.1

Gosrai Gorai.009G132400.1 Riccom 29841.m002744 Thecac Thecc1EG028605t1

Manesc Manes.11G051500.1 Datglo Datgl1163S19000

Poptri Potri.001G177900.2 Poptri Potri.001G177600.1

Bradis Bradi4g03210.1

Setita Seita.9G277100.1

Zeamay Zm00008a038810

Horvul HORVU2Hr1G120140.2

Zeamay Zm00008a038812 Bradis Bradi2g13720.1

Setita Seita.5G175400.1

Zeamay Zm00008a024809 Setita Seita.9G276700.1 Sorbic Sobic.006G259300.1 Selkra 2000459 ZFGK Lycophytes.p1 Orysat LOC Os01g31760.1

Setita Seita.4G226300.1 Zeamay Zm00008a034549

Orysat LOC Os06g39520.2Horvul HORVU7Hr1G084830.1 Sorbic Sobic.010G180400.1

Bradis Bradi1g36950.1 Sorbic Sobic.004G088100.1

Selsel 2005267 KUXM Lycophytes.p1

Musacu GSMUA Achr3T29060 001

Selwil 2003611 KJYC Lycophytes.p1

Selapo 2003844 LGDQ Lycophytes.p1

Selaca 2005078 ZYCD Lycophytes.p1 Sellep 2011008 ABIJ Lycophytes.p1

Selwal 2181108 JKAA Lycophytes.p1

Selsta 2004143 ZZOL Lycophytes.p1

Selkra 2009063 ZFGK Lycophytes.p1 Selmoe 24354 Anacom Aco023937.1

Bradis Bradi1g51170.1

Horvul HORVU7Hr1G019830.1

Setita Seita.4G031400.1 Orysat LOC Os06g05130.1

Sorbic Sobic.010G033300.1

Cepfol Cfol v3 35500

Anacom Aco014328.1

Cepfol Cfol v3 31266 Ambtri evm 27.model.AmTr v1.0 scaffold00006.68 Nelnuc NNU 26267-RA

Orysat LOC Os02g43090.1 Carpap evm.model.supercontig 65.88

Orysat LOC Os11g43820.1

Cucmos CmoCh04G021870.1 Cucmos CmoCh04G021880.1

Helann HanXRQChr01g0013271 Gosrai Gorai.008G157700.1

Riccom 29660.m000782 Citcle Ciclev10015449m Manesc Manes.06G063300.1 Cucmos CmoCh15G009770.1 Dencat lcl NW 021319385.1 XP 028553242.1 17586 Humlup HL.SW.v1.0.G017458.1 Citsin orange1.1g015302m Gosrai Gorai.005G194200.1 Manesc Manes.14G109400.1 Dencat lcl NW 021319779.1 XP 020694462.2 24137 Begfuc Begfu2310S09683

Lagsic Lsi09G006360.1

Begfuc Begfu1341S18398 Casgla Casgl825S26092 Dencat lcl NW 021319682.1 XP 028554965.1 22913 Cucmax CmaCh04G020860.1

Poptri Potri.008G126200.1 Thecac Thecc1EG009021t1 Momcha lcl NW 019104575.1 XP 022152342.1 22362 Cucmax CmaCh15G009370.1 Cucsat evm.model.Chr5.1947 Poptri Potri.010G117400.1 Anacom Aco009798.1

Dencat lcl NW 021319944.1 XP 020699689.1 26539 Citlan Cla003904 Cucmel MELO3C005331.2.1 Phaequ PEQU 26731 Querob Qrob P0504620.2 Ginbil Gb 17544

Datglo Datgl406S30044 Aposhe lcl KZ453894.1 PKA46788.1 20471 Casmol maker-scaffold02823-snap-gene-0.33-mRNA-1Alnglu Alngl18766S01622

Dencat lcl NW 021319483.1 XP 020691792.1 19062 Jugreg g47889.t1 Jugreg g27068.t1 Phaequ PEQU 11349

Aposhe lcl KZ451908.1 PKA63436.1 3748

Spipol Spipo27G0017100 Musacu GSMUA Achr5T24910Musacu GSMUA 001 Achr6T00720 001

Zosmar Zosma178g00130.1 Musacu GSMUA Achr2T16970 001 Humlup HL.SW.v1.0.G017459.1

Humlup HL.SW.v1.0.G036301.1 Zizjuj lcl NC 029688.1 XP 015895576.1 27943 Maldom MDP0000819112 Distri Distr530S32154

Pyrcom PCP009771.1 Pyrbre lcl NW 008988040.1 XP 009357447.1 1162

Mornot L484 025851 Musacu GSMUA Achr9T28630 001 Potmic 3372 t Pruavi Pav sc0001181.1 g510.1.mk Helann HanXRQChr17g0553141

Parand lcl JXTB01000032.1 PON73737.1 5625 Zosmar Zosma1g01370.1 Maldom MDP0000172275 Prumum lcl NW 007362496.1 XP 008243434.1 26929 Treori lcl JXTC01000754.1 PON38388.1 34527 Prudul Prudul26A018872P1 Pyrbre lcl NW 008988084.1 XP 009356195.1 9298 Pyrcom PCP038934.1 Pruper Prupe.1G319800.1 Pyrcom PCP005439.1

Daucar DCAR 007275 Drydru Drydr94S24727 Daucar DCARDaucar 026759 DCAR 023624

Fraana FAN iscf00332986.1.g00001.1

Poptri Potri.012G051400.1 Ambtri evm 27.model.AmTr v1.0 scaffold00142.75 Roschi RchiOBHm Chr4g0434051 Potmic 3365 t Thecac Thecc1EG012529t1 Spipol Spipo21G0008900 Rubocc Bras G02762 Fraana FAN iscf00047417.1.g00001.1

Fraves FvH4 4g26420.1 Fraves FvH4 Fraana4g26490.1 FAN iscf00374138.1.g00001.1

Fraana FANFraana iscf00072896.1.g00001.1 FAN iscf00078601.1.g00001.1 Zizjuj lcl NC 029683.1 XP 015882941.2 14747 Distri Distr238S19355

Fraana FAN icon20457385.1.g00001.1

Nicben Niben101Scf01460g02004.1 Capann CA11g00150 Nicben Niben101Scf04024g01005.1 Sollyc Solyc05g008570.1.1 Solpen Sopen05g004410.1

Petaxi Peaxi162Scf00205g01124.1

Fraexc FRAEX38873 v2 000097460.1

Chafas Chafa2653S02065

Mimpud Mimpu5657S25710

Chafas Chafa4100S22404

Cercan Cerca314S21306 Aradur Aradu.B3QR0

Arahyp arahy.Tifrunner.gnm1.ann1.75YJ3Z.1 Trisub lcl DF973341.1 GAU26776.1 15834 Cercan Cerca295S20502

Araipa Araip.S1TFK Nissch Nissc3271S02093 Casaus Castanospermum11068-PA Arahyp arahy.Tifrunner.gnm1.ann1.SJ2WML.1 Trisub lcl DF974136.1 GAU45623.1 34681

Cajcaj Ccajan 07595

Cicari Ca 10681.1

Glymax Glyma.20G122900.1Phavul Phvul.007G034100.1 Cicari Ca 10617.1 Vigung Vigun09g104200.1 Glymax Glyma.10G268200.1 Vigang vigan.Vang0173s00220.1 Casaus Castanospermum12457-PA Vigung Vigun07g263500.1 Vigang vigan.Vang06g01430.1

Vigrad Vradi08g20850.1Lotjap Lj5g3v2169500.1 Phavul Phvul.009G164800.2 Tripra Tp57577 TGAC v2 TrisubmRNA32779 lcl DF973287.1 GAU24348.1 13406 Ambtri evm 27.model.AmTr v1.0 scaffold00142.76

Medtru MtrunA17 Chr1g0208941 Tripra Tp57577 TGAC v2 mRNA5041

Glymax Glyma.04G197400.1 Tripra Tp57577 TGAC v2 mRNA22709

Cicari Ca 14809.1

Glymax Glyma.06G168100.1

Cajcaj Ccajan 08454

Ambtri evm 27.model.AmTr v1.0 scaffold00016.2 Medtru MtrunA17 Chr3g0132041

Lotjap Lj1g3v1498440.1

Arahyp arahy.Tifrunner.gnm1.ann1.0R09FV.1 Araipa Araip.3B5IK Arahyp arahy.Tifrunner.gnm1.ann1.R2IV6A.1

Lotjap Lj1g3v1498440.2

Aradur Aradu.D1B7C

Lupang Lup008278.1 Lupang Lup000188.1

Vigang vigan.Vang0173s00230.1

Vigrad Vradi05g05400.1

Nissch Nissc8731S31829 Vigung Vigun09g104100.1

Phavul Phvul.009G164200.1

Cajcaj Ccajan 28623 Glymax Glyma.06G168000.1 Cajcaj Ccajan 45758

Glymax Glyma.04G197500.1

Nissch Nissc8731S31832

Lupang Lup008279.1

Chafas Chafa6597S25573 Casaus Castanospermum04025-PA

Casaus Castanospermum29115-PA

Lagsic Lsi02G005160.1 Cercan Cerca4S25746

Citlan Cla002633

Cucsat evm.model.Chr1.951

Cucmel MELO3C002373.2.1 Cucmos CmoCh13G008490.1

Cucpep Cp4.1LG20g02890.1

Begfuc Begfu1163S16871 Cucmax CmaCh13G008190.1

Begfuc Begfu2204S25339

Datglo Datgl562S32360

Pyrbre lcl NW 008988297.1 XP 009375182.2 26669

Pyrbre lcl NW 008988796.1 XP 009344285.2 40613

Pyrcom PCP042064.1 Maldom MDP0000312412

Pyrcom PCP012389.1 Pyrbre lcl NW 008988108.1 XP 009359401.2 12275

Maldom MDP0000229149

Prumum lcl NC 024132.1 XP 016651155.1 23348

Prumum lcl NC 024132.1 XP 008239504.1 23347

Metcra 2008447 NRWZ Liverworts.p1 Prudul Prudul26A002407P1

Pruper Prupe.5G148400.1

Pruavi Pav sc0000740.1 g220.1.mk Pelepi 2092299 PIUF Liverworts.p1 Pelnee 2009687 JHFI Liverworts.p1 Pelnee 2009686 JHFI Liverworts.p1

Drydru Drydr405S21579 Fraana FAN iscf00254464.1.g00001.1

Fraana FAN iscf00110507.1.g00001.1 Schisp. 2013866 LGOW Liverworts.p1 Mixspe 2007921 NWQC Liverworts.p1 Pornav 2009924 KRUQ Liverworts.p1 Ptipul 2136807 HPXA Liverworts.p1 Fraves FvH4 5g08660.1 Odopro 2129264 YBQN Liverworts.p1 Porpin 2016476 UUHD Liverworts.p1 Baztri 2090737 WZYK Liverworts.p1 Fraana FAN iscf00131306.1.g00001.1 Porpin 2016475 UUHD Liverworts.p1 Scanem 2007321 IRBN Liverworts.p1 Fraana FAN iscf00002140.1.g00001.1

Potmic 20628 t

Roschi RchiOBHm Chr7g0189721

Parand lcl JXTB01000014.1 PON77247.1 2866 BlaspNW c315982 g1 i6 m.42926 BlaspNW c315982 g1 i5 m.42923

Rubocc Bras G01898 BlaspNW c315982 g1 i3 m.42918 BlaspNW c315982 g1 i2 m.42915 Humlup HL.SW.v1.0.G037692.1 BlaspNW c315982 g1 i1 m.42912 BlaspNW c315982 g1 i4 m.42920

Parand lcl JXTB01000014.1 PON77246.1 2865

Treori lcl JXTC01000043.1 PON95736.1 8566 Luncru 2005855 TXVB Liverworts.p1

Luncru 2005854 TXVB Liverworts.p1 Zizjuj lcl NC 029683.1 XP 015882517.2 14294 Mornot L484 010129

Zizjuj lcl NC 029683.1 XP 015882177.1 13909 Mongot 2116813 TFDQRicnat Liverworts.p1 2003542 WJLO Liverworts.p1

Distri Distr46S09056

Concon 2002999 ILBQ Liverworts.p1

Concon 2002998 ILBQ Liverworts.p1

Alnglu Alngl1583S17303 Casgla Casgl20S11120 Marpol 2009878 JPYU Liverworts.p1

Marema 2075242 TFYI Liverworts.p1 Marpol Mapoly0023s0056.1

Jugreg g14850.t1

Marpal 2010269 LFVP Liverworts 2 samples combined.p1 Querob Qrob P0275140.2 Casmol augustus masked-scaffold03121-abinit-gene-0.10-mRNA-1 Marpal 2007372 IHWO Liverworts mycorrizal.p1

Marpal 2054140 HMHL Liverworts non mycorrizal.p1

Marpal 2007371 IHWO Liverworts mycorrizal.p1

Marpal 2010270 LFVP Liverworts 2 samples combined.p1

Citcle Ciclev10033687m Marpal scaff16002 FGenesh3.1

Citsin orange1.1g019296m Thecac Thecc1EG014679t1

Manesc Manes.14G049100.1 Cepfol Cfol v3 25698 Selwil 2009505 KJYC Lycophytes.p1 Selapo 2000354 LGDQ Lycophytes.p3

Riccom 30147.m014468 Isoteg 2099017 PKOX Lycophytes.p1

Poptri Potri.015G099600.1 Isoesp. 2074235 PYHZ Lycophytes.p1

Trelac 2011727 FITN Liverworts.p1 Sellep 2000604 ABIJ Lycophytes.p1Sellep 2000605 ABIJ Lycophytes.p1 Poptri Potri.012G101500.1 Selmoe 406992 Selmoe 15558

Selsta 2003613 ZZOL Lycophytes.p3

Solpen Sopen03g028150.1

Sollyc Solyc03g097390.2.1

Capann CA03g22070

Petaxi Peaxi162Scf00516g00330.1

Nicben Niben101Scf12983g00003.1

Nicben Niben101Scf10950g00010.1

Taklep 2007321 SKQD Mosses.p1

Fraexc FRAEX38873 v2 000337300.1

Fraexc FRAEX38873 v2 000055120.1 Sphfal Sphfalx0065s0133.1 Fraexc FRAEX38873 v2 000114570.1 Sphfal Sphfalx0012s0004.1

Sphfal Sphfalx0106s0001.1Sphfal Sphfalx0242s0007.1 Chequi AUR62038840-RA Sphrec 2022248 UHLI Mosses.p1 Sphfal Sphfalx0016s0039.1

Sphfal Sphfalx0000s0721.1 Chequi AUR62029569-RA Sphfal Sphfalx0092s0063.1 Sphfal Sphfalx0043s0062.1Sphfal Sphfalx0319s0005.1

Sphfal Sphfalx0000s0237.1 Spiole Sp 082660 aore.t1 Sphfal Sphfalx0292s0004.1

Sphpal 2017155 RCBT Mosses.p1 Betvul Bv5 126440 pjpn.t1 Sphpal 2017154 RCBT Mosses.p1 Sphpal 2019997 RCBT Mosses.p1 Sphfal Sphfalx0662s0001.1

Sphrec 2004498 UHLI Mosses.p1 Daucar DCAR 016376 Sphfal Sphfalx0068s0112.1 Sphfal Sphfalx0114s0044.1 Sphfal Sphfalx0060s0054.1 Sphfal Sphfalx0407s0001.1 Sphfal Sphfalx0241s0024.1 Sphfal Sphfalx0027s0099.1 Sphfal Sphfalx0603s0001.1 Sphfal Sphfalx0326s0001.1 Sphfal Sphfalx0115s0041.1

Carpap evm.model.supercontig 4.167 Sphfal Sphfalx0105s0063.1 Sphfal Sphfalx0012s0226.1

Sphfal Sphfalx0260s0001.1

Musacu GSMUA Achr7T23000 001 Zeamay Zm00008a008465

Sorbic Sobic.002G111500.1

Setita Seita.2G108900.1

Spipol Spipo0G0147200

Anacom Aco025496.1

Anacom Aco006658.1

Phaequ PEQU 02427

Dencat lcl NW 021319195.1 XP 020686336.2 14376

Aposhe lcl KZ451 906.1 PK A6380 3.1 3119

Dipfol 2013645 AWOI Mosses.p1

Andrup 2095128 WOGB Mosses.p1

Tetpel 2009973 HVBQ Mosses.p1

Tetpel 2009974 HVBQ Mosses.p1

Atrang 2084689 ZTHV Mosses.p1

Polcom 2001597 SZYG Mosses gametophyte.p1

Buxaph 2016501 HRWG Mosses.p1

Dipfol 2007076 AWOI Mosses.p1

Dipfol 2007077 AWOI Mosses.p1

Timaus 2003497 ZQRI Mosses.p1 Racvar 2119185 RDOO Mosses.p1

Racelo 2075784 ABCD Mosses.p1 Dicsco 2101312 NGTD Mosses.p1 Synpri 2019185 GRKU Mosses.p1

Cerpur 2013829 FFPD Mosses.p1

Leugla 2059701 RGKI Mosses.p1

Leualb 2129979 VMXJ Mosses.p1

Leugla 2009001 RGKI Mosses.p1 Phypat Pp3c19 20600V3.1

Phypat Pp3c22 11160V3.1

Physsp. 2016639 YEPO Mosses.p1

Phypat Pp3c21 15300V3.1

Physsp. 2000812 YEPO Mosses.p1

Phypat Pp3c18 15010V3.1

Scoaqu 2090372 BPSG Mosses.p1 Dicsco 2095909 NGTD Mosses.p1

Racvar 2019729 RDOO Mosses.p1

Racelo 2075734 ABCD Mosses.p1

Phifon 2057974 ORKS Mosses.p1

Plains 2077849 BGXB Mosses.p1

Aulhet 2089621 WNGH Mosses.p1 Ortlye 2009905 CMEQ Mosses.p1

Ortlye 2009904 CMEQ Mosses.p1 Hedcil 2012800 YWNF Mosses.p1

Bryarg 2042714 JMXW Mosses.p1

Roscap 2010452 XWHK Mosses.p1

Pseele 2008330 QKQO Mosses.p1

Pseele 2008329 QKQO Mosses.p1

Fonant 2008676 DHWX Mosses.p1

Leujul 2167283 IGUH Mosses.p1

Leubra 2099767 ZACW Mosses.p1

Necdou 2016023 TMAJ Mosses.p1

Anoatt 2061231 QMWB Mosses.p1

Loebre 2046872 WSPM Mosses.p1

Cliden 2085561 MIRS Mosses.p1

Stesub 2069462 LNSF Mosses.p1 FatM Thudel 2008737 EEMJ M osses.p1 Rhyser 2000876 JADL Mosses.p1

Anocla 2053553 VBMM Mosses.p1

Calcor 2015699 TAVP Mosses.p1

Luncru 2008494 TXVB Liverworts.p1

Luncru 2008493 TXVB Liverworts.p1

Sphtex 2045081 HERT Liverworts.p1

Ricnat 2037902 WJLO Liverworts.p1

Concon 2006034 ILBQ Liverworts.p1

Concon 2006035 ILBQ Liverworts.p1

Marema 2075147 TFYI Liverworts.p1

Marpol Mapoly0168s0018.1

Marpal scaff9402 FGenesh5.1

Marpal 2010262 IHWO Liverworts mycorrizal.p1

Marpal 2013755 LFVP Liverworts 2 samples combined.p1

Marpal 2009479 HMHL Liverworts non mycorrizal.p1

BlaspNW c328153 g1 i6 m.78388 BlaspNW c328153 g1 i3 m.78380

BlaspNW c328153 g1 i1 m.78372

BlaspNW c328153 g1 i5 m.78385

BlaspNW c328153 g1 i2 m.78376

Metcra 2014793 NRWZ Liverworts.p1

Calfis 2018525 RTMU Liverworts.p1

Scanem 2165580 IRBN Liverworts.p1

Barbar 2130757 OFTV Liverworts.p1

Mixspe 2160203 NWQC Liverworts.p1

Baztri 2091320 WZYK Liverworts.p1 Fruspp 2020176 CHJJ Liverworts.p1

Radlin 2087219 BNCU Liverworts.p1

Schisp. 2011998 LGOW Liverworts.p1

Ptipul 2018799 HPXA Liverworts.p1

Pornav 2019022 KRUQ Liverworts.p1 Pelnee 2113733 JHFI Liverworts.p1 Pelepi 2016543 PIUF Liverworts.p1

Pallye 2004402 YFGP Liverworts.p1

Taklep 2010999 SKQD Mosses.p1

Taklep 2010998 SKQD Mosses.p1

Sphles 2009044 GOWD Mosses.p1

Sphfal Sphfalx0075s0070.1 Sphrec 2002319 UHLI Mosses.p1

Sphles 2009043 GOWD Mosses.p1

Sphfal Sphfalx0065s0134.1

Andrup 2095023 WOGB Mosses.p1

Atrang 2016598 ZTHV Mosses.p1

Polcom 2006569 SZYG Mosses gametophyte.p1

Tetpel 2009975 HVBQ Mosses.p1

Dipfol 2073350 AWOI Mosses.p1

Phypat Pp3c25 6570V3.1

Timaus 2010073 ZQRI Mosses.p1 Physsp. 2010657 YEPO Mosses.p1

Physsp. 2010658 YEPO Mosses.p1

Encstr 2010761 KEFD Mosses.p1 Physsp. 2005779 YEPO Mosses.p1 Phypat Pp3c6 5010V3.1 Timaus 2018026 ZQRI Mosses.p1

Leualb 2131344 VMXJ Mosses.p1

Cerpur 2012432 FFPD Mosses.p1

Racvar 2117605 RDOO Mosses.p1

Aulhet 2006109 WNGH Mosses.p1Phifon 2059220 ORKS Mosses.p1

Leualb 2003252 VMXJ Mosses.p1

Scoaqu 2022591 BPSG Mosses.p1 Ortlye 2012424 CMEQ Mosses.p1

Hedcil 2009214 YWNF Mosses.p1

Dicsco 2098068 NGTD Mosses.p1

Hedcil 2004257 YWNF Mosses.p1

Hedcil 2004256 YWNF Mosses.p1

Phifon 2006577 ORKS Mosses.p1

Aulhet 2088566 WNGH Mosses.p1

Roscap 2010513 XWHK Mosses.p1

Bryarg 2003340 JMXW Mosses.p1 Pseele 2009061 QKQO Mosses.p1 Fonant 2073697 DHWX Mosses.p1 Calcor 2014896 TAVP Mosses.p1

Anoatt 2059270 QMWBNecdou Mosses.p1 2181754 TMAJ Mosses.p1

Anocla 2053105 VBMM Mosses.p1

Leubra 2001547 ZACW Mosses.p1

Leubra 2001546 ZACW Mosses.p1 Rhyser 2010396 JADL Mosses.p1

Loebre 2006821 WSPM Mosses.p1

Stesub 2069763 LNSF Mosses.p1

Thudel 2007546 EEMJ Mosses.p1

Phacar 2003665 RXRQ Hornworts sporophyte.p1

Megfla 2008843 UCRN Hornworts.p2

Parhal 2056902 FAJB Hornworts.p1

Phacar 2012147 RXRQ Hornworts sporophyte.p1

Phacar 2012148 RXRQ Hornworts sporophyte.p1

Phacar 2001543 WCZB Hornworts gametophyte.p1

Phacar 2001542 WCZB Hornworts gametophyte.p1

Hupluc 2098417 GKAG Lycophytes.p1

Hupsel 2030336 YHZW Lycophytes 2 samplesHupmyr combined.p1 2014733 CBAE Lycophytes.p1

Hupsel 2023302 GTUO Lycophytes.p1 Phydru 2008658 ZZEI Lycophytes.p1

Lycann 2013753 ENQF Lycophytes.p1

Dipdig 2015434 WAFT Lycophytes.p1

Lycdeu 2081908 PQTO Lycophytes.p1

Lycann 2003724 ENQF Lycophytes.p1

Psecar 2019629 UPMJ Lycophytes.p1

Lycapp 2001087 ULKT Lycophytes.p1 Lycapp 2001945 ULKT Lycophytes.p1 Lycapp 2001088 ULKT Lycophytes.p1

Psecar 2001150 UPMJ Lycophytes.p1

Psecar 2001149 UPMJ Lycophytes.p1

Isoteg 2099127 PKOX Lycophytes.p1

Isoesp. 2075025 PYHZ Lycophytes.p1

Trelac 2091254 FITN Liverworts.p1

Osmjav 2077410 VIBO Leptosporangiate Monilophytes.p1

Sellep 2010924 ABIJ Lycophytes.p1 Selkra 2041492 ZFGK Lycophytes.p1 Osmsp. 2075527 UOMY Leptosporangiate Monilophytes gametophyte.p1 Selwil 2008234 KJYC Lycophytes.p1 Selwal 2015290 JKAA Lycophytes.p1 Selsta 2010222 ZZOL Lycophytes.p1 Phydru 2125030 ZZEI Lycophytes.p1 Selmoe 103466

Lycann 2083747 ENQF Lycophytes.p1

Selapo 2012042 LGDQ Lycophytes.p1

Psecar 2009153 UPMJ Lycophytes.p1

Pyrcom PCP000789.1 Pyrbre lcl NW 008988045.1 XP 009371919.1 2478 Maldom MDP0000912251 Maldom MDP0000943090

Pyrcom PCP012645.1 Pyrbre lcl NW 008988387.1 XP 009379360.1 30532 Maldom MDP0000200228 Dipcon 2001119 MEKP Leptosporangiate Monilophytes.p1 Prudul Prudul26A000605P1 Pruper Prupe.8G199400.1 Prumum lcl NC 024131.1 XP 008235447.1 19519

Drydru Drydr380S11284 Pruavi Pav sc0000558.1 g890.1.mk Lycapp 2018540 ULKT Lycophytes.p1

Fraana FAN iscf00146261.1.g00001.1 Fraves FvH4 2g18600.1 Potmic 25058 t Roschi RchiOBHm Chr6g0284171 Rubocc Bras G22523

Parand lcl JXTB01000586.1 PON36042.1 33146 Treori lcl JXTC01000376.1 PON59383.1 28871 Mornot L484 007018 Humlup HL.SW.v1.0.G023672.1

Distri Distr226S06890

Zizjuj lcl NC 029687.1 XP 015892448.1 24449

Thyele 2019848 EWXK Leptosporangiate Monilophytes.p1 Lygjap 2009237 PBUU Leptosporangiate Monilophytes.p1

Cucsat evm.model.Chr7.1407 Dipcon 2008080 MEKP Leptosporangiate Monilophytes.p1 Cucmel MELO3C021059.2.1 Citlan Cla014934

Lagsic Lsi02G021010.1 Anetom 2000705 CQPW Leptosporangiate Monilophytes.p1

Cucmos CmoCh17G012430.1 Cucmax CmaCh17G012720.1 Cucpep Cp4.1LG12g10890.1 Cucmos CmoCh08G002250.1 Cucpep Cp4.1LG17g11040.1 Cucmax CmaCh08G002260.1

Momcha lcl NW 019104489.1 XP 022147807.1 2340

Datglo Datgl107S17979

Begfuc Begfu28140S28660 Datglo Datgl107S17980 Begfuc Begfu444S35049

Casmol maker-scaffold13974-augustus-gene-0.4-mRNA-1Casmol maker-scaffold09667-augustus-gene-0.8-mRNA-1Querob Qrob P0037250.2

Querob Qrob P0255410.2 Alnglu Alngl60713S33272 Casgla Casgl230S11904

Jugreg g49810.t1 Pilglo 2006697 KIIX Leptosporangiate Monilophytes.p1 Jugreg g38506.t1

Azocar 2032771 CVEG Leptosporangiate Monilophytes.p1

Salcuc Sacu v1.1 s0034.g011238

Azofil Azfi s0247.g060103

Psinud 2009640 QVMR Eusporangiate Monilophytes.p1 Vigung Vigun05g134400.1 Tripra Tp57577 TGAC v2 mRNA16275 Vigang vigan.Vang04g10610.1 Phavul Phvul.008G130800.1 Glymax Glyma.08G349200.1 Scedis 2011988 EEAQ Eusporangiate Monilophytes.p1 Dendav 2009736 MTGC Leptosporangiate Monilophytes.p1 Glymax Glyma.18G167300.1 Cajcaj Ccajan 38678 Scedis 2011989 EEAQ Eusporangiate Monilophytes.p2 Linlin 2011186 NOKI Leptosporangiate Monilophytes.p1 Linmic 2007539 YIXP Leptosporangiate Monilophytes.p1

Tripra Tp57577 TGAC v2 mRNA6635 Cicari Ca 05488.1 Lotjap Lj1g3v3557070.1 Trisub lcl DF974137.1 GAU45640.1 34698 Medtru MtrunA17 Chr7g0235761 Lupang Lup010451.1

Osmsp. 2080267 UOMY Leptosporangiate Monilophytes gametophyte.p1

Araipa Araip.D1M07

Casaus Castanospermum21231-PA Arahyp arahy.Tifrunner.gnm1.ann1.QR9F0J.1Aradur Aradu.J7RE1 Nissch Nissc3979S22769 Cryacr 2068231 WQML Leptosporangiate Monilophytes.p1 Casaus Castanospermum26875-PA Arahyp arahy.Tifrunner.gnm1.ann1.YI95N7.1 Polacr 2008194 FQGQ Leptosporangiate Monilophytes.p1 Chafas Chafa4019S09651 Myrruf 2009421 GSXD Leptosporangiate Monilophytes.p1 Gymdry 2013597 HEGQ Leptosporangiate Monilophytes.p1 Argniv 2005916Notmon XDDT 2063781 Leptosporangiate YCKE Leptosporangiate Monilophytes.p1Ptevit 2019163 Monilophytes.p1 POPJ Leptosporangiate Monilophytes.p1

Cercan Cerca480S25317 Adiale 2006746 WCLG Leptosporangiate Monilophytes.p1 Mimpud Mimpu9366S28577Chafas Chafa19855S01460

Mimpud Mimpu6569S26607 Cysree 2009545 RICC Leptosporangiate Monilophytes.p1 Cysfra 2019262 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Ophpet 2018347 WTJG Eusporangiate Monilophytes.p1 Cysfra 2085492 XXHP Leptosporangiate Monilophytes Stewart.p1 Athfil 2013424 URCP Leptosporangiate Monilophytes.p1 Blespi 2013576 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1

Nepexa 2034974 NWWI Leptosporangiate Monilophytes.p1 Hymbiv 2007735 QIAD Leptosporangiate Monilophytes.p1

Dipwic 2088042 UFJN Leptosporangiate Monilophytes.p1 Wooilv 2076089 YQEC Leptosporangiate Monilophytes.p1 Davfej 2008549 OQWW Leptosporangiate Monilophytes.p1 Woosco 2001167 YJJY Leptosporangiate Monilophytes.p1

Adirad 2007152 BMJR Leptosporangiate Monilophytes.p1

Blespi 2002681 VITX Leptosporangiate Monilophytes.p1 Blespi 2013575 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Asppla 2009331 KJZG Leptosporangiate Monilophytes.p1

Adirad 2007153 BMJR Leptosporangiate Monilophytes.p1

Plepol 2074220 UJWU Leptosporangiate Monilophytes dehydrating fronds.p1

Pittri 2013808 UJTT Leptosporangiate Monilophytes.p1 Polgly 2079381 CJNT Leptosporangiate Monilophytes.p1

Equhye 2009400 JVSZ Eusporangiate Monilophytes.p1

Brarap Brara.G00672.1Eutsal Thhalv10002587m Brarap Brara.C03986.1 Braolecap Bol028190 Aralyr AL3G40800.t1 Equdif 2008127 CAPN Eusporangiate Monilophytes.p1 Brarap Brara.J00818.1 Cyaspi 2013462 GANB Leptosporangiate Monilophytes.p1 Arahal Araha.40054s0002.1 Aratha AT3G25110.1

Boestr Bostr.6879s0001.1 Capgra Cagra.4586s0007.1 Braolecap Bol031594 Polamo 2016283 YLJA Leptosporangiate Monilophytes.p1 Caprub Carub.0003s2544.1 Boestr Bostr.19424s0123.1 Adirad 2007154 BMJR Leptosporangiate Monilophytes.p1

Braolecap Bol042479

Caprub Carub.0007s2970.1 Carpap evm.model.supercontig 428.2 Thecac Thecc1EG002853t1 Capgra Cagra.8284s0002.1 Boestr Bostr.2021s0046.1

Arahal Araha.7068s0002.1Aralyr AL9U11220.t1 Citsin orange1.1g017534m Citcle Ciclev10020691m

Aratha AT4G13050.1 Tarhas lcl NW 010971390.1 XP 010527253.1 40825

Gosrai Gorai.004G226800.1 Cepfol Cfol v3 14220 Braolecap Bol040323 Brarap Brara.D00738.1 Tarhas lcl NW 010966542.1 XP 010550894.1 25341 Gosrai Gorai.004G059000.1

Gosrai Gorai.004G226700.1 Poptri Potri.002G245600.1

Cepfol CfolCepfol v3 14221 Cfol v3 14222

Riccom 30217.m000262 Azofil Azfi s0003.g007903 Cepfol CfolCepfol v3 11885 Cfol v3 14223 Manesc Manes.13G049100.1 Azocar 2020991 CVEG Leptosporangiate Monilophytes.p1

Azocar 2020992 CVEG Leptosporangiate Monilophytes.p1

Linmic 2006469 YIXP Leptosporangiate Monilophytes.p1 Linlin 2013472 NOKI Leptosporangiate Monilophytes.p1

Linlin 2009249 NOKI Leptosporangiate Monilophytes.p1

Cryacr 2010784 WQML Leptosporangiate Monilophytes.p1 Linmic 2006470 YIXP Leptosporangiate Monilophytes.p1

Sollyc Solyc06g083380.2.1 Solpen Sopen06g034750.1 Gymdry 2007408 HEGQ Leptosporangiate Monilophytes.p1 Capann CA06g26640Petaxi Peaxi162Scf00517g00629.1

Ptevit 2002089 POPJ Leptosporangiate Monilophytes.p1 Nicben Niben101Scf08799g00002.1 Nicben Niben101Scf03479g05042.1 Fraexc FRAEX38873 v2 000268670.1 Fraexc FRAEX38873 v2 000145450.1 Pteens 2002462 FLTD Leptosporangiate Monilophytes.p1 Nicben Niben101Scf01063g09001.1 Hompyc 2012787 OCZL LeptosporangiateDendav 2046084 Monilophytes.p1 MTGC Leptosporangiate Monilophytes.p1 Nicben Niben101Scf04915g00003.1 Pteens 2002461 FLTD Leptosporangiate Monilophytes.p1

Cysree 2065686 RICC Leptosporangiate Monilophytes.p1 Argniv 2015791 XDDT Leptosporangiate Monilophytes.p1

Cysuta 2029712 HNDZ Leptosporangiate Monilophytes.p1 Myrruf 2012365 GSXD Leptosporangiate Monilophytes.p1 Petaxi Peaxi162Scf00238g00413.1 Cysfra 2017984 LHLE Leptosporangiate Monilophytes.p1

Daucar DCAR 004735 Cysfra 2023453 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Adiale 2010197 WCLG Leptosporangiate Monilophytes.p1 Cysfra 2090175 XXHP Leptosporangiate Monilophytes Stewart.p1 Notmon 2066108 YCKE Leptosporangiate Monilophytes.p1 Cyspro 2006686 YOWV Leptosporangiate Monilophytes.p1

Gagari 2002506 DCDT Leptosporangiate Monilophytes.p1

Onosen 2005944 HTFH Leptosporangiate Monilophytes.p1 Adirad 2063705 BMJR Leptosporangiate Monilophytes.p1 Daucar DCAR 012668 Leuimm 2013000 WGTU Leptosporangiate Monilophytes.p1 Parcor 2009802 ZXJO Leptosporangiate Monilophytes.p1 Nelnuc NNU 17226-RA Chequi AUR62001130-RA Woosco 2077912 YJJY Leptosporangiate Monilophytes.p1

Blespi 2099608 VITX Leptosporangiate Monilophytes.p1 Chequi AUR62016551-RA Cyaspi 2011494 GANB Leptosporangiate Monilophytes.p1 Dipwic 2089667 UFJN Leptosporangiate Monilophytes.p1 Betvul Bv7 179730 pddx.t1 Deplob 2012208 FCHS Leptosporangiate Monilophytes crenata.p1 Wooilv 2077309 YQEC Leptosporangiate Monilophytes.p1 Blespi 2017323Athfil 2065171 RWYZ Leptosporangiate URCP Leptosporangiate Monilophytes Monilophytes.p1 2 samples combined.p1 Spiole Sp 020050 ngft.t1 Helann HanXRQChr01g0015251

Utrgib Utricularia gibba unitig 749 997434 999407 unitig 749.g13490.t1 1 CDS 875844589 18156 Polacr 2011568 FQGQ Leptosporangiate Monilophytes.p1

Didtru 2034365 RFRB Leptosporangiate Monilophytes.p1 Utrgib Utricularia gibba unitig 26 2175029 2177806 unitig 26.g9580.t1 -1 CDS 875813213 28277

Vitlin 2010443 SKYV Leptosporangiate Monilophytes.p1 Asppla 2010355 KJZG Leptosporangiate Monilophytes.p2 Diacar Dca53120.1 Vitapp 2102465 NDUV Leptosporangiate Monilophytes.p1 Diacar Dca4238.1 Vitlin 2000506 SKYV Leptosporangiate Monilophytes.p1

Phacar 2136196 RXRQ Hornworts sporophyte.p1 Bolrep 2016177 JBLI Leptosporangiate Monilophytes.p1 Vitapp 2106197 NDUV Leptosporangiate Monilophytes.p1

Diacar Dca47860.1

Phacar 2140143 RXRQ Hornworts sporophyte.p1 Nepexa 2021603 NWWI Leptosporangiate Monilophytes.p1 Daucar DCAR 022922 Nelnuc NNU 17225-RA Anacom Aco006639.1

Daucar DCAR 028324

Polamo 2071854 YLJA Leptosporangiate Monilophytes.p1 Phygro 2014248 ORJE Leptosporangiate Monilophytes.p1 Musacu GSMUA Achr8T08690 001 Phlpse 2002756 ZQYU Leptosporangiate Monilophytes.p1 Taklep 2012209 SKQD Mosses.p1 Polhes 2024689 GYFU Leptosporangiate Monilophytes A type.p1 Davfej 2002236 OQWW Leptosporangiate Monilophytes.p1 Phlpse 2002758 ZQYU Leptosporangiate Monilophytes.p1 Polhes 2030322 ZRAV LeptosporangiatePhlpse 2002757 Monilophytes ZQYU Leptosporangiate 2 samples combined.p1 Monilophytes.p1

Taklep 2012210 SKQD Mosses.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00117.19 Polhes 2004576 IXLH Leptosporangiate Monilophytes B type.p1 Polgly 2080683 CJNT Leptosporangiate Monilophytes.p1

Spipol Spipo7G0045800 Orysat LOC Os09g32760.1 Phaequ PEQU 05415 Setita Seita.2G264600.1 Bradis Bradi4g34500.1

Zeamay Zm00008a009167Sorbic Sobic.002G256800.2 Aposhe lcl KZ453230.1 PKA47430.1 19861 Horvul HORVU5Hr1G076030.2 Zeamay Zm00008a028518 Tetpel 2020931 HVBQ Mosses.p1

Sorbic Sobic.002G256900.1 Zosmar Zosma77g00830.1 Dencat lcl NW 021318676.1 XP 020675019.2 4117 Sphfal Sphfalx0031s0119.1

Polcom 2003437 SZYG Mosses gametophyte.p1

Atrang 2017207 ZTHV Mosses.p1

Phaequ PEQU 00025

Spipol Spipo4G0050900 BlaspNW c328763 g1 i1 m.83029

Phaequ PEQU 41991

BlaspNW c328763 g1 i3 m.83031 Pelnee 2113894 JHFI Liverworts.p1 Pelepi 2008011 PIUF Liverworts.p1 BlaspNW c328763 g1 i2 m.83030

Pelepi 2008010 PIUF Liverworts.p1

Pelepi 2091601 PIUF Liverworts.p1

Parhal 2011198 FAJB Hornworts.p1

Auschi 2068968 YYPE Conifers.p1 Disarc 2001255 GKCZPiluvi Conifers.p12061863 ETCJ Conifers.p1 Pelnee 2016622 JHFI Liverworts.p1 Pallye 2006642 YFGP Liverworts.p1 Widced 2059878 AUDE Conifers.p1

Chalaw 2068025 AIGO Conifers.p1

Fokhod 2058690 UEVI Conifers.p1 Sphtex 2008771 HERT Liverworts.p1 Pappap 2083446 OVIJ Conifers.p1 Luncru 2075392 TXVB Liverworts.p1 Calgra 2143238 IFLINeopan Conifers 2070157 March.p1 JDQB Conifers.p1

Calmac 2055825 RMMV Conifers March.p1 Pallye 2006641 YFGP Liverworts.p1

Caldec 2059826 FRPM Conifers.p1

Plaori 2052308 BUWV Conifers.p1 Calfis 2183108 RTMU Liverworts.p1 PhaequPhaequ PEQU PEQU 33788 38651 Tetsp. 2069997 CGDN Conifers.p1 Micdec 2054016 XQSG Conifers.p1Thupli 2040621 VFYZ Conifers.p1 Cupdup 2011988 QNGJ Conifers.p1Thudol 2012864 NKIN Conifers.p1 Junsco 2058691 XMGP Conifers.p1Cryjap 2075148 DSXO Conifers.p1 Dencat lcl NW 021318676.1 XP 028548852.1 4116

Cryjap 2010393 HOUF Conifers leaf.p1 Taxdis 2014162 FHST Conifers.p1

Cryjap 2018758 GMHZ Conifers 2 samples combined.p1 Glypen 2046659 OXGJ Conifers.p1

Cunlan 2052084 OUOI Conifers.p1 Marpal 2003464 IHWO Liverworts mycorrizal.p1

Marpal 2005131 LFVP Liverworts 2 samples combined.p1 Marpal scaff4206 FGenesh6.1 Taicry 2067271 QSNJ Conifers.p1 Marpal 2003366 HMHL Liverworts non mycorrizal.p1 Cunlan 2088305Cunlan 2018457 ESYX Conifers ZQVF Conifers branch apex 2 samples with needles.p1 combined.p1 Marpol Mapoly0023s0057.1

Metgly 2063911 NRXL Conifers.p1 Seqgig 2007584 QFAE Conifers Glaucum.p1 Ricnat 2034790 WJLO Liverworts.p1 Athcup 2011015 XIRK Conifers.p1

Concon 2045407 ILBQ Liverworts.p1

Cephar 2060117 GJTI Conifers.p1

Tortax 2008306 EFMS Conifers.p1 Amearg 2018705 IAJW Conifers.p1Cephar 2090765 WYAJ Conifers.p1 Psechi 2006845 YLPM Conifers.p1 Megfla 2002490 UCRN Hornworts.p1 Taxcus 2011755 ZYAX Conifers.p1

Taxbac 2011279 WWSS Conifers.p1Cephar 2111120 NVGZ Conifers 2 samples combined.p1 Sciver 2043232 YFZK Conifers.p1

Faltax 2013747 QHBI Conifers A.p1 Faltax 2062442 ROWR Conifers.p1

Dacbal 2010853 IZGN Conifers.p1 Faltax 2083617 PLYX Conifers 2 samples combined.p1

Daccom 2009998 FMWZ Conifers.p1

Podrub 2059213 XLGK Conifers.p1 Podcor 2011931Nagnag SCEB2115305 Conifers.p1 UUJS Conifers.p1 Acmpan 2018666 HILW Conifers.p1 Retmin 2009409 VGSX Conifers.p1

Mictet 2001193 MHGD Conifers.p1 Mictet 2001191 MHGD Conifers.p1

Saxcon 2013222 QCGM Conifers.p1Mictet 2001192 MHGDSunama Conifers.p1 2002248 KLGF Conifers.p1 Sunama 2002251Parust 2003246 KLGF Conifers.p1 JZVE Conifers.p1 Sunama 2002249 KLGF Conifers.p1Parust 2003247 JZVELagfra Conifers.p1 2090818 ZQWM Conifers.p1

Phyhyp 2006616 JRNA Conifers.p1 Mancol 2063112 CDFR Conifers.p1 Halbid 2011789 OWFC Conifers.p1

Phyhyp 2006615 JRNA Conifers.p1

Pruand 2004103 EGLZ Conifers.p1

Agamac 2069220 ACWS Conifers.p1 Agarob 2074369 MIXZ Conifers.p1 Ararul 2011525 XTZO Conifers.p1

Barbar 2020875 OFTV Liverworts.p1

Saxcon 2011890 QCGM Conifers.p1

Saxcon 2011891 QCGM Conifers.p1

Barbar 2009650 OFTV Liverworts.p1

Pinpin PPI00031929 Picsit PSI00016862 BlaspNW c327701 g1 i5 m.75505 Abilas 2006186 VSRH Conifers.p1 Pintae PTA00041028 Pinsyl PSY00012326 BlaspNW c327701 g1 i9 m.75521 BlaspNW c327701 g1 i8 m.75517

BlaspNW c327701 g1 i7 m.75512 Tsuhet 2055649 GAMHPseama Conifers.p1 2006982 AQFM Conifers.p1 Pseama 2006984 AQFM Conifers.p1 Notlon 2067799 AREG Conifers.p1 Pinpon 2004479 JBND Conifers.p1 Piceng 2005457 AWQB Conifers.p1 Keteve 2004203 JUWL Conifers.p1 Pinrad 2008957 DZQM Conifers.p1 Catagr 2003215 NPRL Conifers.p1 Marpal scaff2511 FGenesh7.1 Abilas 2006187 VSRH Conifers.p1 Pinpar 2005316 IIOL Conifers.p1 Cedlib 2003544 GGEA Conifers.p1

Pinpar 2005318 IIOL Conifers.p1

Pseama 2006983 AQFM Conifers.p1 Pintae PTA00034320

Pinjef 2004634 MFTM Conifers.p1 Marpol Mapoly0094s0076.1 Pinpon 2071864 JBND Conifers.p1Pinsyl PSY00035454 Picsit PSI00016250 Marpol 2008393 JPYU Liverworts.p1 Pinrad 2008956 DZQM Conifers.p1 Sphtex 2044584 HERT Liverworts.p1 Pinsyl PSY00011135Pinpin PPI00006390 Luncru 2075346 TXVB Liverworts.p1

Piceng 2005456 AWQB Conifers.p1

Catagr 2003213 NPRL Conifers.p1 Ginbil Gb 27405 Catagr 2003214 NPRL Conifers.p1 Pinpar 2005317 IIOL Conifers.p1 Sphfal Sphfalx0010s0170.1

Dioedu 2018336 WLIC Cycadales.p1

Pseama 2006985 AQFM Conifers.p1

Psemen PME00019677 Ginbil 2005767 SGTW Ginkgoales.p1

Encbar 2086405 GNQG Cycadales.p1

Cycmic CMI00028031 Psewil 2009408Larspe IOVS2053573 Conifers.p1 WVWNCedlib Conifers.p1 2013451 GGEA Conifers.p1 BlaspNW c327701 g1 i4 m.75501 Calfis 2171048 RTMU Liverworts.p1 Staeri 2011701 KAWQ Cycadales.p1 BlaspNW c327701 g1 i6 m.75509

BlaspNW c327701 g1 i3 m.75496

Cycmic 2013089 XZUY Cycadales.p1

Parhal 2010832 FAJB Hornworts.p1 Polcom 2003005 SZYG Mosses gametophyte.p1

Phacar 2024591 RXRQ Hornworts sporophyte.p1

Phacar 2118606 WCZB Hornworts gametophyte.p1

Phacar 2011851 RXRQ Hornworts sporophyte.p1

Notaen 2006434 DXOU Hornworts.p1 Notvin 2005221 TCBC Hornworts.p1

Megfla 2002545 UCRN Hornworts.p1

Megfla 2002544 UCRN Hornworts.p1

Dipfol 2009494 AWOI Mosses.p1

Parhal 2055726 FAJB Hornworts.p1

Phacar 2006653 WCZB Hornworts gametophyte.p1 Phacar 2138072 RXRQ Hornworts sporophyte.p1

Gnemon TnS000594241t09

Timaus 2010012 ZQRI Mosses.p1

Gnemon 2007606 GTHK Gnetales.p1

Timaus 2005172 ZQRI Mosses.p1

Welmir 2013189 TOXE Gnetales.p1 Scoaqu 2022769 BPSG Mosses.p1

Phacar 2006652 WCZB Hornworts gametophyte.p1

Phifon 2055451 ORKS Mosses.p1

Cerpur 2013148 FFPD Mosses.p1

Aulhet 2087798 WNGH Mosses.p1

Physsp. 2016941 YEPO Mosses.p1 Leubra 2098660 ZACW Mosses.p1

Loebre 2008736Leujul 2014143 WSPM Mosses.p1 IGUH Mosses.p1

Ortlye 2006347 CMEQ Mosses.p1 Phypat Pp3c17 23790V3.1

Rhyser 2047273 JADL Mosses.p1

Stesub 2068439 LNSF Mosses.p1

Leujul 2020378 IGUH Mosses.p1 Leubra 2008322 ZACW Mosses.p2

Loebre 2046524 WSPM Mosses.p1

Pseele 2007794 QKQO Mosses.p1

Leubra 2008323 ZACW Mosses.p2

Osmjav 2076767 VIBO Leptosporangiate Monilophytes.p1

Phypat Pp3c15 18050V3.1

Andrup 2000816 WOGB Mosses.p1

Andrup 2000817 WOGB Mosses.p1

Andrup 2000814 WOGB Mosses.p1

Andrup 2000815 WOGB Mosses.p1

Osmsp. 2013413 UOMY Leptosporangiate Monilophytes gametophyte.p1

Athfil 2002331 URCP Leptosporangiate Monilophytes.p1 Dipwic 2089427 UFJN Leptosporangiate Monilophytes.p1

Woosco 2007548 YJJY Leptosporangiate Monilophytes.p1 Hompyc 2009636 OCZL Leptosporangiate Monilophytes.p1 Woosco 2007549 YJJY Leptosporangiate Monilophytes.p1 Wooilv 2077192 YQEC Leptosporangiate Monilophytes.p1

Blespi 2014679 VITX LeptosporangiateDeplob 2012923 Monilophytes.p1 FCHS Leptosporangiate Monilophytes crenata.p1 Angeve 2011773 NHCM Eusporangiate Monilophytes.p1

Cysfra 2010067 LHLE Leptosporangiate Monilophytes.p1

Theacu 2003412 MROH Leptosporangiate Monilophytes.p1 Cysree 2010567Cysuta 2030525RICCGymdry Leptosporangiate HNDZ2004450 Leptosporangiate HEGQ Monilophytes.p1 Leptosporangiate Monilophytes.p1 Monilophytes.p1 Cyspro 2012004 YOWV Leptosporangiate Monilophytes.p1

Cysfra 2015356 XXHP Leptosporangiate Monilophytes Stewart.p1

Thyele 2020253 EWXK Leptosporangiate Monilophytes.p1

Plajap 2025315 UWOD Leptosporangiate Monilophytes.p1 Botvir 2102906 BEGM Eusporangiate Monilophytes.p1 Culmac 2152388 PNZO Leptosporangiate Monilophytes.p1

Taklep 2079699 SKQD Mosses.p1

Cysfra 2022610 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Cyaspi 2003301 GANB Leptosporangiate Monilophytes.p1

Scedis 2003313 EEAQ Eusporangiate Monilophytes.p1

Hymbiv 2058738 QIAD Leptosporangiate Monilophytes.p1 Lycdeu 2013226 PQTO Lycophytes.p2

Polacr 2000703 FQGQ Leptosporangiate Monilophytes.p1

Polacr 2000704 FQGQ Leptosporangiate Monilophytes.p1 Cyaspi 2003299 GANB Leptosporangiate Monilophytes.p1 Cyaspi 2003300 GANB Leptosporangiate Monilophytes.p1

Didtru 2003491 RFRB Leptosporangiate Monilophytes.p1 Tmepar 2024624 ALVQ Eusporangiate Monilophytes.p1

Lycdeu 2013291 PQTO Lycophytes.p1

Bolrep 2020463 JBLI Leptosporangiate Monilophytes.p1

Tmepar 2101001 ALVQ Eusporangiate Monilophytes.p1 Hupsel 2004858 GTUO Lycophytes.p1

Hupsel 2002816 GTUO Lycophytes.p1 Dipdig 2006611 WAFT Lycophytes.p1

Psinud 2003456 QVMR Eusporangiate Monilophytes.p1 Asppla 2004501 KJZG Leptosporangiate Monilophytes.p1 Polamo 2072573 YLJA Leptosporangiate Monilophytes.p1 Hupsel 2000250 NYBX Lycophytes A.p1 Hupsel 2024878 NYBX Lycophytes A.p1

Hupluc 2002614 GKAG Lycophytes.p1 Leuimm 2009639 WGTU Leptosporangiate Monilophytes.p1 Hupluc 2003676 GKAG Lycophytes.p1 Hupluc 2003680 GKAG Lycophytes.p1 Polgly 2080249 CJNT Leptosporangiate Monilophytes.p1

Polhes 2011970 GYFU Leptosporangiate Monilophytes A type.p1 Aspnid 2014117 PSKY Leptosporangiate Monilophytes.p1 Polhes 2107063 IXLH Leptosporangiate Monilophytes B type.p1 Phlpse 2023360 ZQYU Leptosporangiate Monilophytes.p1

Equhye 2014793 JVSZ Eusporangiate Monilophytes.p1

Polhes 2033268 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Equhye 2007128 JVSZ Eusporangiate Monilophytes.p1 Phygro 2017070 ORJE Leptosporangiate Monilophytes.p1

Dendav 2009385 MTGC Leptosporangiate Monilophytes.p1 Hupsel 2007866 YHZW Lycophytes 2 samples combined.p1 Hupsel 2035573 YHZW Lycophytes 2 samples combined.p1 Hupsel 2035572 YHZW Lycophytes 2 samples combined.p1

Hupsel 2007865 YHZW Lycophytes 2 samples combined.p1 Adiale 2066349 WCLG Leptosporangiate Monilophytes.p1

BlaspNW c331133 g1 i5 m.105951 BlaspNW c331133 g1 i1 m.105940 BlaspNW c331133 g1 i8 m.105959 BlaspNW c331133 g1 i7 m.105956

Equdif 2010070 CAPN Eusporangiate Monilophytes.p1 Sphtex 2045531 HERT Liverworts.p1

Denobs 2013476 XNXF Lycophytes.p1

Hupmyr 2060598 CBAE Lycophytes.p1

BlaspNW c331133 g1 i9 m.105962 BlaspNW c331133 g1 i2 m.105942

Myrruf 2003838 GSXD Leptosporangiate Monilophytes.p1 Psinud 2009882 QVMR Eusporangiate Monilophytes.p1 Hupsqu 2016859 GAON Lycophytes.p1

Hupsqu 2006413 GAON Lycophytes.p1

BlaspNW c331133 g1 i10 m.105965

Cyaspi 2015795 GANB Leptosporangiate Monilophytes.p1

Adirad 2062671 BMJR Leptosporangiate Monilophytes.p1 Hupsel 2004859 GTUO Lycophytes.p1 Plepol 2074575 UJWU Leptosporangiate Monilophytes dehydrating fronds.p1 Hupsel 2004856 GTUO Lycophytes.p1 Hupmyr 2061410 CBAE Lycophytes.p1

Argniv 2010587 XDDT Leptosporangiate Monilophytes.p1

BlaspNW c324682 g1 i4 m.61036 BlaspNW c324682 g1 i2 m.61033

Gagari 2076089 DCDT Leptosporangiate Monilophytes.p1 BlaspNW c324682 g1 i7 m.61039 BlaspNW c324682 g1 i1 m.61030

Marema 2002328 TFYI Liverworts.p1 Notmon 2065807 YCKE Leptosporangiate Monilophytes.p1 Athfil 2062721 URCP Leptosporangiate Monilophytes.p1

Phydru 2128634 ZZEI Lycophytes.p1

Psecar 2018525 UPMJ Lycophytes.p1 Taklep 2075700 SKQD Mosses.p1

Lycapp 2010564 ULKT Lycophytes.p1 Marpal 2085585 LFVP Liverworts 2 samples combined.p1 Linlin 2019102 NOKI Leptosporangiate Monilophytes.p1 Marpal 2011482 IHWO Liverworts mycorrizal.p1 Parcor 2012943 ZXJO Leptosporangiate Monilophytes.p1

Marpal 2054680 HMHL Liverworts non mycorrizal.p1 Marpal scaff5078 FGenesh10.1

Adirad 2006921 BMJR Leptosporangiate Monilophytes.p1 Luncru 2075740 TXVB Liverworts.p1

Deplob 2011811 FCHS Leptosporangiate Monilophytes crenata.p1

Dipwic 2014142 UFJN Leptosporangiate Monilophytes.p1 Pteens 2012025 FLTD Leptosporangiate Monilophytes.p1 Atrang 2011480 ZTHV Mosses.p1

Marpol 2038911 JPYU Liverworts.p1 Marpol Mapoly0020s0090.1 Phydru 2024928 ZZEI Lycophytes.p1 Vitapp 2015537 NDUV Leptosporangiate Monilophytes.p1 Gymdry 2015122 HEGQ Leptosporangiate Monilophytes.p1 Azofil Azfi s0022.g016103

Cysuta 2029636 HNDZ LeptosporangiateBlespi 2216906 Monilophytes.p1RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Lycdeu 2079387 PQTO Lycophytes.p1

Cysfra 2014853 LHLE Leptosporangiate Monilophytes.p1 Polcom 2009338 SZYG Mosses gametophyte.p1

Concon 2046469 ILBQ Liverworts.p1 Pallye 2107497 YFGP Liverworts.p1 Atrang 2016914 ZTHV Mosses.p1 Pelepi 2014220 PIUF Liverworts.p1

Cysree 2065052 RICC Leptosporangiate Monilophytes.p1 Ophvul 2001817 QHVSOphvul Eusporangiate 2001818 QHVS Monilophytes Eusporangiate leaf.p1 Monilophytes leaf.p1 Ptipul 2136124 HPXA Liverworts.p1

Phydru 2024927 ZZEI Lycophytes.p1 Cyspro 2010199 YOWV Leptosporangiate Monilophytes.p1 Tetpel 2019254 HVBQ Mosses.p1 Pelnee 2018911 JHFI Liverworts.p1 Pelepi 2014221 PIUF Liverworts.p1

Cysfra 2087768 XXHP Leptosporangiate Monilophytes Stewart.p1 Azofil Azfi s0035.g025566 Pittri 2021830 UJTT Leptosporangiate Monilophytes.p1 Phacar 2006915 RXRQ Hornworts sporophyte.p1

Ricnat 2007370 WJLO Liverworts.p1

Cysfra 2009701 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Vitapp 2014871 NDUV Leptosporangiate Monilophytes.p1

Tetpel 2004084 HVBQ Mosses.p1

Atrang 2011481 ZTHV Mosses.p1 Vitlin 2001342 SKYV Leptosporangiate Monilophytes.p1

Azocar 2029974 CVEG Leptosporangiate Monilophytes.p1

Pilglo 2090549 KIIX Leptosporangiate Monilophytes.p1

Anetom 2011958 CQPW Leptosporangiate Monilophytes.p1 Anetom 2011959 CQPW Leptosporangiate Monilophytes.p1 Notvin 2082677 TCBC Hornworts.p1

Leuimm 2071559 WGTU Leptosporangiate Monilophytes.p1 Cysfra 2013297Gymdry XXHP 2011065 Leptosporangiate HEGQ Leptosporangiate Monilophytes Stewart.p1 Monilophytes.p1

Cysree 2062898 RICC Leptosporangiate Monilophytes.p1 Cyspro 2007425 YOWV Leptosporangiate Monilophytes.p1

Hompyc 2057952 OCZL Leptosporangiate Monilophytes.p1 Linlin 2095765 NOKI Leptosporangiate Monilophytes.p1 Cysuta 2007094 HNDZ Leptosporangiate Monilophytes.p1 Lygjap 2078625 PBUU Leptosporangiate Monilophytes.p1

Pornav 2113345 KRUQ Liverworts.p1

Hupluc 2020345 GKAG Lycophytes.p1

Hupsel 2004857 GTUO Lycophytes.p1 Adiale 2008444 WCLG Leptosporangiate Monilophytes.p1

Timaus 2013366 ZQRI Mosses.p1 Woosco 2014943 YJJY Leptosporangiate Monilophytes.p1

Dicsco 2101352 NGTD Mosses.p1

Linmic 2052452 YIXP Leptosporangiate Monilophytes.p1 Megfla 2001924 UCRN Hornworts.p1

Argniv 2016393 XDDT Leptosporangiate Monilophytes.p1

Scoaqu 2020067 BPSG Mosses.p1 Myrruf 2065224 GSXD Leptosporangiate Monilophytes.p1 Porpin 2149953 UUHD Liverworts.p1

Gagari 2016663 DCDT Leptosporangiate Monilophytes.p1 Parhal 2010349 FAJB Hornworts.p1

Hupsel 2025565 YHZW Lycophytes 2 samples combined.p1

Isoesp. 2074866 PYHZ Lycophytes.p1

Selsel 2003129 KUXM Lycophytes.p1 Notmon 2064226 YCKE Leptosporangiate Monilophytes.p1

Hedcil 2007778YWNF Mosses.p1

BlaspNW c331133 g1 i3 m.105945

Phifon 2010696 ORKS Mosses.p1

Aulhet 2010372 WNGH Mosses.p1 Pilglo 2010894 KIIX Leptosporangiate Monilophytes.p1 Phacar 2136228 RXRQ Hornworts sporophyte.p1 Polgly 2078924 CJNT Leptosporangiate Monilophytes.p1

Isoteg 2098528 PKOX Lycophytes.p1

Hedcil 2007779YWNF Mosses.p1

Phacar 2117291 WCZB Hornworts gametophyte.p1 Odopro 2013499 YBQN Liverworts.p1

Baztri 2091162 WZYK Liverworts.p1

Marpal 2006207 IHWO Liverworts mycorrizal.p1 Mixspe 2156477 NWQC Liverworts.p1 Parcor 2007781 ZXJO Leptosporangiate Monilophytes.p1 Sphtex 2007176 HERT Liverworts.p1 Salcuc Sacu v1.1 s0130.g022050 Marpal 2011356 LFVP Liverworts 2 samples combined.p1 Sphles 2005931 GOWD Mosses.p1 Marpal scaff502 FGenesh5.1 Polhes 2003170 GYFU Leptosporangiate Monilophytes A type.p1 Phypat Pp3c16 25110V3.1 Calfis 2013712 RTMU Liverworts.p1 Polhes 2003169 GYFU Leptosporangiate Monilophytes A type.p1

Polhes 2021858 IXLH Leptosporangiate Monilophytes B type.p1 Hupmyr 2013558 CBAE Lycophytes.p1 Sphles 2005932 GOWD Mosses.p1

Physsp. 2018534YEPO Mosses.p1 Fruspp 2138326 CHJJ Liverworts.p1

Linmic 2053438 YIXP Leptosporangiate Monilophytes.p1 Trelac 2011439 FITN Liverworts.p1 Azofil Azfi s0007.g011165 Linlin 2095959 NOKI Leptosporangiate Monilophytes.p1 Sphrec 2018832 UHLI Mosses.p1

Phypat Pp3c25 14890V3.1 Barbar 2133121 OFTV Liverworts.p1

Sphfal Sphfalx0040s0004.1

Polhes 2012736 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1

Frusp. 2137741 TGKW Liverworts.p1 Luncru 2073804 TXVB Liverworts.p1

Pittri 2090773 UJTT Leptosporangiate Monilophytes.p1

Metcra 2010157 NRWZ Liverworts.p1 Asppla 2013081 KJZG Leptosporangiate Monilophytes.p1 Ortlye 2009249 CMEQ Mosses.p1 Concon 2043324 ILBQ Liverworts.p1 Marpal 2011357 LFVP Liverworts 2 samples combined.p1 Marpal 2010728 HMHL Liverworts non mycorrizal.p1 Ptevit 2100573 POPJ Leptosporangiate Monilophytes.p1

Sphfal Sphfalx0020s0088.1 Trelac 2090201 FITN Liverworts.p1 Marpol Mapoly0049s0080.1

Isoesp. 2073276 PYHZ Lycophytes.p1 Sphrec 2019429 UHLI Mosses.p1

Andrup 2093974 WOGB Mosses.p1 Scanem 2015176 IRBN Liverworts.p1

Radlin 2017329 BNCU Liverworts.p1

Odopro 2013498 YBQN Liverworts.p1

Isoteg 2097772 PKOX Lycophytes.p1

Atrang 2007565 ZTHV Mosses.p1 Atrang 2007566 ZTHV Mosses.p1 Atrang 2007564 ZTHV Mosses.p1 Polcom 2041734 SZYG Mosses gametophyte.p1

Sphfal Sphfalx0003s0108.1

Selsel 2009784 KUXM Lycophytes.p1

Ricnat 2005165 WJLO Liverworts.p1

Ricnat 2005166 WJLO Liverworts.p1 Tetpel 2131250 HVBQ Mosses.p1

Salcuc Sacu v1.1 s0064.g015816

Selmoe 88332

Selwal 2179504 JKAA Lycophytes.p1

Selaca 2041783 ZYCD Lycophytes.p1

Selsta 2009413 ZZOL Lycophytes.p1

Selkra 2008354 ZFGK Lycophytes.p1

Sellep 2007301 ABIJ Lycophytes.p1 Dipfol 2072335 AWOI Mosses.p1

Timaus 2012618 ZQRI Mosses.p1

Scoaqu 2089418 BPSG Mosses.p1

Phifon 2058524 ORKS Mosses.p1

Selwil 2012693 KJYC Lycophytes.p1

Selapo 2006653 LGDQ Lycophytes.p1

Buxaph 2014228 HRWG Mosses.p1 Hedcil 2050950 YWNF Mosses.p1

Aulhet 2089293 WNGH Mosses.p1

Leualb 2008461 VMXJ Mosses.p1

Dicsco 2100626 NGTD Mosses.p1

Plains 2081771 BGXB Mosses.p1

Racvar 2013636 RDOO Mosses.p1

Racelo 2006819 ABCD Mosses.p1

Pseele 2049922 QKQO Mosses.p1

Anocla 2007250 VBMM Mosses.p1 Cliden 2011343 MIRS Mosses.p1 Necdou 2022955 TMAJ Mosses.p1

Loebre 2005256 WSPM Mosses.p1 Anoatt 2061394 QMWB Mosses.p1 Calcor 2006755 TAVP Mosses.p1 Stesub 2009778 LNSF Mosses.p1

Leubra 2099089 ZACW Mosses.p1

Leujul 2167170 IGUH Mosses.p1

Cerpur 2012522 FFPD Mosses.p1

Physsp. 2014776 YEPO Mosses.p1 Rhyser 2011047 JADL Mosses.p1 Phypat Pp3c17 6430V3.1 Phypat Pp3c14 14380V3.1

Ortlye 2008025 CMEQ Mosses.p1

Thudel 2039353 EEMJ Mosses.p1

Roscap 2046750 XWHK Mosses.p1

Fonant 2015519 DHWX Mosses.p1

Bryarg 2004899 JMXW Mosses.p1

Synpri 2078347 GRKU Mosses.p1

Selmoe 444039

Selsta 2010168 ZZOL Lycophytes.p1

Tree scale: 0.1 Supplementary Figure 26: Maximum likelihood tree of NFP.

Phacar 2016863 WCZB Hornworts gametophyte.p2 Phacar 2016864 WCZB Hornworts gametophyte.p1

Phacar 2020498 RXRQ Hornworts sporophyte.p1

Phacar 2020497 RXRQ Hornworts sporophyte.p1

Marpal 2086070 LFVP Liverworts 2 samples combined.p1

Marpal 2055051 HMHL Liverworts non mycorrizal.p1

Hupsel 2010932 GTUO Lycophytes.p1

Lycapp 2004835 ULKT Lycophytes.p1 Psecar 2018349 UPMJ Lycophytes.p1 Psecar 2016118 UPMJ Lycophytes.p1 Lycapp 2004836 ULKT Lycophytes.p1

Dipdig 2012099 WAFT Lycophytes.p1 Dipdig 2012099 WAFT

Megfla 2052896 UCRN Hornworts.p1 Notvin 2006475 TCBC Hornworts.p1 Parhal 2005844 FAJB Hornworts.p1 Notvin 2006476 TCBC Hornworts.p1 Parhal 2005845 FAJB Hornworts.p1 Notvin 2006474 TCBC Hornworts.p1 Marpal 2068129 IHWO Liverworts mycorrizal.p1 Frusp. 2016359 TGKW Liverworts.p1 Frusp. 2016860 TGKW Liverworts.p1Fruspp 2017153 CHJJ Liverworts.p1 Fruspp 2018874 CHJJ Liverworts.p1 Pornav 2016146 KRUQ RadlinLiverworts.p1 2007390 BNCU Liverworts.p1 Radlin 2007389 BNCU Liverworts.p1 Mixspe 2161013 NWQCPorpin Liverworts.p1 2150727 UUHD Liverworts.p1

Odopro 2015740Scanem YBQN 2011482 Liverworts.p1 IRBN Liverworts.p1Ptipul 2017736 HPXA Liverworts.p1 Baztri 2091787 WZYK Liverworts.p1

Pelnee 2114000 JHFI Liverworts.p1 Pelepi 2092794 PIUF Liverworts.p1 Pallye 2018438Pelepi 2091815 YFGP Liverworts.p1 PIUF Liverworts.p1 Pallye 2018439 YFGP Liverworts.p1

Marpol 2006573 JPYU Liverworts.p1 Ricnat 2037847 WJLO Liverworts.p1 Concon 2005994 ILBQ Liverworts.p1 Luncru 2076322 TXVB Liverworts.p1 Marpal scaff3063 FGenesh4.1

Anocla 2054341BlaspNW VBMM c323267 Mosses.p1 g1 i1 m.57034 BlaspNW c323267 g1 i2 m.57036 Marpol Mapoly0008s0038.1 LoebreRhyser 2008996 2049321 WSPM JADL Mosses.p1 Mosses.p1 Pseele 2010798 QKQO Mosses.p1

Leubra 2000551 ZACW Mosses.p1 Leubra 2000552Calcor ZACW 2021114 Mosses.p1 TAVP Mosses.p1

Necdou 2184080 TMAJ Mosses.p1 Anoatt 2009647Leujul QMWB 2167825 Mosses.p1 IGUH Mosses.p1 Stesub 2070205 LNSF Mosses.p1 FonantThudel 2015195 2040361 DHWX EEMJ Mosses.p1 Mosses.p1

Tetpel 2006095 HVBQ Mosses.p1 Lycann 2017681 ENQF Lycophytes.p1 Lycdeu 2009831 PQTO Lycophytes.p1 Denobs 2010387 XNXF Lycophytes.p1 Aulhet 2090741 WNGH Mosses.p1 Isoteg 2100600 PKOX Lycophytes.p1 Isoesp. 2076023 PYHZ Lycophytes.p1 Trelac 2016033 FITN Liverworts.p1 Selkra 2009255 ZFGK Lycophytes.p1 Selaca 2005668 ZYCD Lycophytes.p1 Selwil 2008274 KJYC Lycophytes.p1 Selmoe 11327 Sellep 2009449 ABIJ Lycophytes.p1 Selapo 2006796 LGDQ Lycophytes.p1 Equdif 2041133 CAPN Eusporangiate Monilophytes.p1 Ortlye 2004466 CMEQ Mosses.p1 Equhye 2132093 JVSZ Eusporangiate Monilophytes.p1 Scedis 2088980 EEAQ Eusporangiate Monilophytes.p1 Ophvul 2004335 QHVS Eusporangiate Monilophytes leaf.p1 Psinud 2005336 QVMR Eusporangiate Monilophytes.p1 Tmepar 2022070 ALVQ Eusporangiate Monilophytes.p1 Ortlye 2004467 CMEQ Mosses.p1 Osmsp. 2080571 UOMY Leptosporangiate Monilophytes gametophyte.p1 Davfej 2226661 OQWW Leptosporangiate Monilophytes.p1 Cryacr 2067978 WQML Leptosporangiate Monilophytes.p1 Adirad 2014273 BMJR Leptosporangiate Monilophytes.p1 Plains 2082170 BGXB Mosses.p1 Osmjav 2003968 VIBO Leptosporangiate Monilophytes.p1 Bryarg 2011858 JMXW Mosses.p1 Osmsp. 2001142 UOMY Leptosporangiate Monilophytes gametophyte.p1 Roscap 2001394 XWHK Mosses.p1 Osmsp. 2001141 UOMY Leptosporangiate Monilophytes gametophyte.p1 Dipcon 2107816 MEKP Leptosporangiate Monilophytes.p1 Lygjap 2002638 PBUU Leptosporangiate Monilophytes.p1 Anetom 2015889 CQPW Leptosporangiate Monilophytes.p1 Dipwic 2088497 UFJN Leptosporangiate Monilophytes.p1 Hedcil 2052211 YWNF Mosses.p1 Pilglo 2090445 KIIX Leptosporangiate Monilophytes.p1 Azofil Azfi s0145.g051647 Phifon 2060148 ORKS Mosses.p1 Pilglo 2091258 KIIX Leptosporangiate Monilophytes.p1 Racvar 2002457 RDOO Mosses.p1 Pilglo 2013483 KIIX Leptosporangiate Monilophytes.p1 Linlin 2096949 NOKI Leptosporangiate Monilophytes.p1 Racvar 2002460 RDOO Mosses.p1 Vitlin 2011660 SKYV Leptosporangiate Monilophytes.p1 Vitapp 2006268 NDUV Leptosporangiate Monilophytes.p1 Racvar 2002459 RDOO Mosses.p1 Ptevit 2019879 POPJ Leptosporangiate Monilophytes.p1 Pteens 2014307 FLTD Leptosporangiate Monilophytes.p1 Racvar 2002458 RDOO Mosses.p1 Adirad 2008399 BMJR Leptosporangiate Monilophytes.p1 Notmon 2066350 YCKE Leptosporangiate Monilophytes.p1 Scoaqu 2019381 BPSG Mosses.p1 Myrruf 2064193 GSXD Leptosporangiate Monilophytes.p1 Asppla 2012780 KJZG Leptosporangiate Monilophytes.p1 Woosco 2015707 YJJY Leptosporangiate Monilophytes.p1 Leualb 2007961 VMXJ Mosses.p1 Gymdry 2008491 HEGQ Leptosporangiate Monilophytes.p1 Cysuta 2009733 HNDZ Leptosporangiate Monilophytes.p1 Synpri 2010193 GRKU Mosses.p1 Cysfra 2007954 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Cyspro 2012123 YOWV Leptosporangiate Monilophytes.p1 Synpri 2010192 GRKU Mosses.p1 Cysfra 2090612 XXHP Leptosporangiate Monilophytes Stewart.p1 Dicsco 2008883 NGTD Mosses.p1 Leuimm 2011157 WGTU Leptosporangiate Monilophytes.p1 Davfej 2008749 OQWW Leptosporangiate Monilophytes.p1 Mixspe 2160982 NWQC Liverworts.p1 Davfej 2008748 OQWW Leptosporangiate Monilophytes.p1 Leugla 2011848 RGKI Mosses.p1 Phlpse 2022784 ZQYU Leptosporangiate Monilophytes.p1 Leualb 2007960 VMXJ Mosses.p1 Polamo 2073221 YLJA Leptosporangiate Monilophytes.p1 Polhes 2014829 GYFU Leptosporangiate Monilophytes A type.p1 Polhes 2000663 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Cerpur 2007479 FFPD Mosses.p1 Polhes 2000662 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Scoaqu 2010376 BPSG Mosses.p1 Polhes 2014828 GYFU Leptosporangiate Monilophytes A type.p1 Scoaqu 2010377 BPSG Mosses.p1 Polhes 2014827 GYFU Leptosporangiate Monilophytes A type.p1 Polgly 2015570 CJNT Leptosporangiate Monilophytes.p1 Polhes 2022136 IXLH Leptosporangiate Monilophytes B type.p1 Physsp. 2003584 YEPO Mosses.p1 Ginbil Gb 18775 Staeri 2055522 KAWQ Cycadales.p1 Encbar 2086554 GNQG Cycadales.p1 Encstr 2004583 KEFD Mosses.p1 Larspe 2055149 WVWN Conifers.p1 Polcom 2012397 SZYG MossesEncstr gametophyte.p1 2014254 KEFD Mosses.p1 Psewil 2007984 IOVS Conifers.p1 Psewil 2007985 IOVS Conifers.p1 Timaus 2013283 ZQRI Mosses.p1 Piceng 2011566 AWQB Conifers.p1 Timaus 2007925 ZQRIPhypat Mosses.p1 Pp3c9 5820V3.1 Picabi MA 9476g0020 Pinpon 2013859 JBND Conifers.p1 AndrupDipfol 2095733 2073568 WOGB AWOI Mosses.p1 Mosses.p1 Pinpar 2007507 IIOL Conifers.p1 Tsuhet 2007504 GAMH Conifers.p1 Tetpel 2022131 HVBQ Mosses.p1 Notlon 2009610 AREG Conifers.p1 Keteve 2004881 JUWL Conifers.p1 Keteve 2004880 JUWL Conifers.p1 Atrang 2085405 ZTHV Mosses.p1 Keteve 2004882 JUWL Conifers.p1 Necdou 2017132 TMAJ Mosses.p1 Ararul 2065994 XTZO Conifers.p1 Necdou 2017133 TMAJ Mosses.p1 Agarob 2075858 MIXZ Conifers.p1 Parust 2039989 JZVE Conifers.p1 Cliden 2001961 MIRS Mosses.p1 Halbid 2056082 OWFC Conifers.p1 Lagfra 2014144 ZQWM Conifers.p1 FonantCalcor 2015548 2016340 DHWX TAVP Mosses.p1 Mosses.p1 Mancol 2009962 CDFR Conifers.p1 Pruand 2010792 EGLZ Conifers.p1 Pseele 2008921 QKQO Mosses.p1 Mictet 2074966 MHGD Conifers.p1 Ortlye 2016916 CMEQ Mosses.p1 Saxcon 2075857 QCGM Conifers.p1 Retmin 2071268 VGSX Conifers.p1 Plains 2010350 BGXB Mosses.p1 Daccom 2003298 FMWZ Conifers.p1 Timaus 2014499 ZQRI Mosses.p1 Daccom 2003299 FMWZ Conifers.p1 Cephar 2091333 WYAJ Conifers.p1 Cephar 2112378 NVGZ Conifers 2 samples combined.p1 Cerpur 2011004 FFPD Mosses.p1 Cephar 2011180 GJTI Conifers.p1 Dicsco 2102234 NGTD Mosses.p1 Cunlan 2021277 ZQVF Conifers 2 samples combined.p1 Racvar 2009800Phypat RDOO Pp3c7 Mosses.p1 26350V3.1 Cunlan 2016650 ESYX Conifers branch apex with needles.p1 Leualb 2131963 VMXJ Mosses.p1 Taicry 2000206 QSNJ Conifers.p1 Athcup 2065054 XIRK Conifers.p1 Physsp. 2014779 YEPO Mosses.p1 Metgly 2065476 NRXL Conifers.p1 Seqgig 2062549 QFAE Conifers Glaucum.p1 Seqsem 2006472 HBGV Conifers.p1 Glypen 2013257 OXGJ Conifers.p1 Sphrec 2009994Phypat UHLI Pp3c1 Mosses.p1 6050V3.1 Taxdis 2012792 FHST Conifers.p1 Sphfal Sphfalx0053s0128.1 Cryjap 2075963 DSXO Conifers.p1 Cryjap 2020484 GMHZ Conifers 2 samples combined.p1 Sphrec 2021113Sphfal Sphfalx0061s0058.1 UHLI Mosses.p1 100 Pappap 2085221 OVIJ Conifers.p1 Sphles 2016852Sphfal GOWD Sphfalx0061s0057.1 Mosses.p2 Auschi 2007522 YYPE Conifers.p1 100 98.2 Andrup 2095759 WOGB Mosses.p1 87.2 Piluvi 2064018 ETCJ Conifers.p1 88.6 99.1 81.4 Disarc 2003816 GKCZ Conifers.p1 100 Tetpel 2132038 HVBQ Mosses.p1 96.4 Calmac 2000176 RMMV Conifers March.p1 Dipfol 2010099 AWOI Mosses.p1 Calmac 2000177 RMMV Conifers March.p1 100 Atrang 2085025 ZTHV Mosses.p1 100 Thupli 2004998 VFYZ Conifers.p1 Scoaqu 2022317 BPSG Mosses.p1 Chalaw 2010678 AIGO Conifers.p1 Cupdup 2074948 QNGJ Conifers.p1

99.1 Caldec 2061671 FRPM Conifers.p1 95.8 Tetsp. 2009019 CGDN Conifers.p1 99.1 100 Plaori 2054512 BUWV Conifers.p1 98.2 99 Micdec 2057517 XQSG Conifers.p1 100 81.6 Ginbil Gb 09695 91.5 Retmin 2072970 VGSX Conifers.p1 99.7 Gnemon TnS000424613t04 98.2 100 Pintae PTA00070518 Psemen PME00008513 Psemen PME00068674 Pintae PTA00022232 100 Pinpin PPI00016556 99 100 100 99.9 Pinsyl PSY00011167 100 Ambtri evm 27.model.AmTr v1.0 scaffold00022.44 100 100 100 Tarhas lcl NW 010966665.1 XP 010551934.1 26281 99.9 99.9 81.3 100 100 Boestr Bostr.1460s0027.1 100 99.9 81.4 100 Aratha AT3G01840.1 100 97.1 96.9 81 100 96.6 100 98.7 100 Aralyr AL3G10290.t1 100 99.5 100 Arahal Araha.1138s0016.1 100 100 93.3 98.6 95.1 Carpap evm.model.supercontig 171.32 95.2 100 Betvul Bv7 166430 zjey.t1 100 95.2 100 Spiole Sp 207520 khcy.t1 99.5 100 Chequi AUR62025400-RA 95.9 93 100 92.4 100 100 100 Micdec 2057909 XQSG Conifers.p1 100 100 100 98 96.2 94.8 Citcle Ciclev10017541m 100 100 99.8 84.6 99.1 99.9 Citsin orange1.1g041830m Plaori 2055018 BUWV Conifers.p1 100 100 99.7 100 100 100 Fraexc FRAEX38873 v2 000229800.1 99.6 99.6 83.7 Tetsp. 2009481 CGDN Conifers.p1 100 100 100 100 97.8 Daucar DCAR 011313 Cupdup 2074398 QNGJ Conifers.p1 90.3 92.2 99.4 100 Solpen Sopen02g038660.1 97.8 100 Caldec 2003941 FRPM Conifers.p1 99.5 96.4 100 99.8

100 Sollyc Solyc02g094010.1.1 96.6 92 93.492.999.684.786.887 100 92.1 92.3 97.199.5 Thupli 2000750 VFYZ Conifers.p1 100 98.6 Nicben Niben101Scf03600g01003.1 100 99 99.2 88.3 Petaxi Peaxi162Scf00420g00445.1 Thudol 2011417 NKIN Conifers.p1 100 100 94 100 Datglo Datgl90S14487 Fokhod 2003348 UEVI Conifers.p1 82.1 100 Begfuc Begfu1135S16621 Fokhod 2003349 UEVI Conifers.p1 95.4 100 80.3 Begfuc Begfu1780S01665

Chalaw 2007429 AIGO Conifers.p1 100 94.6 91.5 99.8 99.7 Begfuc Begfu2538S10055 97.7 98.4 Auschi 2003050 YYPE Conifers.p1 98.7 99.8 Momcha lcl NW 019104493.1 XP 022134272.1 6360

90.8

Auschi 2003051 YYPE Conifers.p1 100 99.6 Cucmos CmoCh04G030840.1 86.5 100 100 99.8 99.5 100 100 100 99.4 Cucmax CmaCh04G029640.1 Piluvi 2003638 ETCJ Conifers.p1 99 99.6 86.5 100 Citlan Cla006516 Piluvi 2003639 ETCJ Conifers.p1 100 100 99 100 Lagsic Lsi03G003850.1 Pappap 2008963 OVIJ Conifers.p1 98.3 100 Calmac 2059243 RMMV Conifers March.p1 82.4 92.4 98.7 Cucsat evm.model.Chr2.2549 Cucmel MELO3C008203.2.1 Calgra 2145780 IFLI Conifers March.p1 86.1 92 100 90.4 100 100 Gosrai Gorai.012G087700.1 91.8 99.9 99.2 Neopan 2010242 JDQB Conifers.p1 100 100 Cepfol Cfol v3 07810 90.3 99.1 87.9 Manesc Manes.17G104300.1 Widced 2008011 AUDE Conifers.p1 97.5 90.3 100 Cryjap 2003966 DSXO Conifers.p1 87 95.8 100 97 98.1 Riccom 30190.m010954 Cryjap 2006170 GMHZ Conifers 2 samples combined.p1 90.5 100 97.3 Poptri Potri.T115100.1 Cryjap 2003965 DSXO Conifers.p1 99.1 Cryjap 2006171 GMHZ Conifers 2 samples combined.p1 80.7 100 100 100 Poptri Potri.001G332800.1 98 100 100 94.7 99.5 Distri Distr1581S05676 99.987.7 99.1 Zizjuj lcl NC 029687.1 XP 015893757.1 26005 Cryjap 2010895 HOUF Conifers leaf.p1 99.2 100 100 100 Zizjuj lcl NC 029687.1 XP 024932869.1 26006 Glypen 2048021 OXGJ Conifers.p1 Mornot L484 017618 100 97.1 94 Treori lcl JXTC01000045.1 PON95340.1 8863 Metgly 2011034 NRXL Conifers.p1 90.8 100 Athcup 2065854 XIRK Conifers.p1 97 100 Parand lcl JXTB01000122.1 PON61341.1 14720 100 100 100 100 95.9 100 Humlup HL.SW.v1.0.G042159.1 Cunlan 2089225 ESYX ConifersTaicry branch 2068771 apex QSNJ with Conifers.p1needles.p1 98.2 96.8 100 Humlup HL.SW.v1.0.G020335.1 99.7 99.9 100 Cunlan 2020950 ZQVF Conifers 2 samples combined.p1 100 Drydru Drydr361S03721 99.2 99.8 99.7 Prumum lcl NC 024129.1 XP 008231201.1 15437 Cunlan 2013666 OUOI Conifers.p1 100 80.2 100 99.5 100 Pruper Prupe.3G303700.1 Cephar 2018433 WYAJ Conifers.p1 99.6 Prudul Prudul26A025891P1 Cephar 2021706 NVGZ Conifers 2 samples combined.p1 97 100 96.6 Maldom MDP0000320123 Pyrbre lcl NW 008988240.1 XP 018506333.1 23449 Cephar 2013094 GJTI Conifers.p1 100 96.4 Pyrcom PCP023229.1 Amearg 2022109 IAJW Conifers.p1 90.4 100 100 100 99.6 92.3 100 Rubocc Bras G03822 Psechi 2002417 YLPM Conifers.p1 94.4 97.4 85.6 Roschi RchiOBHm Chr2g0175211 Ausspi 2012596 BTTS Conifers.p1 100 97.3 Potmic 27254 t 100 97.1 Fraves FvH4 6g53170.1 Taxcus 2000841 ZYAX Conifers.p1 98.9 94.6 Taxbac 2008087 WWSS Conifers.p1 99.294 95.9 Casmol augustus masked-scaffold05126-abinit-gene-0.4-mRNA-1 98.9 88 Alnglu Alngl73950S11992 Chalaw 2007223 AIGO Conifers.p1 100 98.2 Casgla Casgl668S05860 Sciver 2010223 YFZK Conifers.p1 100 92.1 99.1 Jugreg g47368.t1 Sciver 2010224 YFZK Conifers.p1 98.7 100 Jugreg g22863.t1 94.1 100 Wolnob 2004514 RSCE Conifers.p1 98.9 100 Jugreg g2818.t1 Wolnob 2004515 RSCE Conifers.p1 Cercan Cerca69S04390 Ararul 2003458 XTZO Conifers.p1 99.8 93 Mimpud Mimpu144933S06775 99.4 100 NFP Casaus Castanospermum01763-PA Agamac 2069409 ACWS Conifers.p1 89.4 95.9 99.9 Casaus Castanospermum21782-PA Agarob 2009321 MIXZ Conifers.p1 100 98.9 Nissch Nissc30641S08034 90.7 97.5 100 Faltax 2005371 PLYX Conifers 2 samples combined.p1 94.4 100 Arahyp arahy.Tifrunner.gnm1.ann1.13YX85.1 99.1 100 95.5 Arahyp arahy.Tifrunner.gnm1.ann1.0ZJG43.1 Faltax 2005372 PLYX Conifers 2 samples combined.p1 82.5 Lupang Lup013618.1 Faltax 2003761 QHBI Conifers A.p1 100 99.9 92 Faltax 2003763 QHBI Conifers A.p1 100 Lupang Lup013616.1 Faltax 2003762 QHBI Conifers A.p1 100 99.9 Tripra Tp57577 TGAC v2 mRNA39653 99.498.589.3 Lotjap Lj1g3v3834250.1 Daccom 2003339 FMWZ Conifers.p1 100 100 100 Cajcaj Ccajan 17424 Daccom 2003338 FMWZ Conifers.p1 100 99.6 Glymax Glyma.19G088300.1 Podrub 2000751 XLGK Conifers.p1 99.8 95.4 97.1 Glymax Glyma.16G059200.1 Podcor 2000074 SCEB Conifers.p1 87.2 Phavul Phvul.001G095500.1 100 92.5 Vigung Vigun01g067100.1 Retmin 2003860 VGSX Conifers.p1 86.9 99.8 100 Retmin 2003861 VGSX Conifers.p1 99.999.199 Vigrad Vradi0007s01320.1 10095.2 95.6 Vigang vigan.Vang0176s00310.1 Lepsp. 2012905 BBDD Conifers.p1 84.4 99.7 Ambtri evm 27.model.AmTr v1.0 scaffold00059.150 Mancol 2003979 CDFR Conifers.p1 95.7 93.9 100 99.9 Anacom Aco011559.1 Phyhyp 2069576 JRNA Conifers.p1 96.4 100 99.8 100 99.8 Musacu GSMUA Achr8T04890 001 Mictet 2009147 MHGD Conifers.p1 100 99.2 97.8 Orysat LOC Os03g13080.1 98.3 89.4 Mictet 2009148 MHGD Conifers.p1 100 96.2 100 Bradis Bradi1g69290.1 86.8 100 100 99.3 Horvul HORVU4Hr1G066170.1 Pruand 2004316 EGLZ Conifers.p1 95.1 Pruand 2004317 EGLZ Conifers.p1 100 100 100 Setita Seita.9G483300.1 97.497.710084.6 99.6 Zeamay Zm00008a035767 Sunama 2011087 KLGF Conifers.p1 92.7 93.2 100 100 Sorbic Sobic.001G449300.1 Halbid 2002399 OWFC Conifers.p1 100 100 Pintae PTA00045488 10098.9 98.5 Zeamay Zm00008a000827 Halbid 2002400 OWFC Conifers.p1 99.2 Helann HanXRQChr04g0128071 99.499.9 100 100 Daucar DCAR 007516 Pinrad 2003784 DZQM Conifers.p1 99.9 100 Daucar DCAR 010965 99.999.9 Pinjef 2002240 MFTM Conifers.p1 99.9 99.4 Fraexc FRAEX38873 v2 000211980.1 99.990.7 100 99.2 Petaxi Peaxi162Scf00019g00153.1 Pinpon 2004002 JBND Conifers.p1 99.5 89.2 Nicben Niben101Scf02215g05018.1 Pinjef 2002241 MFTM Conifers.p1 87.4 92.899.9 100 99.9 Nicben Niben101Scf14594g00003.1 Pinrad 2003785 PinpinDZQM PPI00013093 Conifers.p1 99.9 86.4 100 Capann CA02g07950 Pinpon 2004005Pinsyl JBND PSY00018880 Conifers.p1 100 95.1 100 Solpen Sopen02g015720.1 98.4 Sollyc Solyc02g065520.1.1 95.2 87.5 Riccom 29250.m000241 99.9 Pinpar 2005038Picabi MAIIOL 475682g0010 Conifers.p1 98.7 Manesc Manes.13G134800.1 Psemen PME00022094 100 Manesc Manes.13G134800.2 98.9 100 Psemen PME00052521 Poptri Potri.007G032300.1 99.9 Poptri Potri.005G128400.1 89 92.5 99.8 99.4 100 Poptri Potri.014G112500.1 Psewil 2009433Pintae IOVS PTA00022352 Conifers.p1 Citcle Ciclev10027414m Pinpin PPI00013455 100 Citsin orange1.1g047629m Larspe 2005778 WVWN Conifers.p1 Carpap evm.model.supercontig 15.133 100 99.8 Picabi MA 793381g0010 98.2 89.5 Thecac Thecc1EG000472t1 99.8 99.4 100 Gosrai Gorai.007G051800.1 100 100 Cercan Cerca46S03403 99.5 Pinjef 2002243 MFTM Conifers.p1 90.3 100 Mimpud Mimpu3206S02941 99.9 99.9 100 Pinjef 2002242 MFTM Conifers.p1 94.7 87.2 100 Chafas Chafa2039S01524 Pinpin PPI00012441 100 100 Chafas Chafa2145S31554 99.2 92.9 89.4 Pinrad 2003786 DZQMPinsyl Conifers.p1PSY00017883 100 96.2 Mimpud Mimpu11398S05491 Pinpon 2004004 JBND Conifers.p1 100 100 90.8 Chafas Chafa95762S05569 Picsit PSI00018913 92.896 97.9 Chafas Chafa95762S13127 Casaus Castanospermum15526-PA Psemen PME00011702 99.9 100 Casaus Castanospermum20155-PA Pinpar 2005039 IIOL Conifers.p1 99.7 100 100 86.2 99.8 Lotjap Lj4g3v0912430.1 99.9 98.7 98.9 99.5 Lotjap Lj0g3v0133269.1 100 99.8 93.7 Cicari Ca 20738.1 Psewil 2006520 IOVS Conifers.p1 99.9 93.5 100 100 Medtru MtrunA17 Chr8g0373711 90 100 100 Trisub lcl DF973128.1 GAU12978.1 2036 Larspe 2003039 WVWN Conifers.p1 84 Tripra Tp57577 TGAC v2 mRNA26301 Notlon 2006882 AREG Conifers.p1 99.9 85.2 98.2 94 Tripra Tp57577 TGAC v2 mRNA32615 Notlon 2006881 AREG Conifers.p1 95.9 100 Lupang Lup012981.1 97.1 Arahyp arahy.Tifrunner.gnm1.ann1.VID2UW.1 Tsuhet 2003885 GAMH Conifers.p1 100 97.1 99.9 98.3 Aradur Aradu.AXP1M Tsuhet 2003883 GAMH Conifers.p1 99.7 Abilas 2004664 VSRH Conifers.p1 100 99.9 Araipa Araip.NL2P7 100 100 Arahyp arahy.Tifrunner.gnm1.ann1.A8RCAK.1 Abilas 2004663 VSRH Conifers.p1 96.6 Lotjap Lj2g3v1828350.1 Psemen PME00017722 90.1 100 Cicari Ca 22860.1 Pseama 2000899 AQFM Conifers.p1 100 100 100 100 Medtru MtrunA17 Chr5g0403371 Larspe 2000879 WVWN Conifers.p1 98 Tripra Tp57577 TGAC v2 mRNA35648 100 Trisub lcl DF973170.1 GAU17450.1 6508 Larspe 2000878 WVWN Conifers.p1 97.9 100 100 96.9 Trisub lcl DF973170.1 GAU17451.1 6509 Psewil 2001132Picabi IOVS MA Conifers.p1 892990g0010 98.8 Cajcaj Ccajan 12621 Pinpin PPI00017071 Glymax Glyma.11G063100.1 Notlon 2006922 AREGPinsyl Conifers.p1 PSY00018322 100 Ginbil Gb 01118 100 100 100 Glymax Glyma.01G179100.1 Tsuhet 2004636 GAMH Conifers.p1 90.9 Phavul Phvul.002G025500.1 Ginbil Gb 20450 100 86.9 Vigung Vigun02g136400.1 Ginbil Gb 20451 100 81.2 100 Vigang vigan.Vang2114s00010.1 100 90.784.298.5 Piceng 2000775 AWQB Conifers.p1 98.4 97.7 99.9 Vigrad Vradi11g05290.1

100 Vigang vigan.Vang07g00280.1 97 Pinpar 2000019 IIOL Conifers.p1 99.6 Casmol augustus masked-scaffold06299-abinit-gene-0.3-mRNA-1 100 99.9 Jugreg g46631.t1 98.7

100 100 Casgla Casgl13S03438 99.4 Alnglu Alngl1669S01357 100 99.6 Zizjuj lcl NC 029686.1 XP 015890225.1 22227 98.3 Distri Distr783S28046

Cycmic CMI00002534 100 99.7 Mornot L484 009156 Treori lcl JXTC01000004.1 POO02616.1 1603 99.9 100 Encbar 2000794 GNQG Cycadales.p1 100 100 Parand lcl JXTB01000530.1 PON37436.1 32027

87.3 Rubocc Bras G00967 Encbar 2000796 GNQG Cycadales.p1 100 Encbar 2000795 GNQG Cycadales.p1 97 100 Roschi RchiOBHm Chr2g0102941 Staeri 2056780 KAWQ Cycadales.p1 Potmic 30581 t Fraana FAN iscf00239457.1.g00001.1 100 Dioedu 2010635 WLIC Cycadales.p1 99.7 100 100 Fraves FvH4 1g14270.1

100 Pruand 2010068 EGLZ Conifers.p1 100 Fraana FAN iscf00087845.1.g00001.1 100 96.9 100 Drydru Drydr368S03767 100 Maldom MDP0000770390 Sunama 2094121 KLGF Conifers.p1 Pyrbre lcl NW 008988383.1 XP 009379171.1 30364 Phyhyp 2068961 JRNA Conifers.p1 100 99.9 87.1 Parust 2006747 JZVE Conifers.p1 100 Pyrcom PCP020476.1 Pruavi Pav sc0000348.1 g980.1.mk Halbid 2012344 OWFC Conifers.p1 100 Prumum lcl NC 024133.1 XP 008241874.1 25283 Mictet 2073405 MHGD Conifers.p1 99.2 Pruper Prupe.7G147300.1 99.9 Prudul Prudul26A026986P1 Podrub 2011318 XLGK Conifers.p1Pintae PTA00020261 100 Casmol snap masked-scaffold05279-abinit-gene-0.7-mRNA-1 98 97.8 Datglo Datgl376S09111 82.7 Parand lcl JXTB01000530.1 PON37437.1 32028 AgamacAgarob 2069137 2010136 ACWS MIXZ Conifers.p1 Conifers.p1 93.6 Drydru Drydr368S03774

Ararul 2011659 XTZO Conifers.p1 100 99.2 Pinsyl PSY00023251 99.7 Drydru Drydr368S11007 Plaori 2006644 BUWV Conifers.p1 96.9 99.8 Pruavi Pav sc0000348.1 g990.1.mk Ginbil Gb 09694 Prumum lcl NC 024133.1 XP 008241875.1 25284 Tetsp. 2068706 CGDN Conifers.p1Psemen PME00017125 Prudul Prudul26A021693P1 Pruper Prupe.7G147400.1 Metgly 2061438 NRXL Conifers.p1 Datglo Datgl978S15045 Picabi MA 97722g0010 Momcha lcl NW 019104492.1 XP 022132556.1 5170 Cucmax CmaCh07G007500.1 Pinpon 2004003 JBND Conifers.p1 Cucpep Cp4.1LG19g11650.1 Cycmic CMI00000420 Cucmos CmoCh07G007720.1 Pinrad 2011004 DZQM Conifers.p1 Citlan Cla008512 Lagsic Lsi01G010490.1 Cucmel MELO3C007495.2.1 Cucsat evm.model.Chr6.2872 Abilas 2057606 VSRH Conifers.p1Riccom 29844.m003180 Datglo Datgl376S09112 Cepfol Cfol v3 13087 Begfuc Begfu1494S01050 Momcha lcl NW 019104546.1 XP 022149487.1 19910 Cucmos CmoCh02G005610.1 Manesc Manes.15G035700.1Poptri Potri.008G160600.1 Cucmax CmaCh02G005490.1 Cucpep Cp4.1LG05g11270.1 Poptri Potri.010G078700.1 Lagsic Lsi10G005780.1 Citlan Cla020178 Cucsat evm.model.Chr2.1440 Cucmel MELO3C020886.2.1 Ephsin 2002197 VDAO Gnetales.p1 Gosrai Gorai.011G164600.1 Jugreg g18993.t2 Welmir 2062692 TOXE Gnetales.p1 Jugreg g18993.t1 Gnemon 2012639 GTHK Gnetales.p1 Gosrai Gorai.006G245600.1Citcle Ciclev10004551m Gnemon TnS000693017t06 Thecac Thecc1EG020764t1Casgla Casgl96S03012 Ambtri evm 27.model.AmTr v1.0 scaffold00001.394 Citsin orange1.1g037224m Zosmar Zosma88g00710.1 Casgla Casgl96S03013 Aposhe lcl KZ451942.1 PKA60161.1 7340 Dencat lcl NW 021319320.1 XP 020701085.1 16628 Musacu GSMUA Achr2T00900 001 Musacu GSMUA Achr5T10270 001 Anacom Aco016632.1 Citlan Cla021574 Setita Seita.1G273200.1 Sorbic Sobic.004G281300.1 Zeamay Zm00008a022641 Alnglu Alngl108585S13721 Orysat LOC Os02g45750.1 Bradis Bradi3g51790.1 Horvul HORVU0Hr1G023200.1 Nelnuc NNU 14293-RA Nelnuc NNU 16517-RA Diacar Dca2263.1 Querob Qrob P0035590.2 Diacar Dca60732.1 Diacar Dca33219.1 Spiole Sp 038280 etzk.t1 Lagsic Lsi05G016580.1 ChequiAUR62025429-RA ChequiAUR62008809-RA ChequiAUR62025432-RA ChequiAUR62008808-RA Faltax 2011937 PLYX Conifers 2 samples combined.p1 ChequiAUR62025430-RA Helann HanXRQChr03g0092501 Helann HanXRQChr13g0424591 Fraexc FRAEX38873 v2 000181550.1 Daucar DCAR 002357 Daucar DCAR 030708 Petaxi Peaxi162Scf01416g00014.1 Nicben Niben101Scf00415g00002.1 Nicben Niben101Scf04941g01011.1 Capann CA03g05970 Sollyc Solyc09g083210.2.1 Solpen Sopen09g032130.1 Solpen Sopen09g032120.1 CucsatCucmel evm.model.Chr3.1252 MELO3C006481.2.1 Begfuc Begfu1S23843 Potmic 3288 t Cucmax CmaCh14G017710.1 Cucmos CmoCh14G018070.1BegfucDatglo Begfu577S38287 Datgl691S33631 Cucmax CmaCh06G013490.1 Cucmos CmoCh06G013620.1

Prudul Prudul26A022636P2 Prudul Prudul26A022636P1Pruper Prupe.1G027000.1 Pyrcom PCP034881.1 Prudul Prudul26A022636P3

Rubocc Bras G13577 Maldom MDP0000135244 Fraves FvH4 4g02230.1 Mornot L484 001673

Cicari Ca 11011.1

Cajcaj Ccajan 38935 Araipa Araip.0T4FD Distri Distr1629S15705

Vigrad Vradi08g00100.1

Aradur Aradu.S0HMQ Lupang Lup019655.1

Pruavi Pav sc0000998.1 g140.1.mk Lotjap Lj0g3v0102179.1

Drydru DrydrC1210588S14895 Vigung Vigun07g001200.1

Roschi RchiOBHm Chr4g0389541 Nissch Nissc4486S23735 Cercan Cerca383S23112 Humlup HL.SW.v1.0.G037406.1 Phavul Phvul.007G280200.1

Chafas Chafa1352S15329 Vigang vigan.Vang06g25690.1 Glymax Glyma.02G000400.1

Sollyc Solyc09g083200.2.1

Mimpud Mimpu1152S14067

Momcha lcl NW 019104533.1 XP 022147269.1 18099

Medtru MtrunA17 Chr5g0418011 Prumum lcl NC 024127.1 XP 008224192.1 8837 Prumum lcl NC 024127.1 XP 008224193.1 8838

Casaus Castanospermum27591-PA

Tripra Tp57577 TGAC v2 mRNA23252 Pyrbre lcl NW 008988492.1 XP 009337287.2 34256 Treori lcl JXTC01000243.1 PON78074.1 23915Zizjuj lcl NC 029681.1 XP 015876533.1 7974 Parand lcl JXTB01000445.1 PON40162.1 29932

Arahyp arahy.Tifrunner.gnm1.ann1.35XI12.1

Arahyp arahy.Tifrunner.gnm1.ann1.2WY12S.1 Zizjuj lcl NW 015454033.1 XP 015868460.1 39037

Tree scale: 0.1 Supplementary Figure 27: Maximum likelihood tree of SEC.

Hupsel 2023794YHZW Lycophytes 2 samples combined.p1

Phacar 2119542 WCZB Hornworts gametophyte.p1

Phacar 2024480 RXRQ Hornworts sporophyte.p1

Phacar 2137181 RXRQ Hornworts sporophyte.p1

Hupsel 2019753 NYBX LycophytesA.p1

Selapo 2008564 LGDQ Lycophytes.p1

Hupsel 2015694 GTUO Lycophytes.p1

Hupmyr 2060712 CBAE Lycophytes.p1 Selaca 2042064 ZYCD Lycophytes.p1 Hupluc 2007956 GKAG Lycophytes.p1 Hupluc 2007957 GKAG Lycophytes.p1

Selsel 2043256 KUXM Lycophytes.p1

Selkra 2040585 ZFGK Lycophytes.p1 Denobs 2070176 XNXF Lycophytes.p1Lycdeu 2081851 PQTO Lycophytes.p1 Selwal 2178810 JKAA Lycophytes.p1 Lycann 2011446 ENQF Lycophytes.p1 Selsta 2053579 ZZOL Lycophytes.p1

Selwil 2000926 KJYC Lycophytes.p1

Psecar 2019837 UPMJ Lycophytes.p1 ABIJ Lycophytes.p2 Sellep 2003266

Dipdig 2069160 WAFT Lycophytes.p1 Phydru 2128611 ZZEI Lycophytes.p1 Isoesp. 2073487 PYHZ Lycophytes.p1 Lycapp 2017887 ULKT Lycophytes.p1

Isoesp. 2004013 PYHZ Lycophytes.p1 Isoteg 2097308 PKOX Lycophytes.p1

Isoteg 2097540 PKOX Lycophytes.p1 Marpal 2007902 LFVP Liverworts 2 samples combined.p1 Selsel 2043104 KUXM Lycophytes.p1 Trelac 2090443 FITN Liverworts.p1 Selwal 2177355 JKAA Lycophytes.p1 Selwil 2048475 KJYC Lycophytes.p1 Trelac 2000770 FITN Liverworts.p1 Notaen 2003416 DXOU Hornworts.p1 Notaen 2003415 DXOU Hornworts.p1 Notvin 2016959 TCBC Hornworts.p1 Notvin 2016960 TCBC Hornworts.p1 Megfla 2012011 UCRN Hornworts.p2

Marpal 2000492 HMHL Liverworts non mycorrizal.p1 Scanem 2012389 IRBN Liverworts.p1 Scanem 2012390 IRBN Liverworts.p1 Parhal 2056858 FAJB Hornworts.p1 Odopro 2005690 YBQN Liverworts.p1 Barbar 2018997 OFTV Liverworts.p1

Scanem 2164142 IRBN Liverworts.p1 Baztri 2014914 WZYK Liverworts.p1 Odopro 2129281 YBQN Liverworts.p1Calfis 2018942 RTMU Liverworts.p1 Mixspe 2160292 NWQC Liverworts.p1Barbar 2013120 OFTV Liverworts.p1

Schisp. 2104933 LGOW Liverworts.p1 Baztri 2019129 WZYK Liverworts.p1 Marpal 2067349 IHWO Liverworts mycorrizal.p1 Pornav 2000643 KRUQ Liverworts.p1 Pornav 2000646 KRUQ Liverworts.p1Calfis 2012266 RTMU Liverworts.p1 Pornav 2000645 KRUQ Liverworts.p1

Porpin 2149488 UUHD Liverworts.p1 Radlin 2006402 BNCU Liverworts.p1 Metcra 2006813Radlin 2006403 NRWZ Liverworts.p1 BNCU Liverworts.p1 Metcra 2006814 NRWZ Liverworts.p1

Frusp. 2139118 TGKW Liverworts.p1

Fruspp 2137897 CHJJ Liverworts.p1 Selmoe 111930

Pelepi 2091382 PIUF Liverworts.p1 Pelnee 2113009 JHFI Liverworts.p1

Selmoe 412840 Marpol 2004715 JPYU Liverworts.p1 Marpol 2004716 JPYU Liverworts.p1

Ricnat 2036971 WJLO Liverworts.p1 Concon 2002655 ILBQ Liverworts.p1 Marema 2004835 TFYI Liverworts.p1 Sphtex 2044368 HERT Liverworts.p1 Marpal scaff1787 FGenesh3.1 Luncru 2075512 TXVB Liverworts.p1

BlaspNW c323182 g1 i2 m.56846 ThudelBlaspNW 2002700 c323182EEMJ Mosses.p1 g1 i1 m.56843 Marpol Mapoly0033s0132.1

scr2178UPMJ Lycophytes.p1 Psecar 2013778 Lycapp 2003095 ULKT Lycophytes.p1 Psecar 2082170 UPMJ Lycophytes.p1 Psecar 2081873 UPMJ Lycophytes.p1 Dipdig 2011109 WAFT Lycophytes.p1 Lycann 2015987 ENQF Lycophytes.p1 Lycdeu 2081222 PQTO Lycophytes.p1 Denobs 2003544 XNXF Lycophytes.p1 Thudel 2002701 EEMJ Mosses.p1 Denobs 2003545 XNXF Lycophytes.p1 Denobs 2003543 XNXF Lycophytes.p1 Hupsqu 2005091 GAON Lycophytes.p1 Hupmyr 2014469 CBAE Lycophytes.p1 Phydru 2127653 ZZEI Lycophytes.p1 Hupsel 2014553 NYBX Lycophytes A.p1 Hupsel 2006340 YHZW Lycophytes 2 samples combined.p1 Stesub 2066808 LNSF Mosses.p1 Hupsel 2004065 GTUO Lycophytes.p1 Phydru 2127819 ZZEI Lycophytes.p1 Hupmyr 2011792 CBAE Lycophytes.p1 Hupsqu 2005654 GAON Lycophytes.p1 Loebre 2009193 WSPM Mosses.p1 Hupluc 2004928 GKAG Lycophytes.p1 Hupluc 2004929 GKAG Lycophytes.p1 Hupsel 2016524 NYBX Lycophytes A.p1 Hupsel 2004067 GTUO Lycophytes.p1 Cliden 2083300 MIRS Mosses.p1 Hupsel 2004063 GTUO Lycophytes.p1 Anocla 2000557 VBMM Mosses.p1 Equhye 2008613 JVSZ Eusporangiate Monilophytes.p1 Scedis 2008058 EEAQ Eusporangiate Monilophytes.p1 Botvir 2101998 BEGM Eusporangiate Monilophytes.p1 Psinud 2001832 QVMR Eusporangiate Monilophytes.p1 Necdou 2007590 TMAJ Mosses.p1 Ophvul 2011565 QHVS Eusporangiate Monilophytes leaf.p1 Ophpet 2022133 WTJG Eusporangiate Monilophytes.p1 Botvir 2002049 BEGM Eusporangiate Monilophytes.p1 Scedis 2008057 EEAQ Eusporangiate Monilophytes.p1 Scedis 2008059 EEAQ Eusporangiate Monilophytes.p1 Osmjav 2077598 VIBO Leptosporangiate Monilophytes.p1 Osmsp. 2005214 UOMY Leptosporangiate Monilophytes gametophyte.p1 Calcor 2019374 TAVP Mosses.p1 Osmsp. 2005213 UOMY Leptosporangiate Monilophytes gametophyte.p1 Leubra 2097497 ZACW Mosses.p1 Hymbiv 2007194 QIAD Leptosporangiate Monilophytes.p1 Hymbiv 2007903 QIAD Leptosporangiate Monilophytes.p1 Anoatt 2001907Leujul QMWB 2164648 Mosses.p1 IGUH Mosses.p1 Dipcon 2012678 MEKP Leptosporangiate Monilophytes.p1 Anetom 2008176 CQPW Leptosporangiate Monilophytes.p1 Lygjap 2008563 PBUU Leptosporangiate Monilophytes.p1 Anetom 2000908 CQPW Leptosporangiate Monilophytes.p1 Anetom 2000907 CQPW Leptosporangiate Monilophytes.p1 Rhyser 2003699 JADL Mosses.p1 Anetom 2000906 CQPW Leptosporangiate Monilophytes.p1 Plajap 2025509 UWOD Leptosporangiate Monilophytes.p1 PseeleRhyser 2048990 2003700 QKQO JADL Mosses.p1 Mosses.p1 Culmac 2016909 PNZO Leptosporangiate Monilophytes.p1 Culmac 2016908 PNZO Leptosporangiate Monilophytes.p1 Fonant 2006807 DHWX Mosses.p1 Cyaspi 2018193 GANB Leptosporangiate Monilophytes.p1 Thyele 2122951 EWXK Leptosporangiate Monilophytes.p1 Fonant 2006806 DHWX Mosses.p1 Pilglo 2086157 KIIX Leptosporangiate Monilophytes.p1 Salcuc Sacu v1.1 s0194.g025408 Linlin 2017825 NOKI Leptosporangiate Monilophytes.p1 Linmic 2054208 YIXP Leptosporangiate Monilophytes.p1 Ortlye 2003178 CMEQ Mosses.p1 Dendav 2046060 MTGC Leptosporangiate Monilophytes.p1 Pittri 2003382 UJTT Leptosporangiate Monilophytes.p1 AulhetOrtlye 2005362 2003179 WNGH CMEQ Mosses.p1 Mosses.p1 Ptevit 2012973 POPJ Leptosporangiate Monilophytes.p1 Roscap 2001499 XWHK Mosses.p1 Pteens 2011006 FLTD Leptosporangiate Monilophytes.p1 Roscap 2001498 XWHK Mosses.p1 Cryacr 2005463 WQML Leptosporangiate Monilophytes.p1 Adirad 2059867 BMJR Leptosporangiate Monilophytes.p1 Adiale 2004920 WCLG Leptosporangiate Monilophytes.p1 Vitlin 2014136 SKYV Leptosporangiate Monilophytes.p1 Bryarg 2008169 JMXW Mosses.p1 Vitapp 2013555 NDUV Leptosporangiate Monilophytes.p1 Argniv 2008115 XDDT Leptosporangiate Monilophytes.p1 Myrruf 2003920 GSXD Leptosporangiate Monilophytes.p1 Plains 2078798 BGXB Mosses.p1 Notmon 2007503 YCKE Leptosporangiate Monilophytes.p1 Phifon 2008581 ORKS Mosses.p1 Parcor 2072415 ZXJO Leptosporangiate Monilophytes.p1 Hedcil 2048186 YWNF Mosses.p1 Gagari 2010850 DCDT Leptosporangiate Monilophytes.p1 Didtru 2034502 RFRB Leptosporangiate Monilophytes.p1 Phygro 2016394 ORJE Leptosporangiate Monilophytes.p1 Leugla 2003403 RGKI Mosses.p1 Phlpse 2014108 ZQYU Leptosporangiate Monilophytes.p1 Leualb 2128436 VMXJ Mosses.p1 Polgly 2077697 CJNT Leptosporangiate Monilophytes.p1 Polhes 2021112 GYFU Leptosporangiate Monilophytes A type.p1 Leugla 2003404 RGKI Mosses.p1 Polhes 2025953 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 RacvarDicsco 2011959 2011307 RDOO NGTD Mosses.p1 Mosses.p1 Polamo 2071304 YLJA Leptosporangiate Monilophytes.p1 Polhes 2000041 IXLH Leptosporangiate Monilophytes B type.p1 Racvar 2011961 RDOO Mosses.p1 Polhes 2000040 IXLH Leptosporangiate Monilophytes B type.p1 Racvar 2011960 RDOO Mosses.p1 Leuimm 2074147 WGTU Leptosporangiate Monilophytes.p1 Bolrep 2020008 JBLI Leptosporangiate Monilophytes.p1 Racelo 2075855 ABCD Mosses.p1 Theacu 2010413 MROH Leptosporangiate Monilophytes.p1 Woosco 2005221 YJJY Leptosporangiate Monilophytes.p1 Physsp. 2080583 YEPO Mosses.p1 Wooilv 2076298 YQEC Leptosporangiate Monilophytes.p1 Deplob 2000989 FCHS Leptosporangiate Monilophytes crenata.p1 Dipwic 2003480 UFJN Leptosporangiate Monilophytes.p1 Athfil 2007656 URCP Leptosporangiate Monilophytes.p1 Encstr 2059662 KEFD Mosses.p1 Blespi 2097003 VITX Leptosporangiate Monilophytes.p1 Timaus 2012422 ZQRI Mosses.p1 Blespi 2025335 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Stesub 2069022 LNSF Mosses.p1 Gymdry 2079983 HEGQ Leptosporangiate Monilophytes.p1 Thudel 2037993 EEMJ Mosses.p1 Aspnid 2014125 PSKY Leptosporangiate Monilophytes.p1 Necdou 2016596 TMAJ Mosses.p1 Cysuta 2019277 HNDZ Leptosporangiate Monilophytes.p1 Phypat Pp3c6 12580V3.1 Cysfra 2001093 LHLE Leptosporangiate Monilophytes.p1 Cysree 2011075 RICC Leptosporangiate Monilophytes.p1 AnoclaCalcor 2051692 2000701 VBMM TAVP Mosses.p1 Mosses.p1 Cysfra 2087261 XXHP Leptosporangiate Monilophytes Stewart.p1 Cyspro 2004156 YOWV Leptosporangiate Monilophytes.p1 Cysfra 2017258 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 LeubraLeujul 2097834 2010778 ZACW IGUH Mosses.p1 Mosses.p1 Lygjap 2007166 PBUU Leptosporangiate Monilophytes.p1 Pseele 2048573 QKQO Mosses.p1 Anetom 2020096 CQPW Leptosporangiate Monilophytes.p1 Fonant 2005891 DHWX Mosses.p1 Anetom 2020095 CQPW Leptosporangiate Monilophytes.p1 Pilglo 2009010 KIIX Leptosporangiate Monilophytes.p1 Bryarg 2004385 JMXW Mosses.p1 Linlin 2011751 NOKI Leptosporangiate Monilophytes.p1 Bryarg 2004386 JMXW Mosses.p1 Linmic 2056021 YIXP Leptosporangiate Monilophytes.p1 Roscap 2005351 XWHK Mosses.p1 Salcuc Sacu v1.1 s0132.g022136 Salcuc Sacu v1.1 s0087.g018457 Plains 2078784 BGXB Mosses.p1 Azocar 2001191 CVEG Leptosporangiate Monilophytes.p1 Ortlye 2006654 CMEQ Mosses.p1 Azofil Azfi s0024.g020391 Aulhet 2085714 WNGH Mosses.p1 Cyaspi 2069778 GANB Leptosporangiate Monilophytes.p1 Thyele 2018915 EWXK Leptosporangiate Monilophytes.p1 Phifon 2010627 ORKS Mosses.p1 Plajap 2000336 UWOD Leptosporangiate Monilophytes.p1 Plajap 2000337 UWOD Leptosporangiate Monilophytes.p1 Hedcil 2010164 YWNF Mosses.p1 Culmac 2010054 PNZO Leptosporangiate Monilophytes.p1 Synpri 2013172 GRKU Mosses.p1 Culmac 2010056 PNZO Leptosporangiate Monilophytes.p1 Dicsco 2011207 NGTD Mosses.p1 Culmac 2010055 PNZO Leptosporangiate Monilophytes.p1 Cerpur 2056025 FFPD Mosses.p1 Linmic 2010934 YIXP Leptosporangiate Monilophytes.p1 Linlin 2003407 NOKI Leptosporangiate Monilophytes.p1 Leugla 2009755 RGKI Mosses.p1 Linlin 2003406 NOKI Leptosporangiate Monilophytes.p1 ScoaquLeualb 2087907 2128772 BPSG VMXJ Mosses.p1 Mosses.p1 Dendav 2000565 MTGC Leptosporangiate Monilophytes.p1 Dendav 2000564 MTGC Leptosporangiate Monilophytes.p1 Racvar 2117636 RDOO Mosses.p1 Pittri 2025063 UJTT Leptosporangiate Monilophytes.p1 Pteens 2009968 FLTD Leptosporangiate Monilophytes.p1 Polcom 2004518 SZYG Mosses gametophyte.p1Timaus 2015810 ZQRI Mosses.p1 Ptevit 2008349 POPJ Leptosporangiate Monilophytes.p1 Encstr 2004228 KEFD Mosses.p1 Cryacr 2067651 WQML Leptosporangiate Monilophytes.p1 Encstr 2004229 KEFD Mosses.p1 Myrruf 2004569 GSXD Leptosporangiate Monilophytes.p1 Gagari 2075243 DCDT Leptosporangiate Monilophytes.p1 Physsp. 2075695 YEPO Mosses.p1 Notmon 2005390 YCKE Leptosporangiate Monilophytes.p1 Vitlin 2064311 SKYV Leptosporangiate Monilophytes.p1 Buxaph 2009985 HRWG Mosses.p1 Vitapp 2103106 NDUV Leptosporangiate Monilophytes.p1 Dipfol 2071946 AWOI Mosses.p1 Adirad 2060164 BMJR Leptosporangiate Monilophytes.p1 Atrang 2017047 ZTHV Mosses.p1 Adiale 2010996 WCLG Leptosporangiate Monilophytes.p1 Phypat Pp3c27 4100V3.1 Aspnid 2008006 PSKY Leptosporangiate Monilophytes.p1 Asppla 2061890 KJZG Leptosporangiate Monilophytes.p1 AndrupAtrang 2014937 2005255 WOGB ZTHV Mosses.p1 Mosses.p1 Didtru 2000268 RFRB Leptosporangiate Monilophytes.p1 Polacr 2073455 FQGQ Leptosporangiate Monilophytes.p1 Bolrep 2016398 JBLI Leptosporangiate Monilophytes.p1 Sphrec 2018799 UHLI Mosses.p1 Leuimm 2009333 WGTU Leptosporangiate Monilophytes.p1 Sphrec 2018798 UHLI Mosses.p1 Davfej 2028563 OQWW Leptosporangiate Monilophytes.p1 Sphles 2019252 GOWD Mosses.p1 Plepol 2012430 UJWU Leptosporangiate Monilophytes dehydrating fronds.p1 Phygro 2019834 ORJE Leptosporangiate Monilophytes.p1 Polamo 2071449 YLJA Leptosporangiate Monilophytes.p1 Sphrec 2092821 UHLI Mosses.p1 Polhes 2007369 GYFU Leptosporangiate Monilophytes A type.p1 Sphpal 2032412 SphfalRCBT Mosses.p1Sphfalx0027s0014.1 Polhes 2007368 GYFU Leptosporangiate Monilophytes A type.p1 Sphles 2019251 GOWD Mosses.p1 Polhes 2007370 GYFU Leptosporangiate Monilophytes A type.p1 Sphfal Sphfalx0008s0180.1 Polhes 2135024 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Taklep 2003911 SKQD Mosses.p3 Polhes 2007417 IXLH Leptosporangiate Monilophytes B type.p1 Taklep 2003910 SKQD Mosses.p1 Polgly 2000833 CJNT Leptosporangiate Monilophytes.p1 Taklep 2010964 SKQD Mosses.p1 Polgly 2000832 CJNT Leptosporangiate Monilophytes.p1 Thudel 2038986 EEMJ Mosses.p1 Polgly 2000831 CJNT Leptosporangiate Monilophytes.p1 Theacu 2010643 MROH Leptosporangiate Monilophytes.p1 Stesub 2068340 LNSF Mosses.p1 Deplob 2005257 FCHS Leptosporangiate Monilophytes crenata.p1 LeubraCliden 2014850 2086552 ZACW MIRS Mosses.p1 Mosses.p1 Woosco 2010814 YJJY Leptosporangiate Monilophytes.p1 98.1 Wooilv 2001079 YQEC Leptosporangiate Monilophytes.p1 Wooilv 2001078 YQEC Leptosporangiate Monilophytes.p1 LoebreLeujul 2001371 2013650 WSPM IGUH Mosses.p1 Mosses.p1 Hompyc 2009288 OCZL Leptosporangiate Monilophytes.p1 Anocla 2010571 VBMM Mosses.p1 Onosen 2041532 HTFH Leptosporangiate Monilophytes.p1 Dipwic 2014596 UFJN Leptosporangiate Monilophytes.p1 Rhyser 2046969 JADL Mosses.p1 Necdou 2182116 TMAJ Mosses.p1 Athfil 2014768 URCP Leptosporangiate Monilophytes.p1 Anoatt 2060351 QMWB Mosses.p1 Blespi 2015480 VITX Leptosporangiate Monilophytes.p1 Blespi 2014586 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Pseele 2048777 QKQO Mosses.p1 Gymdry 2014892 HEGQ Leptosporangiate Monilophytes.p1 Fonant 2012526 DHWX Mosses.p1 Cysree 2005027 RICC Leptosporangiate Monilophytes.p1 Tetpel 2129410 HVBQ Mosses.p1 Cysree 2005028 RICC Leptosporangiate Monilophytes.p1 Aulhet 2088505 WNGH Mosses.p1 Cysfra 2001203 LHLE Leptosporangiate Monilophytes.p1 Roscap 2047959 XWHK Mosses.p1 Cysfra 2088826 XXHP Leptosporangiate Monilophytes Stewart.p1 Cysfra 2006729 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Bryarg 2001474 JMXW Mosses.p1 Cysfra 2006731 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Plains 2008997 BGXB Mosses.p1 Cyspro 2001318 YOWV Leptosporangiate Monilophytes.p1 Phifon 2057840 ORKS Mosses.p1 Cysfra 2006730 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Hedcil 2008818 YWNF Mosses.p1 Gnemon 2012850 GTHK Gnetales.p1 Synpri 2019956 GRKU Mosses.p2 Gnemon TnS000301319t05 Dicsco 2101690 NGTD Mosses.p1 Welmir 2008345 TOXE Gnetales.p1 Welmir 2008346 TOXE Gnetales.p1 Cerpur 2008784 FFPD Mosses.p1 Ginbil 2007484 SGTW Ginkgoales.p1 Leugla 2011474 RGKI Mosses.p1 Ginbil Gb 02528 MixspeLeualb 2155732 2129776 NWQC VMXJ Liverworts.p1 Mosses.p1 Encbar 2004649 GNQG Cycadales.p1 Cycmic 2013323 XZUY Cycadales.p1 Racelo 2077026 ABCD Mosses.p1 Cycmic CMI00001569 Racvar 2118302 RDOO Mosses.p1 Ginbil 2001254 SGTW Ginkgoales.p1 Scoaqu 2014701 BPSG Mosses.p1 Ginbil Gb 18009 Cycmic 2008887 XZUY Cycadales.p1 RacvarEncstr 2014190 2059989 RDOO KEFD Mosses.p1 Mosses.p1 Cycmic CMI00014935 Dioedu 2018126 WLIC Cycadales.p1 Racelo 2074975 ABCD Mosses.p1 Encbar 2015775 GNQG Cycadales.p1 Synpri 2008435 GRKU Mosses.p1 Staeri 2011957 KAWQ Cycadales.p1 Cerpur 2001953 FFPD Mosses.p1 Larspe 2001754 WVWN Conifers.p1 Scoaqu 2015538 BPSG Mosses.p1 Psewil 2014722 IOVS Conifers.p1 100 Psemen PME00025015 Leugla 2006863 RGKI Mosses.p1 Notlon 2067622 AREG Conifers.p1 Leualb 2003311 VMXJ Mosses.p1 Tsuhet 2054894 GAMH Conifers.p1 Timaus 2067037 ZQRI Mosses.p1 Abilas 2056132 VSRH Conifers.p1 Encstr 2013576 KEFD Mosses.p1 Pseama 2081375 AQFM Conifers.p1 Keteve 2091146 JUWL Conifers.p1 Physsp. 2000021 YEPO Mosses.p1 Cedlib 2015352 GGEA Conifers.p1 Catagr 2125541 NPRL Conifers.p1 Physsp. 2080438Phypat YEPO Pp3c3 Mosses.p1 26700V3.1 Picsit PSI00017946 Polcom 2041842 SZYG Mosses gametophyte.p1 Piceng 2054256 AWQB Conifers.p1 BuxaphDipfol 2003022 2071781Phypat HRWG AWOI Pp3c13 Mosses.p1 Mosses.p1 20180V3.1 Picabi MA 865g0010 Pinpar 2078015 IIOL Conifers.p1 Tetpel 2011187 HVBQ Mosses.p1 Pinpon 2071661 JBND Conifers.p1 Tetpel 2009697 HVBQ Mosses.p1 Pinjef 2013538 MFTM Conifers.p1 98.5 Pinpin PPI00043571 Atrang 2082738 ZTHV Mosses.p1 Pinrad 2003467 DZQM Conifers.p1 Andrup 2015062 WOGB Mosses.p1 91.6 86.5 95 Pinsyl PSY00005852 89.4 87.3 Pintae PTA00015631 100 90.9 Ararul 2062317 XTZO Conifers.p1 Sphrec 2005528 UHLI Mosses.p1 Wolnob 2010100 RSCE Conifers.p1 Sphles 2005596Sphfal GOWD Sphfalx0012s0093.1 Mosses.p1 90.7 Sphles 2005595 GOWD Mosses.p1 92.1 99.5 Agamac 2069804 ACWS Conifers.p1 Agarob 2073386 MIXZ Conifers.p1 Sphrec 2005530 UHLI Mosses.p1 Mancol 2062686 CDFR Conifers.p1 Sphrec 2005529 UHLI Mosses.p1 98.3 Parust 2040064 JZVE Conifers.p1 99.9 90.8 Mictet 2073751 MHGD Conifers.p1 Sphles 2005594 GOWD Mosses.p1 Saxcon 2012512 QCGM Conifers.p1 Sphfal Sphfalx0085s0101.1 100 Lepsp. 2007734 BBDD Conifers.p1 Sphpal 2024120 RCBT Mosses.p1 100 Sphpal 2024121 RCBT Mosses.p1 Halbid 2054503 OWFC Conifers.p1 Sphles 2016855 GOWD Mosses.p1 100 Phyhyp 2068380 JRNA Conifers.p1 Sunama 2009118 KLGF Conifers.p1 100 Pruand 2037275 EGLZ Conifers.p1 Sphrec 2020999 UHLI Mosses.p1 94 Acmpan 2113512 HILW Conifers.p1 Sphfal Sphfalx0227s0008.1 99.9 93 Daccom 2009336 FMWZ Conifers.p1 100 84.1 97.6 Dacbal 2007808 IZGN Conifers.p1 88.8 Faltax 2012601 QHBI Conifers A.p1 94.887.8 91.4 88.1 Faltax 2002269 ROWR Conifers.p1 100 98.7 96.9 Faltax 2015981 PLYX Conifers 2 samples combined.p1 100 98.1 Podrub 2001548 XLGK Conifers.p1 82.8 89.4 Podcor 2053519 SCEB Conifers.p1 100 86.3 Retmin 2009222 VGSX Conifers.p1 100 90.1 100 Nagnag 2002283 UUJS Conifers.p1 93.5 Nagnag 2002282 UUJS Conifers.p1 96.4 93.3 98.1 97 99.8 97.596.6 Sciver 2043934 YFZK Conifers.p1 86.3 99 Amearg 2005446 IAJW Conifers.p1 100 97.7 Tornuc 2003554 HQOM Conifers.p1 Tortax 2010332 EFMS Conifers.p1 86.1 85.4 100 Cephar 2015218 WYAJ Conifers.p1 100 95.6 Cephar 2111176 NVGZ Conifers 2 samples combined.p1 100 Cephar 2060382 GJTI Conifers.p1 100 100 99.9 99.9 Taxcus 2074782 ZYAX Conifers.p1 99.9 Taxbac 2006780 WWSS Conifers.p1 Ausspi 2076639 BTTS Conifers.p1 100 97.6 100 100 96.4 99.3 96.9 Psechi 2000610 YLPM Conifers.p1 100 Psechi 2000613 YLPM Conifers.p1 100 80.7 Taicry 2012286 QSNJ Conifers.p1 88.6 86.9 Cunlan 2052530 OUOI Conifers.p1 99.9 Cunlan 2012484 ZQVF Conifers 2 samples combined.p1 85.5 Cunlan 2088710 ESYX Conifers branch apex with needles.p1 92.3 99.5 Cunlan 2012483 ZQVF Conifers 2 samples combined.p1 100 88.1 100 100 Athcup 2010468 XIRK Conifers.p1 86.9 98.9 Metgly 2007021 NRXL Conifers.p1 99.6 100 95.2 85.8 Seqgig 2059335 QFAE Conifers Glaucum.p1 99.498 90.6 Taxdis 2064402 FHST Conifers.p1 91.6 100 91.2 100 93.4 89.5 96.3 95 Glypen 2012529 OXGJ Conifers.p1 96.5 99.7 99.8 94.596.8 100 92.3 100 93.4 Cryjap 2014531 DSXO Conifers.p1 91.7 95.8 Cryjap 2110963 HOUF Conifers leaf.p1 96.6 Cryjap 2015773 GMHZ Conifers 2 samples combined.p1 93.2 81.4 100 Auschi 2069145 YYPE Conifers.p1 99.5 94.3 96.7 99.7 100 86.8 Widced 2060291 AUDE Conifers.p1 100100 80.2 99.9 99.3 Pappap 2011209 OVIJ Conifers.p1 99.9 100 99.8 99.3 99.2 Disarc 2075564 GKCZ Conifers.p1 100 Piluvi 2062370 ETCJ Conifers.p1 Trisub lcl DF974552.1 GAU49359.1 38417 100 98.4 97.7 100 100 94.3 91 90.4 Neopan 2070353 JDQB Conifers.p1

99.2 Tripra Tp57577 TGAC v2 mRNA36177 98.4 100 Calgra 2144195 IFLI Conifers March.p1 84.5 96.5 97.4 95.4 Calmac 2056864 RMMV Conifers March.p1 88.9 100 Medtru MtrunA17 Chr8g0373391 99.6 100 98.9 Thudol 2010169 NKIN Conifers.p1 Thupli 2040903 VFYZ Conifers.p1 83.9 85.1 99.6 100 96.5 100 Chalaw 2003163 AIGO Conifers.p1 84.3 91.5 Fokhod 2006978 UEVI Conifers.p1 Cicari Ca 20680.1 94.2 95.7 99.7 99.3 96.8 98.5 Cupdup 2073577 QNGJ Conifers.p1 Lotjap CicariLj4g3v0949950.1 Ca 20695.1 90.1 100 100 Junsco 2011830 XMGP Conifers.p1

95.4 Lotjap Lj4g3v0949950.2 100 87.8 Caldec 2007853 FRPM Conifers.p1

96.4 98 Vigang vigan.Vang11g02860.1Lupang Lup007655.1 99.9 Tetsp. 2007340 CGDN Conifers.p1 97.9 98.7 100 Plaori 2052931 BUWV Conifers.p1 100 100 100 Vigrad Vradi07g00490.1 91.4 83.7 100 92.1 98.6 Micdec 2056433 XQSG Conifers.p1

Vigung Vigun03g267200.1 98.4 99.8 92.4 96.5 100 100 Spipol Spipo0G0105900 Phavul Phvul.003G253300.1 93.4 Glymax Glyma.02G057200.1 99.4 97.4 Aposhe lcl KZ451923.1 PKA61838.1 5527 91.3 96.9 Arahyp arahy.Tifrunner.gnm1.ann1.A25KZS.1Glymax Glyma.16G140300.1 100 Phaequ PEQU 10687 93.9 Dencat lcl NW 021319910.1 XP 020692936.1 25940 100 99.7 91.8 Dencat lcl NW 021319910.1 XP 020692937.1 25941 Arahyp arahy.Tifrunner.gnm1.ann1.68QIGD.1Cajcaj Ccajan 24171 Musacu GSMUA Achr9T17070 001 98.7 91 100 96.9 100 Musacu GSMUA Achr8T01630 001 98.3 Araipa Araip.K22F0 96.1 91.7 99.4 Musacu GSMUA Achr10T05150 001 Casaus Castanospermum20192-PA 96.7 86 86.6 100 Anacom Aco001696.1 Aradur Aradu.IC00B 97.9 100 Setita Seita.5G052200.1 83.3 Sorbic Sobic.003G121800.1 Nissch Nissc2023S17390 95.3 100 98.6 97.5 10090.2 100 Zeamay Zm00008a011502 Arahyp arahy.Tifrunner.gnm1.ann1.DYU645.1 100 81.1 97.4 Arahyp arahy.Tifrunner.gnm1.ann1.TJQ42N.1Aradur Aradu.3N6NA Orysat LOC Os01g16000.1 Araipa Araip.Q655H 91.7 92.985.899.989.4 Bradis Bradi2g09760.1 97.5 83.7 99.8 96.3 98.9 100 Horvul HORVU3Hr1G037050.3 99.6 100 100 99.8 100 80.2 Horvul HORVU7Hr1G021120.5 Nissch Nissc2089S06812 97.1 100 93.6 96.2 Bradis Bradi2g31770.1 83.2 90.8 89.2 Casaus Castanospermum03720-PA 95.4 100 100 Orysat LOC Os05g18294.1 Lupang Lup025146.1 98 99.9 99.8 95.1 Orysat LOC Os05g18470.1 Chafas Chafa6329S25284 92.5 100 81.9 98.7 99.9 99.9 Sorbic Sobic.008G088000.5 Mimpud Mimpu4325S24131 99.9 82 100 99.382.799.6 Zeamay Zm00008a025498 Cercan Cerca46S25055 97.4 100 97.7 Sorbic Sobic.009G090800.1 91.8 Zeamay Zm00008a031460 Lagsic Lsi01G006780.1 100 99.9 99.4 99.2 Sorbic Sobic.008G086700.2 Cucmel MELO3C007825.2.1Citlan Cla014207 93.3 86.7 Setita Seita.3G296300.1 Cucsat evm.model.Chr6.3218 99.290.2 100 94 100 Fraexc FRAEX38873 v2 000056810.1 Cucmos CmoCh03G007810.1 97 99.9 99.7 82.6 93.4100 Petaxi Peaxi162Scf00003g05365.1 100 99.9 98.9 100 Momcha lcl NW 019104492.1Cucpep XP Cp4.1LG10g00890.1 022133231.1 4741 95.9 86.3 99.6 Nicben Niben101Scf08203g00019.1 Cucmax CmaCh03G007530.1 100 81.1 99.7 99.7 100 100 Capann CA10g22390 Momcha lcl NW 019104492.1 XP 022133233.1 4743 96.598.499.9 94.8 98.6 96 99.6 96.386.8 Solpen Sopen09g036510.1 Momcha lcl NW 019104492.1 XP 022133232.1 4742 97.8 100 92.896.8 100 Sollyc Solyc09g098600.2.1 100 97.4 95.3 99 87.6 86.8 100 93.5 99.8 100 99.6 Carpap evm.model.supercontig 73.38 Begfuc Begfu12332S00595 97.1 98.3 83 Carpap evm.TU.contig 29302.2 97.1 97.9 Daucar DCAR 009090 Begfuc Begfu2019S01970 98.8 9994.3 Daucar DCAR 020634 99.9 99.6 Begfuc Begfu206S24485 83.8 88.4 100 86.497.199.6 97.8 96.9 Cepfol Cfol v3 01022 Cucmel MELO3C017562.2.1 95.6 Poptri Potri.013G068700.2 Cucsat evm.model.Chr4.489 98.897 93.9 96.9 93 88.7 99.9 100 Manesc Manes.09G134200.1 Lagsic Lsi07G001980.1 99.7 Riccom 29818.m000412 97.2 97.5 100 Citlan Cla014514 100 Thecac Thecc1EG025759t2 Cucmax CmaCh16G006600.1 100 99.5 Gosrai Gorai.013G197600.1 Cucpep Cp4.1LG14g01510.1 100 Citcle Ciclev10032042m 98.9 100 Momcha lcl NW 019104496.1Cucmos XP CmoCh16G007170.1 022136351.1 8351 100 100 99.7 96.9 Citsin orange1.1g019727m 97.2 Mornot L484 028007 Pyrbre lcl NW 008989041.1 DatgloXP 018500976.1 Datgl936S36473 43533 Parand lcl JXTB01000067.1 PON67926.1 9924 Pyrbre lcl NW 008989041.1 XP 018500977.1 43534 94.7 100 Treori lcl JXTC01000417.1 PON55734.1 29867 Pyrbre lcl NW 008988609.1 XP 009340754.1 37380 99.9 95.3 100 97 94.8 Humlup HL.SW.v1.0.G006512.1 89.8 100 90 84.198.8 Humlup HL.SW.v1.0.G033819.1 Drydru Drydr6S13404 Pyrcom PCP010076.1 100 Maldom MDP0000703737 89.6 100 Rubocc Bras G20749 99.9 99.8 99.7 Roschi RchiOBHm Chr3g0495481 Pyrcom PCP016281.1 100 SEC Pyrbre lcl NW 008988239.1 XP 009371592.1 23375 100 Fraana FAN iscf00094916.1.g00001.1 100 95.7 95.5 Fraana FAN iscf00214856.1.g00001.1 Maldom MDP0000232756 89.5 99.9 Pruper Prupe.7G025600.1 Pruper Prupe.7G154300.1 84.3 84.1 95.8 Pruavi Pav sc0000231.1 g1290.1.mk Prudul Prudul26A006733P1 95.4 99.5 100 Prumum lcl NC 024133.1 XP 016651464.1 24316 Pruavi Pav sc0000099.1 g880.1.mk 91.9 92.6 100 Prumum lcl NC 024133.1 XP 008241671.1 25350 89.1 100 94.1 Prumum lcl NC 024133.1 XP 008240593.1 24317 99.6 99.9100 Prumum lcl NC 024133.1 XP 016651463.1 24315 Fraves FvH4 1g13330.1 84.799.9 96.1 99.6 93.8 Pyrbre lcl NW 008988064.1 XP 009353029.1 6361 Fraana FAN iscf00280498.1.g00001.1 91.1 93.8 100 99.4 99.8 Pyrcom PCP026063.1 Potmic 32633 t 95.8 82.9 99.8 Maldom MDP0000260135 Roschi RchiOBHm Chr2g0101611 99.9 Pyrcom PCP016687.1 Rubocc Bras G01033 99.3 96.1 Pyrbre lcl NW 008988161.1 XP 009365376.1 17646 Drydru Drydr282S09701 98.593.9 99.9 94.3 100 Jugreg g1775.t1 Humlup HL.SW.v1.0.G008503.1 97.8 98.9 100 Querob Qrob P0112930.2 Humlup HL.SW.v1.0.G006946.1 100 99.686.9 Casmol maker-scaffold00390-snap-gene-1.19-mRNA-1 Treori lcl JXTC01000004.1 POO02536.1 1520 96.8 Datglo Datgl3151S28144 100 92.5 98.8 98.2 99.7 Momcha lcl NW 019104603.1 XP 022154468.1 24315 Parand lcl JXTB01000069.1 PON67667.1 10092 100 Cucmos CmoCh03G002190.1 Zizjuj lcl NC 029686.1 XP 015889927.1 22002 99.9 86 95.3 100 100 Cucpep Cp4.1LG10g10900.1 Alnglu Alngl3025S23523 99.8 96.8 Cucmax CmaCh03G002090.1 Alnglu Alngl3025S23525 96 94.8 90.4 Citlan Cla012177 Jugreg g32500.t1 95.5 84.299.6 Lagsic Lsi01G017140.1 Casgla Casgl428S17645 100 100 95.2 Cucmel MELO3C008874.2.1 Casmol augustus masked-scaffold32043-abinit-gene-0.0-mRNA-1 Cucsat evm.model.Chr4.2122.1 Querob Qrob P0570470.2 99.6 88.8 Cucsat evm.model.Chr4.2122 Chequi AUR62007563-RA 98.7 100 100 Cercan Cerca37S22986 Chequi AUR62004048-RA Chafas Chafa4590S23019 Spiole Sp 056620 kdnk.t1 99.5 99.4 100 100 Araipa Araip.DFV0B Betvul Bv6 128720 sqes.t1 96.6 Arahyp arahy.Tifrunner.gnm1.ann1.C6R2SB.1 Diacar Dca43598.1 95.3 100 Casaus Castanospermum10146-PA Diacar Dca51061.1 96.3 96.7 9893.1 Lupang Lup000068.1 Diacar Dca36257.1 90.3 100 Cajcaj Ccajan 18075 Cepfol Cfol v3 27898 94.698.2 94.7 100 93 Glymax Glyma.03G004600.1 Cepfol Cfol v3 12271 92.8 100 Phavul Phvul.001G101900.1 95.2 95.5 90 99.9 100 Arahal Araha.18319s0006.1 100 Vigung Vigun01g097400.1 Aralyr AL7G14400.t1 100 80.7 100 84.5 95.4 Vigang vigan.Vang0216s00030.1 Aratha AT4G36640.1 99.9 90.1 Vigrad Vradi0007s01040.1 99.9 80 100 100 Cicari Ca 06847.1 Boestr Bostr.7867s1520.1 87.6 100 99.7 Medtru MtrunA17 Chr7g0254621 Capgra Cagra.1695s0028.1 100 95.6 100 99.9 94.5 Tripra Tp57577 TGAC v2 mRNA24479 Caprub Carub.0007s0369.1 100 88 Trisub lcl DF973237.1 GAU21735.1 10793 Brarap Brara.H01684.1 95 95.6 Lotjap Lj1g3v4027110.1 Braolecap Bol028984 100 98.2 98 100 Lotjap Lj1g3v4027110.3 Brarap Brara.A00206.1 99.5 93.9 Lotjap Lj1g3v4027110.4 Braolecap Bol018655 99.9 Lotjap Lj1g3v4027110.2 Brarap Brara.K01306.1 95.3 Ambtri evm 27.model.AmTr v1.0 scaffold00010.184 Eutsal Thhalv10025882m 100 100 Helann HanXRQChr02g0044701 99.9 95.9 Helann HanXRQChr05g0162201 99.7 100 Diacar Dca51600.1 Tarhas lcl NW 010966177.1 XP 019058696.1 23162 100 92.8 Diacar Dca17622.1 Tarhas lcl NW 010966177.1Carpap evm.model.supercontig XP 019058697.1 23163 6.111 Diacar Dca34219.1 Gosrai Gorai.003G015300.1 Diacar Dca2904.1 Gosrai Gorai.007G050700.1 100 Betvul Bv1 009550 niny.t1 Thecac Thecc1EG000393t1 94.4 Citcle Ciclev10026226m 88.999.5 Spiole Sp 115890 xhre.t1 95.682.5 100 97.7 Chequi AUR62027723-RA Poptri Potri.007G025800.1 97.5 100 Zosmar Zosma224g00210.1 Poptri Potri.005G123200.1 96.7 94.7 Phaequ PEQU 25264 Poptri Potri.007G025900.1 83.4 99.8 99.7 98.1 84.8 81.9 Dencat lcl NW 021318921.1 XP 028550177.1 8397 Manesc Manes.01G135200.1 97.6 92.8 91.4 99.4 Dencat lcl NW 021318921.1 XP 020700548.1 8395 Riccom 29634.m002152 99.6 89.9 82.7 Dencat lcl NW 021318921.1 XP 020700547.1 8394 99.9 100 99.1 87 Sollyc Solyc02g085300.2.1 99.4 99.9 100 Dencat lcl NW 021318921.1 XP 020700549.1 8396 Solpen Sopen02g029990.1 99.3 99.2 99.9 Dencat lcl NW 021318921.1 XP 028550180.1 8400 Capann CA02g22670 100 99.8 94 97.5 80.9 98.294.7 Dencat lcl NW 021318921.1 XP 028550181.1 8401 83.8 Dencat lcl NW 021318921.1 XP 028550178.1 8398 Nicben Niben101Scf03693g00005.1 98.7 99.8 100 99.299.9 Dencat lcl NW 021318921.1 XP 028550179.1 8399 Nicben Niben101Scf08162g00017.1 97.7 100 100 Musacu GSMUA Achr3T04420 001 Petaxi Peaxi162Scf00366g00001.1 84.4 91.9 Musacu GSMUA Achr10T24490 001 100 Anacom Aco002830.1 FraexcHelann FRAEX38873 HanXRQChr16g0530361Daucar v2 DCAR000190970.1 017281 100 100 94.8 Orysat LOC Os02g51610.1 97.5 Horvul HORVU6Hr1G075070.2 Vigang vigan.Vang01g15920.1 91.5 94.2 Bradis Bradi3g59030.5 Vigrad Vradi06g15810.1 99.6 99.3 99.9 99.9 100 99.8 95.5 100 99.7 91.2 Setita Seita.1G323100.1 Vigung Vigun08g016100.1 99.6 92.8 80.2 Sorbic Sobic.004G233900.1 Phavul Phvul.001G014800.1 93.5 81.4 100 100 96.4 Zeamay Zm00008a009705 Glymax Glyma.17G250100.1 100 Nelnuc NNU 22452-RA Glymax Glyma.14G075300.1Cajcaj Ccajan 08616 91.880.497.1 96.199.7 90.7 84.3 95.6 Nelnuc NNU 20235-RA 91.9 93 92.9 100 99 Spipol Spipo4G0012700 100 100 97.5 Tarhas lcl NW 010971898.1 XP 010527376.1 40938 84.9 100 Eutsal Thhalv10008258m Tripra Tp57577 TGAC Cicariv2 mRNA20861 Ca 08756.1 99.7 98.7 Brarap Brara.G01047.1 Trisub lclMedtru DF973150.1 MtrunA17 GAU15312.1 Chr1g0155071 4370 98.3 100 Brarap Brara.I03371.1 97.7 100 Lotjap Lj0g3v0092239.1 99.2 100 98.1 97.9 100 10099.8 100 99.2 Braolecap Bol009721 Lotjap Lj0g3v0092239.2 98.8 97 98.8 82.6 Boestr Bostr.12659s0069.1 95.1 99.9 99.4 Capgra Cagra.1707s0002.1 84.299.6 Caprub Carub.0001s2173.1 Aradur Aradu.MC6VZ 99.3 100 Araipa Araip.A87CL 97.1 96.3 98.9 99.9 Aratha AT1G22180.2 Arahyp arahy.Tifrunner.gnm1.ann1.P0KEMF.1 95.5 85 100 99.8 Aralyr AL1G35630.t1 93.6 99.9 Arahyp arahy.Tifrunner.gnm1.ann1.U4QIQ0.1Nissch Nissc776S30888 100 88.7 100 Arahal Araha.1325s0007.1 Lupang Lup024438.1 95.8 96.7 Tarhas lcl NW 010965372.1 XP 010538954.1 14782 Lupang Lup014711.1 96 100 99.5 99.9 91.9 Tarhas lcl NW 010965372.1 XP 010538953.1 14781 100 96.5 100 Tarhas lcl NW 010965372.1 XP 010538955.1 14783 Mimpud Mimpu53781S25500 98.7 87.1 85.8 99.7 Tarhas lcl NW 010965372.1 XP 010538952.1 14780 100 Eutsal Thhalv10028819m 100 99.6 98.3 Casaus Castanospermum02075-PA 99.8 99.9 100 99.3 94.5 Braolecap Bol025598 Casaus GlymaxCastanospermum13883-PA Glyma.04G032500.1 92.4 98.2100 Brarap Brara.C02575.1 Glymax Glyma.06G032400.1 100 92.5 100 99.8 Boestr Bostr.3877s0001.1 NisschLupang Nissc16276S06042 Lup012382.1 98.9 92.5 94.894.2 Caprub Carub.0006s2720.1 100 98.3 93.2

91.4

93.7 99.8 8799.5 83.8 98.8 89.6 82.3 96.6 Capgra Cagra.8879s0001.1 100 99.2 82.7 97.7 98 Aralyr AL6G42470.t1 93.2 100 99.2 90.2 83.3 Mimpud Mimpu144613S15836 96 Chafas Chafa12408S14859 80.1 Aratha AT4G08690.2 Riccom 30170.m014221 91.199.4 99.8 92 Arahal Araha.37940s0001.1 98 100 98.9 99.9 100 Cepfol Cfol v3 02810 100 98.9 100 Manesc Manes.05G159900.1 99.8 100 Gosrai Gorai.009G239300.1 Poptri Potri.002G261000.2 99.1 98.7 99.8 99.9 Thecac Thecc1EG034950t1 87.3 100 100 100 81.7 98.6 95.5 100 100 Gosrai Gorai.010G043500.1 83.1

Pyrcom PCP004908.1 98 97.3 Carpap evm.model.supercontig 66.84 99.2 99.9 80.7 99.7 97 95 100 99.8 99.2 Citcle Ciclev10001758m 99.1 89.7 99.4 83 Maldom MDP0000749404 100 87.3 97.5 100 Citsin orange1.1g019678m 99.9 98.5 100 97.8 86.2 99.8 99.5 88.9 99.6 Riccom 29908.m005999 Pyrbre lcl NW 008988041.1 XP 009364759.1 1842 100 98.7 99.1 100 92.9 97.6 92.2 98.4 Manesc Manes.18G069500.1 Pyrbre lcl NW 008988050.1 XP 018498562.1Pyrcom PCP024523.1 3471 86.9 95.3 97.8 100 93 98.8 95.8 99.6 97.7 Poptri Potri.002G093400.4 Maldom MDP0000279644 98.9 99.4 97.8 96.8 98.5 100 Poptri Potri.005G168100.1 99.7 100 87.483.4 84.2 84.994 99.399.8 87.3 Daucar DCAR 008713 Pyrbre lcl NW 008988164.1 XP 018504991.1 17898 90.5 98.9 99.9 100 Fraexc FRAEX38873 v2 000065340.1 99.9 95.1 96 87.8 99.7 95.4 Pyrbre lcl NW 008988164.1 XP 009365577.1 17899 99.7 91.4 90.484.9 99.9 Utrgib Utricularia gibba unitig 26 1373770 1375170 unitig 26.g9265.t1 1 CDS 875812619 2130 99.4 99.1 86.1 99.2 98.7 Pruper Prupe.1G379800.1 100 83.287.187.5 84.3 Utrgib Utricularia gibba unitig 749 786075 787313 unitig 749.g13412.t1 1 CDS 875844459 9630 81.8 100 97.7 99.9 95.4 83.1 99 95.2 99.8 Petaxi Peaxi162Scf00041g00217.1 Prumum lcl NC 024127.1Prudul XP 016647681.1 Prudul26A003622P1 5727 99.9 99.9 98.1 Nicben Niben101Scf06375g02001.1 Potmic 9335 t 99.9 98.1 99.2 Prumum lcl NC 024127.1 XP 008220794.1 5729 87.8 83.5 99.9 Nicben Niben101Scf00630g02004.1 Prumum lcl NC 024127.1 XP Fraves008220793.1 FvH4 2g39850.15728 82.8 Capann CA04g15030 Pruavi Pav sc0000078.1 g050.1.mk 100 100 95.5 99.1 99.8 Solpen Sopen04g028980.1 Fraana FAN iscf00062326.1.g00001.1 Sollyc Solyc04g072810.2.1 Rubocc Bras G02375 Datglo Datgl27346S26163 100 Drydru Drydr549S04845 100 Begfuc Begfu4295S04243 Roschi RchiOBHm Chr6g0300991 98.9 100 Begfuc Begfu91863S06480 83.7 Begfuc Begfu91372S44023 85.1 95.6 83.2 100 94.3 Begfuc Begfu2873S03068 95.7 86.5 87.9 87 Momcha lcl NW 019104488.1 XP 022140282.1 348 Distri Distr82S28399 Momcha lcl NW 019104488.1 XP 022140273.1 347 91.5 85.5 99.3 100 Cucmos CmoCh01G014670.1 Zizjuj lcl NC 029684.1 XP 015884677.1 16529 99.6 100 Cucmax CmaCh01G014170.1 96.6 Zizjuj lcl NC 029684.1 XP 015884681.1 16532 97.2 93.9 97 Citlan Cla023132 99.9 100 100 Zizjuj lcl NC 029684.1 XP 015884678.1Mornot 16530L484 003333 97 Lagsic Lsi04G023510.1 Zizjuj lcl NC 029684.1 XP 015884680.1 16531 98.4 99.1 100 Cucmel MELO3C010421.2.1 Humlup HL.SW.v1.0.G012477.1 100 96.7 Cucsat evm.model.Chr4.1825 99.9 89.3 Cucsat evm.model.Chr4.1825.1 Cucsat evm.model.Chr3.4183 85.1 93.1 Parand lcl JXTB01000437.1 PON40487.1 29732 100 88.4 Mornot L484 021547 Treori lcl JXTC01000366.1 PON60290.1 28516 95.6 Parand lcl JXTB01000120.1 PON61603.1 14521 Cucsat evm.model.Chr3.4183.2.1Citlan Cla020758 98.6 99.3 Cucsat evm.model.Chr3.4183.2 86.9 98.5 Treori lcl JXTC01000001.1 POO04035.1 339 Distri Distr3583S02675 Cucsat evm.model.Chr3.4183.1 99.4 100 86.2 100 84.9 Cucmel MELO3C003839.2.1 Zizjuj lcl NC 029684.1 XP 015885536.1 17486 Lagsic Lsi04G016570.1 84.4 100 96.3 96.2 100 99.2 Zizjuj lcl NC 029684.1 XP 024931006.1 17487 99.8 94.3 Zizjuj lcl NC 029684.1 XP 015885534.1 17485 Cucpep Cp4.1LG02g07270.1 96.3 83.6 Drydru Drydr40S04034 98.5 84.2 99.9 100 Rubocc Bras G26584 Cucmos CmoCh01G019680.1 99.9 87.5 100 86.6 Roschi RchiOBHm Chr7g0239851 100 Cucmax CmaCh01G019050.1 88.7 98.6 Potmic 32273 t 97.7 Fraves FvH4 5g37870.1 Datglo Datgl2102S24342 98 89.8 89.3 99.2 99.4 Pruavi Pav sc0000030.1 g070.1.mk Alnglu Alngl10153S12864Jugreg g32879.t1 Casgla Casgl305S14614 Prudul Prudul26A007419P1 Pruper Prupe.1G512800.1 Prumum lcl NC 024130.1 XP 008234017.1 18215 98.2 97.2 Maldom MDP0000191424 Querob AralyrQrob P0624260.2 AL2G35080.t1 90.8 Pyrcom PCP003703.1 Momcha lcl NW 019104488.1 XP 022136456.1 1181 86.4 99.9 Pyrbre lcl NW 008988262.1 XP 009373172.1 24826 Momcha lcl NW 019104488.1 XP 022136463.1Arahal Araha.49879s0006.1Aratha 1182 AT1G75170.1 Pyrbre lcl NW 008988262.1 XP 009373173.1 24827 Pyrbre lcl NW 008988262.1 XP 018506663.1 24825 Maldom MDP0000302730 Capgra Cagra.0402s0013.1 99.8 Pyrbre lcl NW 008988209.1 XP 018505850.1 21594 Caprub Carub.0002s2198.1Braolecap Bol027750 Pyrbre lcl NW 008988209.1 XP 018505849.1 21595 Boestr Bostr.3288s0165.1 Pyrcom PCP031915.1 Brarap Brara.G03331.1 Pyrcom PCP000594.1 Alnglu Alngl7802S36004 Eutsal Thhalv10018941m Casgla Casgl148S08917 Jugreg g36354.t1 Casmol augustus masked-scaffold00873-abinit-gene-0.3-mRNA-1 100 Jugreg g47809.t1 Querob Qrob P0214970.2 Gosrai Gorai.009G202600.1 Casmol snap masked-scaffold04137-abinit-gene-0.7-mRNA-1 Gosrai Gorai.010G010500.1 Cercan Cerca257S19439 CitcleCepfol Ciclev10002080m Cfol v3 02409 Carpap evm.model.supercontigThecac Thecc1EG034028t2 36.72 Chafas Chafa12630S14951 Mimpud Mimpu405S23771 Lupang Lup004987.1 Sollyc Solyc12g089130.1.1Capann CA12g17130 Nissch Nissc2467S18941 Solpen Sopen12g031000.1 Arahyp arahy.Tifrunner.gnm1.ann1.4S1Z6L.1 Tarhas lcl NW 010965373.1 XP 010539916.1 15541 Araipa Araip.HH5DC Arahyp arahy.Tifrunner.gnm1.ann1.K0LQZB.1 Aradur Aradu.K2K8G Cicari Ca 04135.1 Medtru MtrunA17 Chr5g0425421 Nicben Niben101Scf00055g03019.1 Trisub lcl DF973553.1 GAU34383.1 23441 Nicben Niben101Scf00219g07014.1 Tripra Tp57577 TGAC v2 mRNA32748 Petaxi Peaxi162Scf00064g00422.1 Lotjap Lj0g3v0032219.1 Sollyc Solyc04g080290.2.1Capann CA04g20560 Lotjap Lj0g3v0105949.1 Nicben Niben101Scf08160g02006.1 Cajcaj Ccajan 05002 Nicben Niben101Scf08376g00012.1Solpen Sopen04g033890.1 Petaxi Peaxi162Scf00417g01210.1 Glymax Glyma.14G170800.1 Glymax Glyma.13G087900.1 Phavul Phvul.008G171700.1 Vigung Vigun08g098200.1 Vigang vigan.Vang0313s00020.1 Vigrad Vradi06g07770.1 Fraexc FRAEX38873 v2 000254620.2 Casaus Castanospermum05320-PA Casaus Castanospermum08497-PA Fraexc FRAEX38873 v2 000254620.1 Nissch Nissc7959S04343 Fraexc FRAEX38873 v2 000245990.1 Lupang Lup004963.1 Fraexc FRAEX38873 v2 000245990.2 Lupang Lup012658.1 Fraexc FRAEX38873 v2 000037970.1 Aradur Aradu.SQ2UE Fraexc FRAEX38873 v2 000037970.2 Araipa Araip.Y5YXN Arahyp arahy.Tifrunner.gnm1.ann1.FTVA6C.1 Fraexc FRAEX38873 v2 000305330.1Daucar DCAR 008757 Helann HanXRQChr02g0042091 Lotjap Lj1g3v0638710.2 Helann HanXRQChr04g0105571Nelnuc NNU 05384-RA Lotjap Lj1g3v0638710.1 Nelnuc NNU 17200-RA Cicari Ca 13290.1 Helann HanXRQChr16g0510661 Medtru MtrunA17 Chr3g0115591 Helann HanXRQChr09g0268881 Trisub lcl DF973292.1 GAU24556.1 13614 Zeamay Zm00008a010127 Tripra Tp57577 TGAC v2 mRNA36398 Glymax Glyma.06G105500.1 Zeamay Zm00008a003504 Glymax Glyma.04G104300.1 Zeamay Zm00008a005039 Setita Seita.9G111500.1 Vigung Vigun09g174500.1 Phavul Phvul.009G029200.1 Sorbic Sobic.001G108500.1 Cajcaj Ccajan 25710 Zeamay Zm00008a005038 Glymax Glyma.04G104400.1 Setita Seita.9G111600.1 Phavul Phvul.009G029100.1 Sorbic Sobic.001G108600.1Setita Seita.9G111700.1 Vigung Vigun09g174400.1 Vigrad Vradi05g07650.1 Vigang vigan.Vang0017s01010.1 Sorbic Sobic.001G108700.1 Equhye 2128245 JVSZ Eusporangiate Monilophytes.p1 Bradis Bradi1g10270.1 Osmsp. 2078243 UOMY Leptosporangiate Monilophytes gametophyte.p1 Osmjav 2074678 VIBO Leptosporangiate Monilophytes.p1 Horvul HORVU4Hr1G009310.9 Scedis 2087229 EEAQ Eusporangiate Monilophytes.p1 Anacom Aco015896.1 Botvir 2101248 BEGM Eusporangiate Monilophytes.p1 Horvul HORVU4Hr1G009190.3 Lygjap 2009103 PBUU Leptosporangiate Monilophytes.p1 Orysat LOC Os03g51430.1 Anetom 2008182 CQPW Leptosporangiate Monilophytes.p1 Horvul HORVU4Hr1G009210.3 Anetom 2008181 CQPW Leptosporangiate Monilophytes.p1 Phaequ PEQU 02621 Thyele 2122283 EWXK Leptosporangiate Monilophytes.p1 Culmac 2017867 PNZO Leptosporangiate Monilophytes.p1 Plajap 2024995 UWOD Leptosporangiate Monilophytes.p1 Pilglo 2088366 KIIX Leptosporangiate Monilophytes.p1 Salcuc Sacu v1.1 s0059.g015058 Zosmar Zosma86g00510.1 Salcuc Sacu v1.1 s0097.g019451 Azocar 2008255 CVEG Leptosporangiate Monilophytes.p1 Azofil Azfi s0388.g067610 UtrgibUtrgib Utricularia Utricularia gibba gibba unitig unitig 21 402445 8 1315677 408283 1317024 unitig unitig 21.g20161.t1 8.g3373.t1 -1 1 CDS CDS 875805111 875848011 2178014645 Spipol Spipo9G0022200 Linlin 2018946 NOKI Leptosporangiate Monilophytes.p1 Spipol Spipo24G0003400 Cryacr 2009114 WQML Leptosporangiate Monilophytes.p1 Phaequ PEQU 19378 Pittri 2009072 UJTT Leptosporangiate Monilophytes.p1 Musacu GSMUA Achr8T26360 001 Pteens 2012476 FLTD Leptosporangiate Monilophytes.p1 Ptevit 2005790 POPJ Leptosporangiate Monilophytes.p1 Ptevit 2005792 POPJ Leptosporangiate Monilophytes.p1 Musacu GSMUA Achr4T03190 001 Adirad 2061173 BMJR Leptosporangiate Monilophytes.p1 Adiale 2064460 WCLG Leptosporangiate Monilophytes.p1 Vitlin 2009376 SKYV Leptosporangiate Monilophytes.p1 Dencat lcl NW 021319127.1 XP 020673116.1 12405 Vitapp 2103686 NDUV Leptosporangiate Monilophytes.p1 Dencat lcl NW 021319127.1 XP 020673114.1 12403 Notmon 2003740 YCKE Leptosporangiate Monilophytes.p1 Gagari 2013757 DCDT Leptosporangiate Monilophytes.p1 Dencat lcl NW 021319127.1Musacu GSMUA XP 020673115.1 AchrUn randomT24020 12404 001 Argniv 2008666 XDDT Leptosporangiate Monilophytes.p1 Myrruf 2003768 GSXD Leptosporangiate Monilophytes.p1 Myrruf 2003767 GSXD Leptosporangiate Monilophytes.p1 Myrruf 2003766 GSXD Leptosporangiate Monilophytes.p1 Asppla 2061239 KJZG Leptosporangiate Monilophytes.p1 Junsco 2057620 XMGP Conifers.p1 Aspnid 2011743 PSKY Leptosporangiate Monilophytes.p1 Nepexa 2030515 NWWI Leptosporangiate Monilophytes.p1 CupdupTetsp. 2072669 2068298 QNGJ CGDN Conifers.p1 Conifers.p1 Davfej 2224136 OQWW Leptosporangiate Monilophytes.p1 Caldec 2011126 FRPM Conifers.p1 Phlpse 2111761 ZQYU Leptosporangiate Monilophytes.p1 Aposhe lcl KZ452026.1 PKA50389.1 16988 Phygro 2019258 ORJE Leptosporangiate Monilophytes.p1 Dencat lcl NW 021318912.1 XP 020674112.1Micdec 8256 2055526 XQSG Conifers.p1 Polamo 2070845 YLJA Leptosporangiate Monilophytes.p1 Plaori 2052106 BUWV Conifers.p1 Polgly 2013958 CJNT Leptosporangiate Monilophytes.p1 Dencat lcl NW 021318912.1 XP 020674111.1 8255Chalaw 2068446 AIGO Conifers.p1 Polhes 2033157 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 FokhodPiluvi 2059475 2060714 UEVI ETCJ Conifers.p1 Conifers.p1 Polhes 2001113 GYFU Leptosporangiate Monilophytes A type.p1 Polhes 2001114 GYFU Leptosporangiate Monilophytes A type.p1 Theacu 2005445 MROH Leptosporangiate Monilophytes.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00059.25Pappap 2083163 OVIJ Conifers.p1 Hompyc 2003304 OCZL Leptosporangiate Monilophytes.p1 Hompyc 2003303 OCZL Leptosporangiate Monilophytes.p1 Auschi 2002037 YYPE Conifers.p1 Gymdry 2080359 HEGQ Leptosporangiate Monilophytes.p1 Disarc 2074586 GKCZ Conifers.p1 Cysfra 2072582 LHLE Leptosporangiate Monilophytes.p1 Cyspro 2067343 YOWV Leptosporangiate Monilophytes.p1 Widced 2003431 AUDE Conifers.p1 Cysfra 2087769 XXHP Leptosporangiate Monilophytes Stewart.p1 Cysfra 2010861 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Blespi 2039752 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 NeopanThupli 2069388 2039513 JDQB VFYZ Conifers.p1 Conifers.p1 Blespi 2013346 VITX Leptosporangiate Monilophytes.p1 Blespi 2039751 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Thudol 2049862 NKIN Conifers.p1 Onosen 2040880 HTFH Leptosporangiate Monilophytes.p1 Deplob 2002861 FCHS Leptosporangiate Monilophytes crenata.p1 Cryjap 2074567 DSXO Conifers.p1 Athfil 2064642 URCP Leptosporangiate Monilophytes.p1 Dipwic 2010643 UFJN Leptosporangiate Monilophytes.p1 Wooilv 2003005 YQEC Leptosporangiate Monilophytes.p1 Calmac 2054233 RMMV Conifers March.p1 Woosco 2004929 YJJY Leptosporangiate Monilophytes.p1 Angeve 2012409 NHCM Eusporangiate Monilophytes.p1 GlypenTaxdis 2045362 2063286 OXGJ FHST Conifers.p1 Conifers.p1 Equhye 2127088 JVSZ Eusporangiate Monilophytes.p1 Cryjap 2109772 HOUF Conifers leaf.p1 Equdif 2038810 CAPN Eusporangiate Monilophytes.p1 Metgly 2062776 NRXL Conifers.p1 Psinud 2012200 QVMR Eusporangiate Monilophytes.p1 Athcup 2061804 XIRK Conifers.p1 Pintae PTA00027166 Tmepar 2102787 ALVQ Eusporangiate Monilophytes.p1 Taicry 2066530 QSNJ Conifers.p1 Ophpet 2008425 WTJG Eusporangiate Monilophytes.p2 Botvir 2102445 BEGM Eusporangiate Monilophytes.p1 Scedis 2014583 EEAQ Eusporangiate Monilophytes.p1 Cunlan 2004437 OUOI Conifers.p1 Pinpin PPI00063958 Osmjav 2076581 VIBO Leptosporangiate Monilophytes.p1 Osmsp. 2078296 UOMY Leptosporangiate Monilophytes gametophyte.p1 Sciver 2007838 YFZK Conifers.p1 Pinpin PPI00005921 Dipcon 2005627 MEKP Leptosporangiate Monilophytes.p1 Dipcon 2005626 MEKP Leptosporangiate Monilophytes.p1 Pinsyl PSY00006947 Hymbiv 2003705 QIAD Leptosporangiate Monilophytes.p1 Lygjap 2015440 PBUU Leptosporangiate Monilophytes.p1 Agarob 2008142 MIXZ Conifers.p1 Picsit PSI00007607 Anetom 2000639 CQPW Leptosporangiate Monilophytes.p1 Anetom 2000638 CQPW Leptosporangiate Monilophytes.p1 Agamac 2001393 ACWS Conifers.p1 Pilglo 2088397 KIIX Leptosporangiate Monilophytes.p1 Salcuc Sacu v1.1 s0076.g017543 Ararul 2006892 XTZO Conifers.p1 Azofil Azfi s0007.g010837 AgamacWolnob 2001394 2056570 ACWS RSCE Conifers.p1 Conifers.p1 Azocar 2016997 CVEG Leptosporangiate Monilophytes.p1 Ararul 2006893 XTZO Conifers.p1 Azocar 2016996 CVEG Leptosporangiate Monilophytes.p1 Cyaspi 2069355 GANB Leptosporangiate Monilophytes.p1 Ptevit 2005791 POPJ Leptosporangiate Monilophytes.p1 Cryacr 2000752 WQML Leptosporangiate Monilophytes.p1 Cryacr 2000753 WQML Leptosporangiate Monilophytes.p1 Psemen PME00021069 Adirad 2011850 BMJR Leptosporangiate Monilophytes.p1 Pinrad 2012758 DZQM Conifers.p1 Adiale 2064219 WCLG Leptosporangiate Monilophytes.p1 Pinpon 2013550 JBND Conifers.p1 Adirad 2007357 BMJR Leptosporangiate Monilophytes.p1 Cryjap 2144714 GMHZ Conifers 2 samples combined.p1 Pinjef 2016747 MFTM Conifers.p1 Adirad 2007356 BMJR Leptosporangiate Monilophytes.p1 Picabi MA 10431096g0010 Gagari 2002587 DCDT Leptosporangiate Monilophytes.p1 Parcor 2010082 ZXJO Leptosporangiate Monilophytes.p1 Ginbil Gb 31937 Myrruf 2064295 GSXD Leptosporangiate Monilophytes.p1 Argniv 2005633 XDDT Leptosporangiate Monilophytes.p1 Pinpar 2013931 IIOL Conifers.p1 Dendav 2001980 MTGC Leptosporangiate Monilophytes.p1 Linlin 2005512 NOKI Leptosporangiate Monilophytes.p1 Linmic 2054588 YIXP Leptosporangiate Monilophytes.p1 Cycmic CMI00014578 Asppla 2013491 KJZG Leptosporangiate Monilophytes.p1 Theacu 2007329 MROH Leptosporangiate Monilophytes.p1 Leuimm 2073461 WGTU Leptosporangiate Monilophytes.p1 Hompyc 2005751 OCZL Leptosporangiate Monilophytes.p1 Catagr 2009148 NPRL Conifers.p1 Athfil 2064695 URCP Leptosporangiate Monilophytes.p1 Dipwic 2086329 UFJN Leptosporangiate Monilophytes.p1 Gymdry 2010939 HEGQ Leptosporangiate Monilophytes.p1 Ginbil Gb 06593 Cysuta 2029810 HNDZ Leptosporangiate Monilophytes.p1 Cysree 2007764 RICC Leptosporangiate Monilophytes.p1 Cysfra 2071546 LHLE Leptosporangiate Monilophytes.p1 Cysfra 2009137 XXHP Leptosporangiate Monilophytes Stewart.p1 Cyspro 2066825 YOWV Leptosporangiate Monilophytes.p1 Piceng 2004426 AWQB Conifers.p1 Cysfra 2006874 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Blespi 2013562 VITX Leptosporangiate Monilophytes.p1 Cunlan 2101266 ZQVF Conifers 2 samples combined.p1 Onosen 2040799 HTFH Leptosporangiate Monilophytes.p1 Woosco 2014790 YJJY Leptosporangiate Monilophytes.p1 Psewil 2008711 IOVS Conifers.p1 Deplob 2006647 FCHS Leptosporangiate Monilophytes crenata.p1 Didtru 2004899 RFRB Leptosporangiate Monilophytes.p1 Polacr 2072755 FQGQ Leptosporangiate Monilophytes.p1 Bolrep 2017592 JBLI Leptosporangiate Monilophytes.p1 Davfej 2000959 OQWW Leptosporangiate Monilophytes.p1 Davfej 2000958 OQWW Leptosporangiate Monilophytes.p1 Cycmic CMI00000722 Davfej 2000960 OQWW Leptosporangiate Monilophytes.p1 Phygro 2010363 ORJE Leptosporangiate Monilophytes.p1 Plepol 2073871 UJWU Leptosporangiate Monilophytes dehydrating fronds.p1 Phlpse 2017022 ZQYU Leptosporangiate Monilophytes.p1 Polgly 2001250 CJNT Leptosporangiate Monilophytes.p1 Polhes 2006985 IXLH Leptosporangiate Monilophytes B type.p1 Polhes 2011512 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Polamo 2071355 YLJA Leptosporangiate Monilophytes.p1 Notlon 2066528 AREG Conifers.p1 Polhes 2003348 GYFU Leptosporangiate Monilophytes type.p1A Polhes 2003347 GYFU Leptosporangiate Monilophytes type.p1A Welmir 2061106TOXE Gnetales.p1 Gnemon 2056110 GTHK Gnetales.p1 GnemonTnS000468567t13 Pinpar 2014438 IIOL Conifers.p1 Larspe 2006037 WVWN Conifers.p1 Pinsyl PSY00005866 Pintae PTA00027135 Pinpin PPI00014679 Pinrad 2006159 DZQM Conifers.p1 Pintae PTA00048217 TsuhetAbilas 2010028 2010132 GAMH VSRH Conifers.p1 Conifers.p1 Pinpon 2014049 JBND Conifers.p1 Pinjef 2016991 MFTM Conifers.p1 Keteve 2015758 JUWL Conifers.p1

Pseama 2014063 AQFM Conifers.p1

Cycmic 2011238 XZUY Cycadales.p1 Staeri 2005255 KAWQ Cycadales.p1 Encbar 2009091 GNQG Cycadales.p1

Ginbil 2039089Staeri 2055793 SGTW KAWQGinkgoales.p1 Cycadales.p1

Dioedu 2120002 WLIC Cycadales.p1 Encbar 2012164 GNQG Cycadales.p1

Cycmic 2007589 XZUY Cycadales.p1 Faltax 2061434 ROWR Conifers.p1 Ginbil 2004150 SGTW Ginkgoales.p1Dacbal 2013694 IZGN Conifers.p1 Faltax 2003104 QHBI Conifers A.p1

Retmin 2006747 VGSX Conifers.p1 Daccom 2009182Retmin FMWZ 2006749 Conifers.p1 VGSX Conifers.p1 Nagnag 2002551Podcor 2052676 UUJS Conifers.p1 SCEB Conifers.p1 Podrub 2057092 XLGK Conifers.p1 Acmpan 2113250Mictet 2073237 HILW MHGD Conifers.p1 Conifers.p1 Picsit PSI00005746

Phyhyp 2067782 JRNA Conifers.p1 Parust 2038763 JZVE Conifers.p1 Saxcon 2074565 QCGM Conifers.p1 Mancol 2062481 CDFR Conifers.p1 Psemen PME00107892 Psemen PME00107899 Psemen PME00107896 Lagfra 2088442 ZQWM Conifers.p1 Psemen PME00107890 Psemen PME00107903 Psemen PME00107894 Psemen PME00107904 Psemen PME00107901 Pruand 2038508 EGLZ Conifers.p1 Sunama 2093455 KLGFLepsp. Conifers.p1 2077036 BBDD Conifers.p1 Halbid 2055247 OWFC Conifers.p1Ararul 2062965 XTZO Conifers.p1

Wolnob 2055365 RSCE Conifers.p1 Agamac 2067290 ACWS Conifers.p1 Glypen 2007371 OXGJ Conifers.p1 Auschi 2067147 YYPE Conifers.p1 Neopan 2004117 JDQB Conifers.p1 Metgly 2060096Athcup NRXL 2062327 Conifers.p1Taicry XIRK 2062497Conifers.p1 QSNJ Conifers.p1

Cunlan 2002329 OUOI Conifers.p1 Taxcus 2003485 ZYAX Conifers.p1

Cryjap 2106985 HOUF Conifers leaf.p1 Taxcus 2003486Ausspi ZYAX 2076966 Conifers.p1 BTTS Conifers.p1 Psechi 2011551 YLPM Conifers.p1 Tortax 2014003 EFMS Conifers.p1 Faltax 2081911 PLYX Conifers 2 samples combined.p1 Cephar 2059913 GJTI Conifers.p1 Taxbac 2008703 WWSS Conifers.p1 Sciver 2043100 YFZK Conifers.p1 Tornuc 2018105 HQOM Conifers.p1 Amearg 2022388 IAJW Conifers.p1

Cephar 2010295 WYAJ Conifers.p1 Psewil 2056064 IOVS Conifers.p1

Abilas 2011441 VSRH Conifers.p1

Catagr 2014123 NPRL Conifers.p1 Cedlib 2015371 GGEA Conifers.p1

Keteve 2015752 JUWL Conifers.p1

Tsuhet 2010540 GAMH Conifers.p1

Piceng 2055493 AWQB Conifers.p1

Larspe 2052702 WVWN Conifers.p1 Calmac 2006888 RMMV Conifers March.p1 Pseama 2013507 AQFM Conifers.p1

Cryjap 2142416 GMHZ Conifers 2 samples combined.p1

Cunlan 2004675 ZQVF Conifers 2 samples combined.p1

Cephar 2110936 NVGZ Conifers 2 samples combined.p1

Tree scale: 0.1 Supplementary Figure 28: Maximum likelihood tree of SYN.

Hupsel 2167000 YHZW Lycophytes 2 samples combined.p1

Marpal 2006701 LFVP Liverworts 2 samples combined.p1

Marpal 2006700 LFVP Liverworts 2 samples combined.p1

Marpal 2000832 HMHL Liverworts non mycorrizal.p1 Hupsqu 2008535 GAON Lycophytes.p1 Hupsqu 2008536 GAON Lycophytes.p1 Marpal 2000833 HMHL Liverworts non mycorrizal.p1 Denobs 2005823 XNXF Lycophytes.p1 Denobs 2005822 XNXF Lycophytes.p1 Lycdeu 2013184 PQTO Lycophytes.p1 Lycann 2002072 ENQF Lycophytes.p1 Marpal 2004072 IHWO Liverworts mycorrizal.p1 Psecar 2005505 UPMJ Lycophytes.p1 Psecar 2005504 UPMJ Lycophytes.p1 Dipdig 2015413 WAFT Lycophytes.p1 Psecar 2005503 UPMJ Lycophytes.p1 Marpal 2004071 IHWO Liverworts mycorrizal.p1 Lycapp 2002868 ULKT Lycophytes.p1

Isoteg 2097194 PKOX Lycophytes.p1 Selapo 2003860 LGDQ Lycophytes.p1 Marpal 2084709 LFVP Liverworts 2 samples combined.p1 Selsta 2053071 ZZOL Lycophytes.p1 Selaca 2007139 ZYCD Lycophytes.p1 Selwal 2002568 JKAA Lycophytes.p1 Sellep 2009135ABIJ Lycophytes.p1 Selkra 2004370 ZFGK Lycophytes.p1

Selsel 2006116Selwil KUXM 2012860 Lycophytes.p1 KJYC Lycophytes.p1 Marpal 2004701 HMHL Liverworts non mycorrizal.p1

Salcuc Sacu v1.1 s0095.g019192

Marpal 2066857 IHWO Liverworts mycorrizal.p1

Marpol 2038923 JPYU Liverworts.p1 Azofil Azfi s0113.g045884 Marema 2075207 TFYI Liverworts.p1 Concon 2045156 ILBQ Liverworts.p1 Marpal scaff12744 FGenesh3.1

Selmoe 443146 Marpol Mapoly0062s0097.1

Marpol Mapoly0009s0005.1 Marpol 2009006 JPYU Liverworts.p1 Marema 2002368 TFYI Liverworts.p1 Selmoe 124666 Ricnat 2004899 WJLO Liverworts.p1Marpal scaff14115 FGenesh4.1 Ricnat 2004897 WJLO Liverworts.p1 Concon 2045873 ILBQ Liverworts.p1 Luncru 2007605 TXVB Liverworts.p1 Marpol Mapoly0055s0091.1 Sphtex 2041567 HERT Liverworts.p2 Sphtex 2008716 HERT Liverworts.p1

Hupmyr 2056098 CBAE Lycophytes.p1 Hupsel 2030274 YHZW Lycophytes 2 samples combined.p1 Hupsel 2030272 YHZW Lycophytes 2 samples combined.p1 usl2018447Hupsel GTUO Lycophytes.p1 Hupsel 2015208 NYBX Lycophytes A.p1 Hupluc 2016118 GKAG Lycophytes.p1 Hupluc 2016119 GKAG Lycophytes.p1 Hupsel 2015209 NYBX Lycophytes A.p1 Barbar 2024680 OFTV Liverworts.p1 Phydru 2023976 ZZEI Lycophytes.p1 Equhye 2003204 JVSZ Eusporangiate Monilophytes.p1 Scanem 2164547 IRBN Liverworts.p1 Equdif 2039299 CAPN Eusporangiate Monilophytes.p1 Angeve 2004197 NHCM Eusporangiate Monilophytes.p1 Psinud 2017668 QVMR Eusporangiate Monilophytes.p1 Tmepar 2007177 ALVQ Eusporangiate Monilophytes.p1 Odopro 2129508 YBQN Liverworts.p1 Tmepar 2007176 ALVQ Eusporangiate Monilophytes.p1 Botvir 2011538 BEGM Eusporangiate Monilophytes.p1 Botvir 2011537 BEGM Eusporangiate Monilophytes.p1 Ophvul 2017880 QHVS Eusporangiate Monilophytes leaf.p1 Ophpet 2006363 WTJG Eusporangiate Monilophytes.p1 Ophpet 2006362 WTJG Eusporangiate Monilophytes.p1 MixspeCalfis 2156689 2182890 NWQC RTMU Liverworts.p1 Liverworts.p1 Osmsp. 2080359 UOMY Leptosporangiate Monilophytes gametophyte.p1 Osmjav 2077625 VIBO Leptosporangiate Monilophytes.p1 Dipcon 2014336 MEKP Leptosporangiate Monilophytes.p1 Hymbiv 2056673 QIAD Leptosporangiate Monilophytes.p1 Lygjap 2011954 PBUU Leptosporangiate Monilophytes.p1 Schisp.Baztri 2104252 2017406 LGOW WZYK Liverworts.p1 Liverworts.p1 Anetom 2015522 CQPW Leptosporangiate Monilophytes.p1 Pilglo 2088888 KIIX Leptosporangiate Monilophytes.p1 Salcuc Sacu v1.1 s0004.g002159 Salcuc Sacu v1.1 s0092.g018921 Azocar 2025400 CVEG Leptosporangiate Monilophytes.p1 Pelnee 2014546 JHFI Liverworts.p1 Azofil Azfi s0059.g034575 Thyele 2009564 EWXK Leptosporangiate Monilophytes.p1 Pelepi 2002813 PIUF Liverworts.p1 Cyaspi 2007756 GANB Leptosporangiate Monilophytes.p1 Linlin 2013466 NOKI Leptosporangiate Monilophytes.p1 MetcraPtipul 2100507 2133751 NRWZ HPXA Liverworts.p1 Liverworts.p1 Linmic 2004729 YIXP Leptosporangiate Monilophytes.p1 Linmic 2004732 YIXP Leptosporangiate Monilophytes.p1 Linlin 2013413 NOKI Leptosporangiate Monilophytes.p1 Porpin 2149342 UUHD Liverworts.p1 Linmic 2004728 YIXP Leptosporangiate Monilophytes.p1 Pornav 2004867 KRUQ Liverworts.p1 Ptevit 2013242 POPJ Leptosporangiate Monilophytes.p1 Pteens 2018128 FLTD Leptosporangiate Monilophytes.p1 Frusp. 2136403 TGKW Liverworts.p1 Pittri 2017305 UJTT Leptosporangiate Monilophytes.p1 Cryacr 2013552 WQML Leptosporangiate Monilophytes.p1 Fruspp 2021863 CHJJ Liverworts.p1 Myrruf 2065475 GSXD Leptosporangiate Monilophytes.p1 Argniv 2000566 XDDT Leptosporangiate Monilophytes.p1 Pelepi 2002814 PIUF Liverworts.p1 Notmon 2065006 YCKE Leptosporangiate Monilophytes.p1 Gagari 2013107 DCDT Leptosporangiate Monilophytes.p1 Pelnee 2016247 JHFI Liverworts.p1 Parcor 2010965 ZXJO Leptosporangiate Monilophytes.p1 Adiale 2063030 WCLG Leptosporangiate Monilophytes.p1 BlaspNW c333196 g1 i6 m.136210 Adirad 2013461 BMJR Leptosporangiate Monilophytes.p1 BlaspNW c333196 g1 i13 m.136218 Adirad 2013460 BMJR Leptosporangiate Monilophytes.p1 Vitapp 2104748 NDUV Leptosporangiate Monilophytes.p1 BlaspNW c333196 g1 i5 m.136208 Vitlin 2064860 SKYV Leptosporangiate Monilophytes.p1 BlaspNW c333196 g1 i4 m.136206 Dendav 2047090 MTGC Leptosporangiate Monilophytes.p1 Leuimm 2012561 WGTU Leptosporangiate Monilophytes.p1 BlaspNW c333196 g1 i8 m.136212 Polacr 2007123 FQGQ Leptosporangiate Monilophytes.p1 BlaspNW c333196 g1 i10 m.136214 Nepexa 2009788 NWWI Leptosporangiate Monilophytes.p1 BlaspNW c333196 g1 i14 m.136221 Nepexa 2009786 NWWI Leptosporangiate Monilophytes.p1 Davfej 2024989 OQWW Leptosporangiate Monilophytes.p1 Plepol 2013008 UJWU Leptosporangiate Monilophytes dehydrating fronds.p1 Physsp. 2082010 YEPO Mosses.p1 Phlpse 2111729 ZQYU Leptosporangiate Monilophytes.p1 Phygro 2016988 ORJE Leptosporangiate Monilophytes.p1 Timaus 2018218 ZQRI Mosses.p1 Polgly 2079134 CJNT Leptosporangiate Monilophytes.p1 Phypat Pp3c4 32180V3.1 Polhes 2106733 GYFU Leptosporangiate Monilophytes A type.p1 Physsp. 2003577 YEPO Mosses.p1 Polhes 2008687 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Polamo 2071929 YLJA Leptosporangiate Monilophytes.p1 Hedcil 2048347 YWNF Mosses.p1 Polhes 2006233 IXLH Leptosporangiate Monilophytes B type.p1 Aulhet 2005762 WNGHPhypat Pp3c3Mosses.p1 13140V3.1 Onosen 2008313 HTFH Leptosporangiate Monilophytes.p1 Woosco 2076588 YJJY Leptosporangiate Monilophytes.p1 BuxaphDipfol 2069385 2012499 HRWG AWOI Mosses.p1 Mosses.p1 Wooilv 2012515 YQEC Leptosporangiate Monilophytes.p1 Theacu 2006482 MROH Leptosporangiate Monilophytes.p1 Tetpel 2004277 HVBQ Mosses.p1 Athfil 2003789 URCP Leptosporangiate Monilophytes.p1 Andrup 2094392 WOGB Mosses.p1 Blespi 2024554 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Blespi 2098283 VITX Leptosporangiate Monilophytes.p1 Blespi 2024553 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Sphpal 2035453 RCBT Mosses.p1 Deplob 2066358 FCHS Leptosporangiate Monilophytes crenata.p1 Sphles 2083461Sphfal GOWD Sphfalx0166s0012.1 Mosses.p1 Dipwic 2014678 UFJN Leptosporangiate Monilophytes.p1 Phacar 2139554 RXRQ Hornworts sporophyte.p1 Aspnid 2014465 PSKY Leptosporangiate Monilophytes.p1 Phacar 2009492 WCZB Hornworts gametophyte.p1 Asppla 2013639 KJZG Leptosporangiate Monilophytes.p1 Taklep 2013110 SKQD Mosses.p1 Gymdry 2079964 HEGQ Leptosporangiate Monilophytes.p1 Taklep 2013111Sphfal SKQD Sphfalx0064s0090.1 Mosses.p1 Cysuta 2130044 HNDZ Leptosporangiate Monilophytes.p1 Cysfra 2072924 LHLE Leptosporangiate Monilophytes.p1 Cysree 2064757 RICC Leptosporangiate Monilophytes.p1 Parhal 2056440 FAJB Hornworts.p1 Cysfra 2002830 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Notaen 2036000 DXOU Hornworts.p2 Cyspro 2067738 YOWV Leptosporangiate Monilophytes.p1 Phacar 2138941 RXRQ Hornworts sporophyte.p1 Cysfra 2088326 XXHP Leptosporangiate Monilophytes Stewart.p1 Notvin 2000402 TCBC Hornworts.p2 Welmir 2061735 TOXE Gnetales.p1 Megfla 2052638 UCRN Hornworts.p2 Gnemon 2008780 GTHK Gnetales.p1 Gnemon 2008781 GTHK Gnetales.p1 Gnemon TnS000244003t01 Larspe 2052308 WVWN Conifers.p1 Psewil 2056010 IOVS Conifers.p1 Psemen PME00108181 Pseama 2000970 AQFM Conifers.p1 Abilas 2055893 VSRH Conifers.p1 Keteve 2090086 JUWL Conifers.p1 Tsuhet 2011034 GAMH Conifers.p1 Notlon 2065082 AREG Conifers.p1 Cedlib 2004733 GGEA Conifers.p1 Catagr 2121099 NPRL Conifers.p1

99.2 Piceng 2055126 AWQB Conifers.p1 Picsit PSI00003640 100 Picabi MA 10427190g0010 100 Pinpar 2015949 IIOL Conifers.p1

100 99.9 Pinpin PPI00065215 89.2 99.1 Pinsyl PSY00012236 92.2 99.2 98.6 Pinpon 2012662 JBND Conifers.p1 97.1 Pinjef 2011562 MFTM Conifers.p1 97.4 100 Pinrad 2053868 DZQM Conifers.p1 99.9 88.4 100 Pintae PTA00045350 Vigang vigan.Vang02g09250.1 100 99.8 100 100 94.2 Ginbil 2039174 SGTW Ginkgoales.p1 99.8 86.3 Ginbil Gb 34888 85.4 Vigrad Vradi01g11590.1 94.281.994.1 100 Cycmic 2011584 XZUY Cycadales.p1 Vigung Vigun04g113100.1 Cycmic CMI00028609 Phavul Phvul.007G067400.1 81.1 99.9 98.3 99.4 Dioedu 2119379 WLIC Cycadales.p1 Phavul Phvul.004G081300.1 99.5 99.4 96.7 84.2 95.2 Encbar 2084414 GNQG Cycadales.p1 96.8 92.8 Glymax Glyma.02G072900.1 99.6 99.6 100 93.5 Staeri 2054235 KAWQ Cycadales.p1 91.6 100 96.6 100 91.8 95.8 Glymax Glyma.16G154200.1 97.3 Sciver 2043395 YFZK Conifers.p1 100 99.9 93.1 87.4 Ararul 2064212 XTZO Conifers.p1 Tripra Tp57577 TGAC v2 mRNA9455 99.6 Trisub lcl DF973364.1 GAU27967.1Cajcaj Ccajan 17025 16143 100 93 96.397.7 Wolnob 2056366 RSCE Conifers.p1 100 98.7 97.1 100 98.9 92.3 97.9

93.9 85 100 91.7 Agamac 2010907 ACWS Conifers.p1

Tripra Tp57577 TGAC v2 mRNA9451 100 93.3

97.5 88.8 Agarob 2073525 MIXZ Conifers.p1 100 100 100 99.9 Halbid 2053268 OWFC Conifers.p1 Medtru MtrunA17 Chr6g0461261 100

100 98.8 85.5 94.7 Sunama 2092549 KLGF Conifers.p1 99.5 99.7 90.8 99.5 100 Lepsp. 2076768 BBDD Conifers.p1 Cicari Ca 04643.1 81.1 87.4 99.9 90.3 96.2 99.3 Lagfra 2088541 ZQWM Conifers.p1 Aradur Aradu.Z06PE 100 91.1 99.9 Arahyp arahy.Tifrunner.gnm1.ann1.55IZK7.1 99.5 92.5 Mancol 2061577 CDFR Conifers.p1 Araipa Araip.DT1LC 99.8 97.7 100 Parust 2037542 JZVE Conifers.p1 Arahyp arahy.Tifrunner.gnm1.ann1.SNC74A.1 97.2 97.4 100 95.7 93.3 100 98.9 99.1 99.9 95.1 Phyhyp 2067036 JRNA Conifers.p1 99.4 84.3 98.8 92.7 94.282.499.3 Saxcon 2073082 QCGM Conifers.p1 Nissch Nissc1917S17072 100 90.4 98.8 99.9 85.2 81 Mictet 2072445 MHGD Conifers.p1 100 93.3 99.9 99 86.598.3 Lupang Lup001525.1 99.6 95.4 Acmpan 2112727 HILW Conifers.p1 99 100 96.6 Lupang Lup006063.1 96.493.1 Podrub 2057782 XLGK Conifers.p1 Casaus Castanospermum10070-PA 91.9 90.7 99.6 91.9 100 Podcor 2053116 SCEB Conifers.p1 100 88.3 Mimpud Mimpu537S25501 95.3 98.6 Nagnag 2006900 UUJS Conifers.p1 81.3 98.696.799.7 Mimpud Mimpu12785S14931 100 Retmin 2008858 VGSX Conifers.p1 99.9 10097.297.5 Daccom 2056737 FMWZ Conifers.p1 Chafas Chafa2509S19358 83.6 100 99.2 98.1 84.7 Dacbal 2072244 IZGN Conifers.p1 Chafas Chafa2647S19818 85.5 89.1 100 100 84.1 Faltax 2057538 QHBI Conifers A.p1 Cercan Cerca43S24584 86.4 Faltax 2061212 ROWR Conifers.p1 Querob Qrob P0414090.2 100 Casmol maker-scaffold05344-augustus-gene-0.14-mRNA-1 99.9 84.2 88.4 81.199.4 Faltax 2082233 PLYX Conifers 2 samples combined.p1 100 Cephar 2016519 NVGZ Conifers 2 samples combined.p1 100 96.4 91.382.6 Alnglu Alngl51846S31566 99.8 Cephar 2089361 WYAJ Conifers.p1 86.3 Casgla Casgl43S17819 99.8 88.9 92.2 Cephar 2008370 GJTI Conifers.p1 81.8 Amearg 2149475 IAJW Conifers.p1 Jugreg g37989.t1 80.3 100 98.5 Tortax 2080186 EFMS Conifers.p1 Pyrcom PCP040120.1 91.391.6 Pyrcom PCP011435.1 90.8 98.7 Tornuc 2135816 HQOM Conifers.p1 83.3 98.9 Taxcus 2010451 ZYAX Conifers.p1 84.7 97.7 10096.4 Pyrbre lcl NW 008988174.1 XP 009366471.1 18732 99.9 Taxbac 2002347 WWSS Conifers.p1 99.2 Pyrbre lcl NW 008988174.1 XP 009366470.1 18731 100 100 Ausspi 2077959 BTTS Conifers.p1 Maldom MDP0000278269 95.9 93.1 97 97.4 85.1100 Psechi 2080051 YLPM Conifers.p1 Maldom MDP0000122104 Taicry 2065275 QSNJ Conifers.p1 100 96.2 Pyrcom PCP016977.1 99.8 Athcup 2061581 XIRK Conifers.p1 99.7 9298.8 Metgly 2062181 NRXL Conifers.p1 Pyrbre lcl NW 008988064.1Maldom XP 009353111.1 MDP0000295664 6451 99.9 Glypen 2045097 OXGJ Conifers.p1 98.4 99.996.5 Pruper Prupe.7G006600.1 99.6 Taxdis 2063312 FHST Conifers.p1 92.9 89.7 Cunlan 2013170 OUOI Conifers.p1 Prudul Prudul26A001937P1 100 100 97.1 100 Cunlan 2011627 ZQVF Conifers 2 samples combined.p1 86.8 Cunlan 2008849 ESYX Conifers branch apex with needles.p1 Prumum lcl NC 024133.1 XP 008240502.1 24227 SYN 88.8 99.6 Cryjap 2013389 DSXO Conifers.p1 Pruavi Pav sc0000575.1 g290.1.mk 89.3 83.6 99.6 100 86.3 Cryjap 2109020 HOUF Conifers leaf.p1 Fraana FAN iscf00142547.1.g00001.1Fraves FvH4 1g28350.1 97.2 Potmic 31966 t Cryjap 2017568 GMHZ Conifers 2 samples combined.p1 100 Thudol 2049776 NKIN Conifers.p1 100 97.7 99.7 99.2 Thupli 2008959 VFYZ Conifers.p1 Roschi RchiOBHmRubocc Chr3g0496741 Bras G20203 99.8 Chalaw 2067634 AIGO Conifers.p1 Drydru Drydr247S08954 Fokhod 2011522 UEVI Conifers.p1 98.9 99.7 Cupdup 2072202 QNGJ Conifers.p1 Drydru Drydr121S15201 84.3 97.3 100 Drydru Drydr127S15358 100 100 Junsco 2011810 XMGP Conifers.p1 Caldec 2059385 FRPM Conifers.p1 100 100 Tetsp. 2010772 CGDN Conifers.p1 97.8 99.4 100 Plaori 2051742 BUWV Conifers.p1 Zizjuj lcl NW 015454350.1 XP 024925359.1 40012 Micdec 2052709 XQSG Conifers.p1 100 Auschi 2067015 YYPE Conifers.p1 Zizjuj lcl NW 015454350.1 XP 015869431.1 40011 94.6 99.7 Zizjuj lcl NW 015454381.1 XP 015869508.1 40081 99.9 Pappap 2011401 OVIJ Conifers.p1 Distri Distr2552S20032 93 Widced 2058049 AUDE Conifers.p1 99.5 85.9 Zizjuj lcl NW 015454391.1 XP 024925384.1 40099 99.6 96.3 98.2 80 100 100 Disarc 2014345 GKCZ Conifers.p1 Zizjuj lcl NW 015454391.1 XP 015869524.1 40098 100 Piluvi 2060499 ETCJ Conifers.p1 Humlup HL.SW.v1.0.G000196.1 95.4 91.5 97.1 88.280.9 99.6 Humlup HL.SW.v1.0.G013726.1 95.5 100 Calgra 2006778 IFLI Conifers March.p1 99.4 100 99.9 85.8 97.3 Calmac 2054461 RMMV Conifers March.p1 100 99.7 97.8 Neopan 2069045 JDQB Conifers.p1 92.6 99.7 Ambtri evm 27.model.AmTr v1.0 scaffold00004.233 Cucsat evm.model.Chr3.3988 100 100 93.6 Parand lcl JXTB01000266.1 PON49130.1 23218 96.2 Aposhe lcl KZ451939.1 PKA60314.1 6966 Cucmel MELO3C026621.2.1 Treori lcl JXTC01000092.1 PON89603.1 14587 Anacom Aco010577.1 Cucsat Lagsicevm.model.Chr3.3989 Lsi03G013190.1Citlan Cla017155 100 Musacu GSMUA Achr10T07900 001 100 93.8 89.8 96.2 Dencat lcl NW 021319982.1 XP 020674262.1 27113 99.4 Phaequ PEQU 42106 97.799.9 98 100 99.2 Phaequ PEQU 05541 Cucmax CmaCh14G011060.1 99.9 83.8 100 88 83 Cucmos CmoCh14G011100.1 100 Dencat lcl NW 021319835.1 XP 028555550.1 24792 100 100 Phaequ PEQU 34379 Cucpep Cp4.1LG03g09390.1 97.2 92.1 100 91.5 Musacu GSMUA Achr9T24850 001 97.3 100 99 92.5 Anacom Aco009072.1 Begfuc Begfu26066S28019Aralyr AL6G18460.t1 99.1 99.4 100 98.5 100 92.1 97.8 99.6 100 Anacom Aco020546.1 83.2 99.5 93.1 93.9 Bradis Bradi1g25880.1 Aratha AT5G08080.3 95.8 Arahal Araha.31158s0002.1 99.9 83.2 100 95 82.9 87.8 98.8 Horvul HORVU2Hr1G045350.3 99.9 Setita Seita.2G337400.1 Momcha lcl NW 019104892.1 XP 022158976.1 28288 98.6 Capgra Cagra.1365s0014.1 100 98.4 Sorbic Sobic.002G323700.1 Caprub Carub.0006s0697.1 100 Zeamay Zm00008a028993 99.8 93 99.4 BoestrBrarap Bostr.13129s0159.1 Brara.J02456.1 Zizjuj lcl NC 029682.1 XP 015881074.1 12734 99.9 97.2 Poptri Potri.007G123000.3 98.6 100 Brarap Brara.B00269.1 96.9 Gosrai Gorai.013G099700.1 93.8 100 Brarap Brara.C00327.1 100 82.8 86.5 86.5 Thecac Thecc1EG011324t1 99.5 Gosrai Gorai.005G150400.1 Eutsal Thhalv10014211m 99.8 Riccom 30086.m000215 86.1 95 100 97.5 85.3 97.1 Manesc Manes.12G075900.1 99.5 93.7 99.6 Manesc Manes.12G075900.2 Brarap Brara.E03504.1 99.8 100 97 Cepfol Cfol v3 24748 Brarap Brara.A03802.1 100 99.2 100 Carpap evm.model.supercontig 8.224 100 99.9 85.5

99.1 100 Citsin orange1.1g038457m Eutsal Thhalv10021203m 100 99.7 95.4 Citcle Ciclev10016039m

100 92.9 Fraexc FRAEX38873 v2 000317470.3 89.3 Caprub Carub.0003s0297.1 98.4

Tarhas lcl NW 010960187.1 XP 010550705.1 2865 86.3 89.2 Fraexc FRAEX38873 v2 000317470.2

Capgra Cagra.2098s0008.1Aralyr AL3G13660.t1 97.5 Tarhas lcl NW 010961290.1 XP 010528744.1 5461 98.8 91.1 100 Fraexc FRAEX38873 v2 000317470.1 Boestr Bostr.17549s0001.1 Fraexc FRAEX38873 v2 000288950.1

84.5 100 Aratha AT3G03800.1 99.4 100 Helann HanXRQChr11g0347181 Arahal Araha.0303s0006.1 80.7 Daucar DCAR 019284 Daucar DCAR 012949 91.4 Petaxi Peaxi162Scf00007g01112.1 100 98.5 Petaxi Peaxi162Scf00558g00218.1 Petaxi Peaxi162Scf01845g00009.1

98.7 96.4 Nicben Niben101Scf07429g00005.1 Gosrai Gorai.004G250800.1 100 Nicben Niben101Scf01926g05001.1 Thecac Thecc1EG025899t2 100 99.4 100 Capann CA07g12020 Carpap evm.model.supercontigGosrai Gorai.007G260300.1 51.144 Citsin orange1.1g023623mCepfol Cfol v3 20758 Solpen Sopen07g026100.1 Citcle Ciclev10021315m Sollyc Solyc07g052470.2.1 Solpen Sopen07g026100.2

99.9 99.2 100 Querob Qrob P0728970.2 Tarhas lcl NW 010966372.1 XP 010549686.1 24240 Casmol maker-scaffold00284-augustus-gene-1.10-mRNA-2 Manesc Manes.08G145800.1 Casmol maker-scaffold00284-augustus-gene-1.10-mRNA-1 Riccom 30072.m000983 Jugreg g11907.t1 Manesc Manes.09G139600.1 Jugreg g11907.t2 Poptri Potri.019G036700.1 Casgla Casgl307S01342 Chequi AUR62036289-RA Alnglu Alngl1357S07287 Chequi AUR62039738-RA Chafas Chafa16703S07263 Spiole Sp 175190Diacar Dca20532.1 czit.t1 Mimpud Mimpu145269S01353 Diacar Dca51659.1 Mimpud Mimpu4440S24224 Betvul Bv5 109450 rngd.t1 Cercan Cerca105S12022 100 Casaus Castanospermum02715-PA Casaus Castanospermum24061-PA Lotjap Lj0g3v0042819.1 Cajcaj Ccajan 13746 Solpen Sopen01g025910.1 Glymax Glyma.12G194800.1 Solpen Sopen01g025910.2 Glymax Glyma.13G307600.1 Sollyc Solyc01g056810.2.1 100 Phavul Phvul.005G114200.1 Vigung Vigun05g225900.1 Vigang vigan.Vang09g03250.1 Vigrad Vradi05g22650.1 Vigung Vigun10g004700.1 Capann CA10g18180 Vigung Vigun04g069200.1 Sollyc Solyc10g081580.1.1 Vigang vigan.Vang08g05390.1 Vigrad Vradi09g05320.1 Nicben Niben101Scf00207g04007.1Solpen Sopen10g032090.1 Nissch Nissc4608S09010 Arahyp arahy.Tifrunner.gnm1.ann1.G2H5J3.1 Nicben Niben101Scf10328g00011.1 Araipa Araip.6GW8K Petaxi Peaxi162Scf00061g01010.1 Aradur Aradu.DET4U Arahyp arahy.Tifrunner.gnm1.ann1.011VCX.1 Cicari Ca 00762.1 Medtru MtrunA17 Chr2g0322801 Tripra Tp57577 TGAC v2 mRNA4309 Trisub lcl DF973166.1 GAU17093.1 6151 Lupang Lup024169.1 Lupang Lup004249.1 Lupang Lup030298.1 Nicben Niben101Scf29098g00002.1 Lupang Lup026446.1 Lupang Lup001354.1 Nicben Niben101Scf09670g02010.1 Datglo Datgl318S08141 Petaxi Peaxi162Scf00060g01215.1 Begfuc Begfu3087S30105 Begfuc Begfu2789S28555 Cucmax CmaCh20G006290.1 Daucar DCAR 013472 Cucmos CmoCh20G006150.1 Cucpep Cp4.1LG16g04480.1 Citlan Cla010492 Cucmel MELO3C019244.2.1 Lagsic Lsi10G001450.1 Momcha lcl NW 019104503.1 XP 022140581.1 11577 Momcha lcl NW 019104503.1 XP 022140582.1 11578 Momcha lcl NW 019104503.1 XP 022140795.1 11580 Momcha lcl NW 019104503.1 XP 022140794.1 11579 Cucmos CmoCh02G001630.1 Cucpep Cp4.1LG05g14450.1 Fraexc FRAEX38873Helann v2 000320830.1 HanXRQChr01g0026321 Cucsat evm.model.Chr2.2632 Cucmel MELO3C034678.2.1 Distri Distr149S14853 Mornot L484 018255 Treori lcl JXTC01000059.1 PON93249.1 10822 Helann HanXRQChr11g0347901 Bradis Bradi1g56720.1 Parand lcl JXTB01000060.1 PON68750.1 9357 Parand lcl JXTB01000060.1 PON68749.1 9356 Treori lcl JXTC01000059.1 PON93248.1 10821 Fraexc FRAEX38873 v2 000291830.1 Humlup HL.SW.v1.0.G009507.1 BlaspNW c375734 g1 i1 m.182171 Rubocc Bras G06771 Roschi RchiOBHm Chr2g0159801 Potmic 25437 t Fraexc FRAEX38873Helann v2 000237370.1 HanXRQChr13g0398801 Horvul HORVU3Hr1G115630.1 Horvul HORVU6Hr1G095330.1 Horvul HORVU2Hr1G057360.2Orysat LOC Os07g07000.1 Zeamay Zm00008a026857 Horvul HORVU2Hr1G057350.3 Anacom Aco008762.1 Anacom Aco005157.1 Sorbic Sobic.002G043300.2Zeamay Zm00008a010484Setita Seita.2G042700.1 Zeamay Zm00008a039994

Phaequ PEQU 09042

Bradis Bradi4g05940.1 Setita Seita.3G347200.1

Sorbic Sobic.008G115500.1Zeamay Zm00008a012446

Musacu GSMUA Achr2T17410 001 Spipol Spipo4G0027300 Pyrcom PCP028071.1 Musacu GSMUA Achr7T16680 001 Orysat LOC Os06g07200.1 Pyrcom PCP014785.1

Zosmar Zosma264g00170.1 Zosmar Zosma116g00550.1

Horvul HORVU5Hr1G026120.1 Fraves FvH4 6g43430.1 Maldom MDP0000163989

Maldom MDP0000216913

Pruper Prupe.3G218900.1

Prudul Prudul26A010695P1

Aposhe lclAposhe KZ452015.1 lcl KZ451888.1 PKA50907.1 PKA66062.1 16339 1408

Musacu GSMUA Achr2T01540 001

Pruavi Pav sc0001073.1 g220.1.mk

Fraana FAN iscf00003279.1.g00001.1

Fraana FAN iscf00108357.1.g00001.1

Dencat lcl NW 021503063.1 XP 020684108.1 32851 Utrgib Utricularia gibba unitig 85 203402 206137 unitig 85.g27221.t1 1 CDS 875851891 27001

Utrgib Utricularia gibba unitig 578 3379351 3381350 unitig 578.g16709.t1 1 CDS 875827969 1619 Ambtri evm 27.model.AmTr v1.0 scaffold00004.123

Pyrbre lcl NW 008988678.1 XP 018499764.1 38759 Pyrbre lcl NW 008988678.1 XP 009342249.1 38760 Pyrbre lcl NW 008988065.1 XP 009353260.1 6585 Prumum lcl NC 024129.1 XP 008230082.1 14425 Pyrbre lcl NW 008988678.1 XP 009342248.1 38761

Tree scale: 0.1 Supplementary Figure 29: Maximum likelihood tree of CYTB561.

Osmsp. 2078236 UOMY Leptosporangiate Monilophytes gametophyte.p1

Dendav 2008164 MTGC Leptosporangiate Monilophytes.p1

Cryacr 2007457 WQML Leptosporangiate Monilophytes.p1

Adiale 2061660 WCLG Leptosporangiate Monilophytes.p1

Azocar 2020700 CVEG Leptosporangiate Monilophytes.p2 Vitapp 2100531 NDUV Leptosporangiate Monilophytes.p1

Adirad 2059137 BMJR Leptosporangiate Monilophytes.p1

Pteens 2016581 LeptosporangiateFLTD Monilophytes.p1

Dipcon 2013458 MEKP Leptosporangiate Monilophytes.p2 Lygjap 2005477 PBUU Leptosporangiate Monilophytes.p1 Lygjap 2005476 PBUU Leptosporangiate Monilophytes.p1 Hymbiv 2054956 QIAD Leptosporangiate Monilophytes.p1 Linmic 2051546YIXP Leptosporangiate Monilophytes.p1

Osmjav 2076306 VIBO Leptosporangiate Monilophytes.p1 2017303 SKYVVitlin Leptosporangiate Monilophytes.p1 Stilob 2033892 XDVM Leptosporangiate Monilophytes.p1 Linlin 2012818 NOKI Leptosporangiate Monilophytes.p1

Pittri 2090088 UJTT Leptosporangiate Monilophytes.p1

Pilglo 2005287 KIIX Leptosporangiate Monilophytes.p1

Tmepar 2096466ALVQ Eusporangiate Monilophytes.p1 Ophpet 2012498 WTJGPsinud Eusporangiate 2012581 QVMR Monilophytes.p1 Eusporangiate Monilophytes.p1 Angeve 2063803 NHCM Eusporangiate Monilophytes.p1

Scedis 2084879 EEAQ Eusporangiate Monilophytes.p1 Equhye 2128619 JVSZ Eusporangiate Monilophytes.p1 Equdif 2039032 CAPN Eusporangiate Monilophytes.p1

Phacar 2116198 WCZB Hornworts gametophyte.p1 Phacar 2116668 WCZB Hornworts gametophyte.p2

Phacar 2136295 RXRQ Hornworts sporophyte.p2 Phacar 2137693 RXRQ Hornworts sporophyte.p2 Phacar 2013311 WCZB Hornworts gametophyte.p1 Phacar 2020824 RXRQ Hornworts sporophyte.p2

Hupsel 2009457 YHZW Lycophytes 2 samples combined.p1

Hupsel 2009454 YHZW Lycophytes 2 samples combined.p1

Notaen 2036900 DXOU Hornworts.p1

Megfla 2050728 UCRN Hornworts.p1 Salcuc Sacu v1.1 s0024.g009175 Notvin 2000016 TCBC Hornworts.p1

Megfla 2050955 UCRN Hornworts.p1 Parhal 2011255 FAJB Hornworts.p2

Notvin 2010081 TCBC Hornworts.p1 Selapo 2001544 LGDQ Lycophytes.p1 Selapo 2001543 LGDQ Lycophytes.p1 Parhal 2001346 FAJB Hornworts.p3 Megfla 2050531 UCRN Hornworts.p1Parhal 2001347 FAJB Hornworts.p3 Selapo 2001545 LGDQ Lycophytes.p2 Notvin 2003496 TCBC Hornworts.p1

AzofilAzfi s0006.g009989 Sellep 2006804 ABIJ Lycophytes.p2 Selsta 2003397 ZZOLSellep Lycophytes.p2 2006805 ABIJ Lycophytes.p2 Selkra 2001530Selwil 2010636ZFGK Lycophytes.p2 KJYC Lycophytes.p1 Selkra 2001533 ZFGK Lycophytes.p2 Selkra 2001531 ZFGK Lycophytes.p2 Selaca 2006129Selkra 2001532 ZYCD Lycophytes.p3 ZFGK Lycophytes.p2 Selaca 2006130 ZYCD Lycophytes.p3

Selwal 2010367 JKAA Lycophytes.p3 Selsel 2006849Selwal 2010366KUXM Lycophytes.p1 JKAA Lycophytes.p3 Hupluc 2016651Selsel 2006848 GKAG Lycophytes.p1KUXM Lycophytes.p1

Hupsel 2023045 NYBXHupluc Lycophytes 2016650 A.p1 GKAG Lycophytes.p1 Hupsel 2022177 GTUO Lycophytes.p1

Hupsqu 2004111 GAON Lycophytes.p1 Hupsqu 2004113 GAONPhydru Lycophytes.p1 2004679 ZZEI Lycophytes.p1 Hupsqu 2004112 GAONPhydru Lycophytes.p1 2004680 ZZEI Lycophytes.p1 Hupmyr 2060738 CBAE Lycophytes.p1 Lycann 2012451 ENQF Lycophytes.p1 Lycann 2012452 ENQF Lycophytes.p1 LycdeuDipdig 2010290 2068431 PQTO WAFT Lycophytes.p1 Lycophytes.p1 Lycdeu 2010289 PQTO Lycophytes.p1 Denobs 2010213 XNXF Lycophytes.p1

Lycapp 2005892 ULKT Lycophytes.p1 Hupsel 2024322 YHZW Lycophytes 2 samples combined.p1 Psecar 2018237 UPMJ Lycophytes.p1 Lycdeu 2012566 PQTO Lycophytes.p1 Lycann 2081093 ENQF Lycophytes.p1 Denobs 2068339 XNXF Lycophytes.p1

Lycdeu 2078114 PQTO Lycophytes.p1 Selmoe 88335

PsecarDipdig 2005389 2066914 UPMJ WAFT Lycophytes.p1 Lycophytes.p1 Hupsel 2009937Lycapp NYBX 2016714 Lycophytes ULKT A.p1Lycophytes.p1

Myrruf 2063994 GSXD Leptosporangiate Monilophytes.p1 Argniv 2010329 XDDT Leptosporangiate Monilophytes.p1 Gagari 2006465 DCDT Leptosporangiate Monilophytes.p1 Parcor 2000816 ZXJO Leptosporangiate Monilophytes.p1 omn2011524 YCKENotmon Leptosporangiate Monilophytes.p1 Leuimm 2072390 WGTU Leptosporangiate Monilophytes.p1 Didtru 2032095 RFRB Leptosporangiate Monilophytes.p1 Cysuta 2007569 HNDZ Leptosporangiate Monilophytes.p1 Hupsel 2009936 NYBX Lycophytes A.p1 Cysree 2063726 RICC Leptosporangiate Monilophytes.p1 Cyspro 2066394 YOWV Leptosporangiate Monilophytes.p1 Cysfra 2087376 XXHP Leptosporangiate Monilophytes Stewart.p1 Lycapp 2013147 ULKT Lycophytes.p1 Cysfra 2008192 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Onosen 2040097 HTFH Leptosporangiate Monilophytes.p1 Asppla 2011006 KJZG Leptosporangiate Monilophytes.p1 Aspnid 2013482 PSKY Leptosporangiate Monilophytes.p1 Blespi 2096871 VITX Leptosporangiate Monilophytes.p1 Athfil 2011485 URCP Leptosporangiate Monilophytes.p1 Woosco 2074986 YJJY Leptosporangiate Monilophytes.p1 Dipwic 2085688 UFJN Leptosporangiate Monilophytes.p1 Theacu 2006036 MROH Leptosporangiate Monilophytes.p1 Bolrep 2100718 JBLI Leptosporangiate Monilophytes.p1 Hupmyr 2059608 CBAE Lycophytes.p1 Nepexa 2013889 NWWI Leptosporangiate Monilophytes.p1 Nepexa 2013888 NWWI Leptosporangiate Monilophytes.p1 Nepexa 2013886 NWWI Leptosporangiate Monilophytes.p1 Hupsqu 2056066 GAON Lycophytes.p1 Nepexa 2013887 NWWI Leptosporangiate Monilophytes.p1 Davfej 2019012 OQWW Leptosporangiate Monilophytes.p1 Plepol 2008845 UJWU Leptosporangiate Monilophytes dehydrating fronds.p1 Phlpse 2026480 ZQYU Leptosporangiate Monilophytes.p1 Polamo 2069539 YLJA Leptosporangiate Monilophytes.p1 Polhes 2025291 IXLH Leptosporangiate Monilophytes B type.p1 Polhes 2012812 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Polgly 2077809 CJNT Leptosporangiate Monilophytes.p1 Polhes 2027445 GYFU Leptosporangiate Monilophytes A type.p1 Dencat lcl NW 021319682.1 XP 020696997.1 22745 Hupluc 2017174 GKAG Lycophytes.p1 Phaequ PEQU 22889 Phydru 2008950 ZZEI Lycophytes.p1 Musacu GSMUA Achr8T29770 001 Spipol Spipo19G0020600 Lycann 2012829 ENQF Lycophytes.p1 Eutsal Thhalv10008642m Braolecap Bol043304 Brarap Brara.G00897.1 Isoesp. 2008765 PYHZ Lycophytes.p1 Brarap Brara.H02120.1 Braolecap Bol024968 Boestr Bostr.12659s0393.1 Caprub Carub.0001s2487.1 Capgra Cagra.11546s0006.1 Arahal Araha.50307s0002.1 Aralyr AL1G39680.t1 Isoesp.Isoteg 2010290 2096649 PYHZ PKOX Lycophytes.p1 Lycophytes.p1 Aratha AT1G26100.1 Betvul Bv6 141230 nfzd.t1 Trelac 2088620 FITN Liverworts.p1 Spiole Sp 144970 jdke.t1 Daucar DCAR 007222 Helann HanXRQChr17g0551321 Fraexc FRAEX38873 v2 000138680.1 Isoteg 2008070 PKOX Lycophytes.p1 Fraexc FRAEX38873 v2 000138680.3 Fraexc FRAEX38873 v2 000138680.2 Hupsel 2021487 TrelacGTUO 2086622 Lycophytes.p1 FITN Liverworts.p1 Nicben Niben101Scf01338g04003.1 Petaxi Peaxi162Scf00367g00727.1 Capann CA11g01760 Hupmyr 2059267 CBAE Lycophytes.p1 Solpen Sopen05g005760.1 Hupsqu 2056717Phydru GAON 2016635 Lycophytes.p1 ZZEI Lycophytes.p1 Sollyc Solyc05g009950.2.1 Nelnuc NNU 00598-RA Datglo Datgl825S35405 Lycdeu 2006598 PQTO Lycophytes.p1 Begfuc Begfu369S49201 Momcha lcl NW 019104556.1 XP 022150472.1 20723 Lycdeu 2006599 PQTO Lycophytes.p1 Cucmax CmaCh18G010500.1 Cucpep Cp4.1LG09g02610.1 Denobs 2011275 XNXF Lycophytes.p1 Cucmos CmoCh18G010700.1 Lagsic Lsi04G002980.1 Lycann 2006129 ENQF Lycophytes.p1 Cucsat evm.model.Chr5.2453 Citlan Cla020358 Psecar 2081405 UPMJ Lycophytes.p1 Thecac Thecc1EG011882t1 Gosrai Gorai.008G187200.1 Lycapp 2013842 ULKT Lycophytes.p1 Cepfol Cfol v3 20943 Carpap evm.model.supercontig 1.232 Citcle Ciclev10032628m Isoesp. 2073182 PYHZ Lycophytes.p1 Citsin orange1.1g030324m Manesc Manes.06G073500.1 Isoteg 2095705Trelac PKOX2090027 Lycophytes.p1 FITN Liverworts.p1 Riccom 29738.m001032 Poptri Potri.008G115200.2 Poptri Potri.010G131100.1 Mornot L484 022942 Selsta 2051532 ZZOL Lycophytes.p1 Zizjuj lcl NC 029688.1 XP 015895774.1 28135 Selapo 2010195 LGDQ Lycophytes.p1 Distri Distr1155S12414 Humlup HL.SW.v1.0.G032094.1 Sellep 2007347 ABIJ Lycophytes.p1 Treori lcl JXTC01000122.1 PON87028.1 17143 Selsel 2003586 KUXM Lycophytes.p1 Parand lcl JXTB01000024.1 PON75407.1 4374 Selsel 2003585 KUXM Lycophytes.p1 Rubocc Bras G02619 Roschi RchiOBHm Chr4g0436011 Potmic 6609 t Selwil 2010247 KJYC Lycophytes.p1 Fraves FvH4 4g28220.1 SelacaSelwal 2006770 2167874 ZYCD JKAA Lycophytes.p1 Lycophytes.p1 Fraana FAN iscf00231620.1.g00001.1 Drydru Drydr94S05980 Selkra 2039043 ZFGK Lycophytes.p1 Maldom MDP0000314476 Pyrbre lcl NW 008988477.1 XP 009336637.1 33666 Isoesp. 2071159 PYHZ Lycophytes.p1 Pyrcom PCP039351.1 Pyrcom PCP007784.1 Trelac 2087138 FITN Liverworts.p1 Pruavi Pav sc0010559.1 g020.1.mk Isoteg 2097764 PKOX Lycophytes.p1 Pruavi Pav co4061725.1 g010.1.mk Prumum lcl NW 007362496.1 XP 008243157.1 26755 Pruper Prupe.1G304000.1 Anocla 2001630 VBMM Mosses.p1 Prudul Prudul26A006910P1 Anocla 2001631 VBMM Mosses.p1 Querob Qrob P0039800.2 Selmoe 109639 Casmol maker-scaffold05674-augustus-gene-0.10-mRNA-1 Jugreg g28910.t1 Rhyser 2004984 JADL Mosses.p1 Casgla Casgl64S20302 Thudel 2037222 EEMJ Mosses.p1 Alnglu Alngl9449S37822 Stesub 2067027 LNSF Mosses.p1 Cercan Cerca45S24885 Lotjap Lj2g3v1172590.1 LoebreCliden 2043418 2011996 WSPM MIRS Mosses.p2 Mosses.p2 Cicari Ca 26709.1 Medtru MtrunA17 Chr5g0422371 Necdou 2009261 TMAJ Mosses.p1 Tripra Tp57577 TGAC v2 mRNA2771 Necdou 2009260 TMAJ Mosses.p1 Chafas Chafa447S22860 Anoatt 2010829 QMWB Mosses.p2 Mimpud Mimpu2373S20444 Casaus Castanospermum11865-PA Casaus Castanospermum02172-PA PseeleCalcor 2047925 2015390 QKQO TAVP Mosses.p1 Mosses.p1 Nissch Nissc524772S27741 Leubra 2005283 ZACW Mosses.p1 Arahyp arahy.Tifrunner.gnm1.ann1.KV992X.1 Leubra 2005285 ZACW Mosses.p1 Glymax Glyma.02G101300.1 Glymax Glyma.01G089700.1 Leubra 2005284 ZACW Mosses.p1 Cajcaj Ccajan 30510 Phavul Phvul.003G025900.1 FonantLeujul 2002002 2005037 DHWX IGUH Mosses.p1 Mosses.p1 Vigung Vigun02g027200.1 Vigrad Vradi11g12060.1 Tetpel 2127866 HVBQ Mosses.p1 Vigang vigan.Vang0004ss01200.1 Aulhet 2085946 WNGH Mosses.p1 Cycmic 2012759 XZUY Cycadales.p1 Bryarg 2006339 JMXW Mosses.p1 Cycmic CMI00012446 Bryarg 2006340 JMXW Mosses.p1 Dioedu 2019748 WLIC Cycadales.p1 Roscap 2047052 XWHK Mosses.p1 Staeri 2055347 KAWQ Cycadales.p1 Encbar 2010397 GNQG Cycadales.p1 Hedcil 2049061 YWNF Mosses.p1 Ginbil Gb 30842 Halbid 2046833 OWFC Conifers.p1 Plains 2078356 BGXB Mosses.p1 Podrub 2054516 XLGK Conifers.p1 Phifon 2002101 ORKS Mosses.p1 Daccom 2054935 FMWZ Conifers.p1 Mixspe 2153122Phifon 2002102 NWQC Liverworts.p2ORKS Mosses.p1 Amearg 2018684 IAJW Conifers.p1 Timaus 2065628 ZQRI Mosses.p1 Taicry 2009567 QSNJ Conifers.p1 Athcup 2056655 XIRK Conifers.p1 Dicsco 2006851 NGTD Mosses.p1 Cunlan 2013372 ZQVF Conifers 2 samples combined.p1 Cunlan 2007048 OUOI Conifers.p1 Synpri 2002979 GRKU Mosses.p1 Psemen PME00113745 Leugla 2061720 RGKI Mosses.p1 Psemen PME00113743 Leualb 2127247 VMXJ Mosses.p1 Psemen PME00113748 Polcom 2010103 SZYG MossesRacvar gametophyte.p1 2116325 RDOO Mosses.p1 Picabi MA 949599g0010 Racelo 2074622 ABCD Mosses.p1 Tsuhet 2052105 GAMH Conifers.p1 Scoaqu 2087013 BPSG Mosses.p1 Abilas 2010473 VSRH Conifers.p1 Abilas 2010474 VSRH Conifers.p1 Physsp. 2076989 YEPO Mosses.p1 Pinjef 2079371 MFTM Conifers.p1 Pintae PTA00016437 Pinpon 2066076 JBND Conifers.p1 Encstr 2059436 KEFD Mosses.p1 Pinsyl PSY00014407 Dipfol 2069948 AWOI Mosses.p1 Ginbil 2034566 SGTW Ginkgoales.p1 Phypat Pp3c16 7180V3.1 Ginbil Gb 30840 Atrang 2082268 ZTHV Mosses.p1 Ephsin 2032413 VDAO Gnetales.p1 Tetpel 2019142 HVBQ Mosses.p1 Welmir 2000042 TOXE Gnetales.p1 Leubra 2013049 ZACW Mosses.p1 Gnemon 2005067 GTHK Gnetales.p1 Gnemon TnS000785287t03 PseeleLeujul 2046040 2165698 QKQO IGUH Mosses.p1 Mosses.p1 Larspe 2049967 WVWN Conifers.p1 Anoatt 2010470 QMWB Mosses.p1 Psewil 2010240 IOVS Conifers.p1 Psemen PME00018077 Necdou 2019924 TMAJ Mosses.p1 Tsuhet 2053225 GAMH Conifers.p1 Anocla 2009572 VBMM Mosses.p1 Pseama 2078830 AQFM Conifers.p1 Roscap 2009271 XWHK Mosses.p1 Abilas 2010803 VSRH Conifers.p1 Keteve 2083305 JUWL Conifers.p1 RacvarPlains 2016359 2076289 RDOO BGXB Mosses.p1 Mosses.p1 Picabi MA 191989g0010 Piceng 2053730 AWQB Conifers.p1 Racelo 2073447 ABCD Mosses.p1 Picsit PSI00013189 Cerpur 2001220 FFPD Mosses.p1 Catagr 2012009 NPRL Conifers.p1 Dicsco 2096176 NGTD Mosses.p1 Pinpar 2076300 IIOL Conifers.p1 Leualb 2117034 VMXJ Mosses.p1 Pinpin PPI00017948 Pinsyl PSY00024330 ScoaquLeugla 2020023 2006574 BPSG RGKI Mosses.p1 Mosses.p1 Pintae PTA00026808 Pinjef 2079534 MFTM Conifers.p1 Timaus 2015844 ZQRI Mosses.p1 Pinpon 2068964 JBND Conifers.p1 Physsp. 2013433 YEPO Mosses.p1 Pinrad 2051948 DZQM Conifers.p1 Ararul 2063771 XTZO Conifers.p1 Encstr 2058186 KEFD Mosses.p1 Wolnob 2053665 RSCE Conifers.p1 Agarob 2073608 MIXZ Conifers.p1 BuxaphDipfol 2069673 2066143 HRWG AWOI Mosses.p1 Mosses.p1 Agamac 2067136 ACWS Conifers.p1 Andrup 2092717 WOGBPhypat Mosses.p1 Pp3c23 400V3.1 Halbid 2051763 OWFC Conifers.p1 Lepsp. 2074561 BBDD Conifers.p1 Polcom 2040752 SZYG Mosses gametophyte.p1 Sunama 2092032 KLGF Conifers.p1 Sphrec 2007835 UHLI Mosses.p1 Pruand 2037859 EGLZ Conifers.p1 Sphles 2082979 GOWD Mosses.p1 Phyhyp 2065019 JRNA Conifers.p1 Andrup 2005204Sphfal WOGB Sphfalx0081s0039.1 Mosses.p1 Parust 2036346 JZVE Conifers.p1 Andrup 2005205 WOGB Mosses.p1 Mancol 2008502 CDFR Conifers.p1 Lagfra 2086126 ZQWM Conifers.p1 Tetpel 2129666 HVBQ Mosses.p1 Acmpan 2016709 HILW Conifers.p1 Mictet 2008208 MHGD Conifers.p1 Atrang 2007422 ZTHV Mosses.p1 Saxcon 2071753 QCGM Conifers.p1 Taklep 2011768 SKQD Mosses.p1 100 Podrub 2000843 XLGK Conifers.p1 Frusp.Taklep 2005010 2077444 TGKW SKQD Liverworts.p1 Mosses.p1 Podcor 2050999 SCEB Conifers.p1 Fruspp 2136770 CHJJ Liverworts.p1 Nagnag 2113122 UUJS Conifers.p1 Retmin 2068969 VGSX Conifers.p1 Fruspp 2010343 CHJJ Liverworts.p1 Dacbal 2070558 IZGN Conifers.p1 Pallye 2107021 YFGP Liverworts.p1 Metcra 2098124 NRWZ Liverworts.p1 99.4 Faltax 2005932 ROWR Conifers.p1 Faltax 2002976 QHBI Conifers A.p1 Pornav 2111522 KRUQ Liverworts.p1 99.9 Faltax 2004636 PLYX Conifers 2 samples combined.p1 Porpin 2147264 UUHD Liverworts.p1 Sciver 2042254 YFZK Conifers.p1 Radlin 2085416 BNCU Liverworts.p1 86.2 Taxbac 2043470 WWSS Conifers.p1 Ausspi 2006794 BTTS Conifers.p1 Vitapp 2095344 NDUV LeptosporangiatePelepi 2088759 Monilophytes.p1 PIUF Liverworts.p1 85.8 Psechi 2005945 YLPM Conifers.p1

Pelnee 2111202 JHFI Liverworts.p1 100 Psechi 2005944 YLPM Conifers.p1 Schisp.Ptipul 2103555 2018180 LGOW HPXA Liverworts.p1 Liverworts.p1 Amearg 2020842 IAJW Conifers.p1 Tortax 2012339 EFMS Conifers.p1 Ptipul 2018179 HPXA Liverworts.p1 Tornuc 2135314 HQOM Conifers.p1 Scanem 2160670 IRBN Liverworts.p1 92.9 Cephar 2009297 WYAJ Conifers.p1 Barbar 2002138 OFTV Liverworts.p1 100 Cephar 2009298 WYAJ Conifers.p1 Marpal 2083004 LFVP Liverworts 2 samples combined.p1 81.8 99.9 99.7 Cephar 2010152 GJTI Conifers.p1 Odopro 2129217 YBQN Liverworts.p1 99.9 Cephar 2008418 NVGZ Conifers 2 samples combined.p1 Baztri 2017782 WZYK Liverworts.p1 95.5 Cephar 2010153 GJTI Conifers.p1 Mixspe 2015462 NWQC Liverworts.p1 93 Cunlan 2011799 ESYX Conifers branch apex with needles.p1 MarpalMarpal 2052167 2064832 HMHL IHWO Liverworts Liverworts non mycorrizal.p1 mycorrizal.p1 99.7 Cunlan 2100474 ZQVF Conifers 2 samples combined.p1 Calfis 2002345 RTMU Liverworts.p1 100 95.4 100 100 86.9 99.9 Cunlan 2051384 OUOI Conifers.p1 98.4 Athcup 2061910 XIRK Conifers.p1 90.7 99.9 81.7 Taicry 2064011 QSNJ Conifers.p1 Marpal scaff9704 FGenesh1.1 98.4 96 100 90.8 Seqgig 2057696 QFAE Conifers Glaucum.p1 Seqsem 2004934 HBGV Conifers.p1

89.4 97.1 99.5 98.2 Metgly 2061670 NRXL Conifers.p1 92.4 99.9 80.5 Cryjap 2107770 HOUF Conifers leaf.p1 Marpol 2037470 JPYU Liverworts.p1 99.1 99.7 85.8 Cryjap 2019678 GMHZ Conifers 2 samples combined.p1 Marema 2003565 TFYI Liverworts.p1 86.3 99.4 97.6 85.8 Glypen 2044084 OXGJ Conifers.p1 Ricnat 2035440Marpol WJLO Mapoly0007s0088.1 Liverworts.p1 99.8 95.4 100 96.2 Taxdis 2009318 FHST Conifers.p1 Concon 2007169 ILBQ Liverworts.p1 99.8 100 95.7 Pappap 2082691 OVIJ Conifers.p1 Luncru 2073011 TXVB Liverworts.p1 99.1 100 Auschi 2065652 YYPE Conifers.p1 Sphtex 2043066 HERT Liverworts.p1 84.8 Piluvi 2003614 ETCJ Conifers.p1 100 91.1 99.5 Widced 2007570 AUDE Conifers.p1 BlaspNW c381490 g1 i1 m.184332 99.2 100 99.8 Disarc 2073580 GKCZ Conifers.p1 99.9 85 99.9 99.8 Calgra 2008222 IFLI Conifers March.p1 99 94.5 Neopan 2068406 JDQB Conifers.p1 89.2 95.2 84.1 Calmac 2053505 RMMV Conifers March.p1 95.1 100 100 Thudol 2048975 NKIN Conifers.p1 95.4 99.9 98.2 84.5 Thupli 2038882 VFYZ Conifers.p1

99.9 95.5

99.9 Fokhod 2011145 UEVI Conifers.p1 100 80.5 97.7 99.8 99.8 97.6 Chalaw 2066883 AIGO Conifers.p1 93.5 99.5 86.5 Tetsp. 2068474 CGDN Conifers.p1 91.4 96.4 Cupdup 2012307 QNGJ Conifers.p1 90.9 90.2 Junsco 2057375 XMGP Conifers.p1 84.1 87.3 94.1 Caldec 2058662 FRPM Conifers.p1 Plaori 2050339 BUWV Conifers.p1 86.2 99.6 Micdec 2053439 XQSG Conifers.p1

95.6 Ambtri evm 27.model.AmTr v1.0 scaffold00024.332 82.1 Zosmar Zosma199g00110.1 Orysat LOC Os08g29520.1 95.3 Bradis Bradi3g34910.1 100 99.1 Horvul HORVU7Hr1G065590.7 98.5 100 Setita Seita.6G126700.1

91.8 100 Sorbic Sobic.007G117800.1 100 Zeamay Zm00008a003876 95 Aposhe lcl KZ451980.1 PKA55133.1 12091 Dencat lcl NW 021477709.1 XP 020682699.1 32591

95.1 Phaequ PEQU 02789 98.2 Spipol Spipo18G0027700

100 Anacom Aco006777.1 98.7 Musacu GSMUA Achr1T25200 001

86.6 Musacu GSMUA Achr4T06470 001 100 99.9 Nelnuc NNU 07598-RA 100 Casmol maker-scaffold05674-augustus-gene-0.9-mRNA-1 99.5 Poptri Potri.008G115300.1 99.9 Manesc Manes.06G073400.1

100 97.3 Daucar DCAR 010973 97.2 98.9 100 Diacar Dca26186.1 96.3 99 100 86.8 Diacar Dca1744.1 94.184.9 86.4 Diacar Dca12703.1 100 96.792.3 83.2 Betvul Bv2 026350 kdtm.t1 91.893.2 Spiole Sp 048400 dgzx.t1 99.5 93.5 99.2 99.8 Chequi AUR62014544-RA 100 100 98.6 99.2100 Chequi AUR62008959-RA 96.8 96.6 100 90.1 Utrgib Utricularia gibba unitig 748 4714973 4715987 unitig 748.g8407.t1 -1 CDS 875843453 10801 Pyrbre lcl NW 008988585.1 XP 009340012.1 36728 100 96.9 Helann HanXRQChr14g0452301 100 99.9 Helann HanXRQChr10g0283771 97.4 99.6 Fraexc FRAEX38873 v2 000290920.1 Pyrbre lcl NW 008988585.1 XP 009340016.1 36729 99.6 100 Fraexc FRAEX38873 v2 000063590.1 Pyrcom PCP030693.1 99.8 99.5 Fraexc FRAEX38873 v2 000225730.3 100 96.9 99.1 96.5 Fraexc FRAEX38873 v2 000225730.2 Maldom MDP0000201928 100 88.8 99.8 97.5 Fraexc FRAEX38873 v2 000225730.1 Pyrbre lcl NW 008989240.1 XP 009349345.1 45219 97.1 Pyrcom PCP030694.1 Petaxi Peaxi162Scf00019g01111.1 Pyrbre lcl NW 008988232.1 XP 009371327.1 23141 100 100 Nicben Niben101Scf13530g01009.1 Maldom MDP0000153630 93.9 98.2 84.9 96.5 Nicben Niben101Scf02215g02008.1 100 97.1 Pyrcom PCP028472.1 92.8 100 98.6 Capann CA02g08030 94.7 100 Solpen Sopen02g015770.1 100 98.2 100 100 Sollyc Solyc02g065580.2.1 Prumum lcl NC 024130.1 MaldomXP 008234253.1 MDP0000119385 18377 100 Gosrai Gorai.001G081800.1 Prudul Prudul26A004677P1 95.7 95.3 99.7 99.5 Thecac Thecc1EG019521t1 100 86.6 89 99.9 Pruper Prupe.2G294100.1 94.9 92.2 Tarhas lcl NW 010961290.1 XP 010528463.1 5180 Pruavi Pav sc0001405.1 g940.1.mk 100100 84 97 98.483.585.2 Fraana FAN iscf00107318.1.g00002.1 83 87.5 99.4 98.8 98.7 81.8 83.384.4 Eutsal Thhalv10027908m 100 87.2 81.7 87.9 99.699.9 Braolecap Bol040150 98.2 100 90.8 88.3 Brarap Brara.D00911.1 98.6 99.9 99.3 88.1 Fraves FvH4 7g29440.1 82.5 90.6 96.9 Boestr Bostr.17584s0018.1 Roschi RchiOBHm Chr1g0377221 100 98.1 99.9 100 100 Caprub Carub.0007s3723.1 Roschi RchiOBHm Chr1g0377231 100 98.8 99.9 Capgra Cagra.4701s0014.1 Potmic 8415 t 88.8 98.8 99.4 87.3 99.9 Aratha AT5G38630.1 Parand lcl JXTB01000889.1 PON31973.1 36534 93.7 92.8 98 99.5 90.2 Aralyr AL7G51910.t1 Treori lcl JXTC01000312.1 RuboccPON66410.1 Bras G0944126762 95 99.7 95.5 Arahal Araha.48355s0001.1 Drydru Drydr2S08090 99.9 91.7 100 99.7 98.7 100 96.3 Cercan Cerca190S16999 Zizjuj lcl NW 015457658.1 XP 015872816.1 43301 99.8 88.6100 97 Casaus Castanospermum06662-PA 100 80.5 86.2 Chafas Chafa38743S22044 Mornot L484 015781 96.9 98.3 99.9 Mimpud Mimpu1631S18092 99.8 100 96.881.698.6 Chafas Chafa7594S26665 87.6 98.4 99.9 99.3 93.1 Mimpud Mimpu145187S16917 Distri Distr1455S14651 100 95.5 91.2 99.9 99.3 Cucmos CmoCh19G004230.1 99.992.4 Casaus Castanospermum01661-PA Cucpep Cp4.1LG15g03170.1 86.8 Nissch Nissc299S07962 Cucmax CmaCh19G004160.1 100 85.494.993.795.8 100 Araipa Araip.U3PCH Cucmos CmoCh02G010800.1 98.998.682.9 98.6 Arahyp arahy.Tifrunner.gnm1.ann1.63EJDF.1 Cucpep Cp4.1LG05g06420.1 97 91.5 100 93 Arahyp arahy.Tifrunner.gnm1.ann1.Y6M3VX.1 Cucsat evm.model.Chr3.4662 99.6 Aradur Aradu.CJJ6J Momcha lcl NW 019104490.1Cucmel XP MELO3C003324.2.1 022159487.1 3096 86.1 99.8 96.8 89.2 99.7 94.7 Lotjap Lj0g3v0264389.1 98.7 98.9 Lupang Lup032435.1 Lagsic Lsi05G000050.1 94.5 94 100 82.5 Lupang Lup026700.1 Begfuc Begfu91433S51321 94.988.7 99.1 100 99.1 Cicari Ca 04771.1 Begfuc Begfu4543S35723 91.9 100 99.5 100 Medtru MtrunA17 Chr6g0456901 91.4 100 90.7 Tripra Tp57577 TGAC v2 mRNA25940 Begfuc Begfu4543S49763 99.6 88.9 100 100 88 87.1 99.9 100 Trisub lcl DF974247.1 GAU46746.1 35804 Begfuc Begfu1433S07837 99.9 100 97.4 93.3 99.1 100 Cajcaj Ccajan 40300 Begfuc Begfu2529S27437 85.5 92.1 87.6 92.9 99.8 99.6 Glymax Glyma.19G044200.1 Datglo Datgl1239S19455 10083 92.7 99.3 99.5 81.698.3 95.793.2 Phavul Phvul.004G072300.1 100 82.4 98.2 Alnglu Alngl14475S16433 96.6 98.284.1 100 80.1 Vigung Vigun04g092300.1 Casgla Casgl53S05646 100 95.4 87.8 98.3 Vigang vigan.Vang02g11980.1 88.9 91.8 82.6 88.3 100 Vigrad Vradi01g09160.1 Jugreg g59149.t1 100 95.1 87.6 85.1 84.2 86.2 Vigrad Vradi0319s00100.1 Casmol maker-scaffold00694-augustus-gene-0.53-mRNA-1Querob QrobJugreg P0007910.2 g39980.t1 100 99.7 96.7 100 Cepfol Cfol v3 19112 Querob Qrob P0372700.2 100 100 94.5 100 Citsin orange1.1g026868m Trisub lcl DF973151.1 GAU15432.1 4490 91.1 98.7 Citcle Ciclev10012646m Tripra Tp57577 TGAC v2 mRNA14826 94.6 100 86.3 98.1 Carpap evm.model.supercontig 818.1 97.2 100 99 89.3 91.494.2 89.2 Riccom 29673.m000912 Medtru MtrunA17 Chr1g0203371 97.4 99.8 85.9 97.2 86.1 91.7 100 Manesc Manes.01G107700.1 88.5 98.6 96.7 Poptri Potri.004G103800.1 Cicari Ca 08736.1 94.3 100 96.1 Poptri Potri.017G111700.1 Lotjap Lj5g3v2013830.1 100 80.7 98.6 99.5 98.2 94.899.6 Querob Qrob P0734060.2 Arahyp arahy.Tifrunner.gnm1.ann1.XGDM8S.2Araipa Araip.HBQ1U 100 98.6 99.9 Casmol maker-scaffold03430-augustus-gene-0.30-mRNA-1 99.3 Jugreg g14535.t1 98.1 Arahyp arahy.Tifrunner.gnm1.ann1.L2LC7G.2Aradur Aradu.RW8B0 94.8 95.9 Jugreg g10983.t1 85.3 97.8 10091.587.388 Casgla Casgl37S16776 Nissch Nissc16986S16163 93.8 88.7 Alnglu Alngl53469S11138 Nissch Nissc8429S04502 82 Alnglu Alngl25538S21988 Vigrad Vradi08g18890.1 94.5 Alnglu Alngl2883S23078 Vigang vigan.Vang06g04970.1 96.5 100 80.4 Begfuc Begfu1504S01161 Vigung Vigun07g227200.1 99.5 99.2 Datglo Datgl428S30615 Phavul Phvul.007G069600.1 97.4 100 99.9 Datglo Datgl298S27536 Glymax Glyma.10G236200.1 97 99.9 100 Begfuc Begfu3231S31000 Glymax Glyma.20G158300.1 84.3 Begfuc Begfu318S30584 100 90.7 Momcha lcl NW 019104493.1 XP 022134497.1 6160 Lupang Lup004679.1 84.393.295.7 99.7 Cajcaj Ccajan 07299 100 88.9 100 Cucpep Cp4.1LG01g22250.1 Casaus Castanospermum19555-PA 95.6 100 98.7 Cucmax CmaCh04G028420.1 Araipa Araip.A9UT9 100 Cucmos CmoCh04G029720.1 Arahyp arahy.Tifrunner.gnm1.ann1.GP1IFW.1 100 98.4 89.7 98.389.4 Cucmax CmaCh15G001930.1 Arahyp arahy.Tifrunner.gnm1.ann1.99ANZ9.1 Cucmos CmoCh15G002060.1 92.5 99.5 94.6 99 89.6 Citlan Cla016460 Araipa Araip.LA2BG 97.5 91.5 91.7 100 Lagsic Lsi03G002250.1 Aradur Aradu.UMK1N 86.9 97.7 100 Arahyp arahy.Tifrunner.gnm1.ann1.HA0JIQ.1 86.3 Cucmel MELO3C022085.2.1 99.9 100 91.6 100 Cucsat evm.model.Chr5.2956 Araipa Araip.296S2 98.9 98.1 Cucsat evm.model.Chr5.2956.1 Arahyp arahy.Tifrunner.gnm1.ann1.MGEP0F.1 95.2 98.4 Zizjuj lcl NC 029682.1 XP 015880565.1 12205 Nissch Nissc113S12965 100 85.4 10093 Distri Distr516S25320 Vigang vigan.Vang0203s00180.1 84.2 94.2 Mornot L484 009146 Vigrad Vradi01g14420.1 99.7 100 Humlup HL.SW.v1.0.G020209.1 Vigung Vigun04g156700.1 97.783.9 98.6 95 Parand lcl JXTB01000513.1 PON37914.1 31663 Phavul Phvul.004G116800.1 100 95.4 83.4 97.3 99.7 Treori lcl JXTC01000058.1 PON93513.1 10792 Lupang Lup020121.1 99.7 86 98.7 100 Roschi RchiOBHm Chr2g0163271 Cercan Cerca93S11448 96.6 98.5 93 100 Potmic 27681 t Chafas Chafa95604S30186 97.3 95.4 100100 Fraves FvH4 6g45440.1 Mimpud Mimpu144931S16522 94.5 88 9989.6 Fraana FAN iscf00164778.1.g00001.1 Mimpud Mimpu1391S15264 99.9 95.3 100 97.3 Drydru Drydr164S16903 Chafas Chafa15816S16300 94.8 99.9 98.2 Prumum lcl NC 024129.1 XP 008230380.1 14696 99 90.2 100 96.1 100 83.3 Pruavi Pav sc0000618.1 g440.1.mk Spiole Sp 019690 imzo.t2 100 98.4 99.4 99.9 Pruper Prupe.3G240600.1 Spiole Sp 019690 imzo.t1 98.9 91 Prudul Prudul26A008325P1 Chequi AUR62021195-RA 100 99.7 100 84.2 90.7 100 88.8 Maldom MDP0000312256 Chequi AUR62015987-RA 100 93 100 95.3 Pyrbre lcl NW 008988089.1 XP 009357027.1 10060 Betvul Bv 009630 xgdu.t1 83.9 93.8 86.1 96.5 100 Pyrcom PCP043143.1 Betvul Bv 009620 cxmc.t1 98 99.5 Maldom MDP0000789056 Diacar Dca43303.1 100 100 100 Pyrbre lcl NW 008988228.1 XP 009371014.1 22859 Diacar Dca22532.1 83.4 99.8 Pyrcom PCP000711.1 Diacar Dca48554.1 99.1 100 Equhye 2127850 JVSZ Eusporangiate Monilophytes.p1 Thecac Thecc1EG015161t1 99.6 98.2 Equdif 2009744 CAPN Eusporangiate Monilophytes.p1 Thecac Thecc1EG015162t2 98.7 95.7 99.5 99.9 Marsp. 2124221 UXCS Eusporangiate Monilophytes.p1 Gosrai Gorai.004G118600.1 98.5 90.7 Angeve 2013859 NHCM Eusporangiate Monilophytes.p1 Poptri Potri.012G141000.1 95.998.9 97.4 Scedis 2085101 EEAQ Eusporangiate Monilophytes.p1 Poptri Potri.015G143700.1 99.9 98.7 Tmepar 2008966 ALVQ Eusporangiate Monilophytes.p1 Cepfol Cfol v3 24720 99.7 97.4 100 100 Psinud 2014055 QVMR Eusporangiate Monilophytes.p1 100 Psinud 2014054 QVMR Eusporangiate Monilophytes.p1 Manesc Manes.06G146900.2 99.498.7 96 98.3 Psinud 2016658 QVMR Eusporangiate Monilophytes.p1 Manesc Manes.06G146900.1 Riccom 30147.m013747 99.9 Tmepar 2015280 ALVQ Eusporangiate Monilophytes.p1 98.7 96.8 Tmepar 2015279 ALVQ Eusporangiate Monilophytes.p1 Citcle Ciclev10005795m 91.2 88.4 Scedis 2011124 EEAQ Eusporangiate Monilophytes.p1 Citsin orange1.1g026979m 98.6 87.4 Ophvul 2016436 QHVS Eusporangiate Monilophytes leaf.p1 Fraexc FRAEX38873 v2 000225820.1 91.586.4 100 Ophpet 2002821 WTJG Eusporangiate Monilophytes.p1 97.485.3 98.8 96.8 97.8 Scedis 2077895 EEAQ Eusporangiate Monilophytes.p1 Fraexc FRAEX38873 v2 000225820.3 99.9 Botvir 2020832 BEGM Eusporangiate Monilophytes.p1 Fraexc FRAEX38873 v2 000225820.2 99.3 99.7 Botvir 2020831 BEGM Eusporangiate Monilophytes.p1 Fraexc FRAEX38873 v2 000008600.1 99.6 100 100 Dipcon 2105245 MEKP Leptosporangiate Monilophytes.p1 Fraexc FRAEX38873 v2 000093410.1 93.5 92.8 100 Cyaspi 2017322 GANB Leptosporangiate Monilophytes.p1 100 80.8 90.9 Culmac 2011576 PNZO Leptosporangiate Monilophytes.p1 Daucar DCAR 018197 99.8 100 Plajap 2018478 UWOD Leptosporangiate Monilophytes.p1 Solpen Sopen03g004650.1 95.1 85 92.7 Thyele 2008399 EWXK Leptosporangiate Monilophytes.p1 Sollyc Solyc03g025840.2.1 100 99.8 Thyele 2008396 EWXK Leptosporangiate Monilophytes.p1 Utrgib Utricularia gibba unitig 0 7483661 7484694 unitig 0.g2482.t1 1 CDSCapann 875800127 CA03g17730 11468 98.7 89.6 Thyele 2008397 EWXK Leptosporangiate Monilophytes.p1 100 99.7 88.3 83 Osmjav 2077358 VIBO Leptosporangiate Monilophytes.p1 Utrgib Utricularia gibba unitig 37 1610216 1611387 unitig 37.g12523.t1 -1 CDS 875819709 8037 99.7 CYTB561 99.6 100 Nicben Niben101Scf04804g00002.1 99.6 100 94.6 95.1 Osmsp. 2009035 UOMY Leptosporangiate Monilophytes gametophyte.p1 Nicben Niben101Scf02910g01009.1 92.690.3 96.3 Stilob 2001862 XDVM Leptosporangiate Monilophytes.p1 Petaxi Peaxi162Scf01464g00028.1Aralyr AL7G27530.t1 100 100 Dipcon 2010629 MEKP Leptosporangiate Monilophytes.p1 100 95.6 92.486.9 Dipcon 2010628 MEKP Leptosporangiate Monilophytes.p1 Arahal Araha.12285s0006.1Aratha AT4G25570.1 98.9 100 100 97 Dipcon 2103222 MEKP Leptosporangiate Monilophytes.p1 86.283.695 100 97.8 Creven 2032646 TWFZ Leptosporangiate Monilophytes.p1 Capgra Cagra.23907s0009.1 94.5 92.198.6 95.5 95.1 99.5 99.9 Hymbiv 2006581 QIAD Leptosporangiate Monilophytes.p1 Caprub Carub.0007s1541.1 100 97.3 98.2 93.2 99.9 94.193.187.9 Hymcup 2049498 TRPJ Leptosporangiate Monilophytes.p1 Boestr Bostr.7867s0368.1 85.6 96.6 81.5 93 10088.9 95.2 99.4 Lygjap 2013415 PBUU Leptosporangiate Monilophytes.p1 Eutsal Thhalv10026122m 100 96.7 95.2 Anetom 2011699 CQPW Leptosporangiate Monilophytes.p1 Braolecap Bol042247 100 99.9 95.2 99.6 85.2 91.9 99.389.7 99.7 91.2 87.8 Anetom 2011698 CQPW Leptosporangiate Monilophytes.p1 Brarap Brara.K00190.1 99.9 99 94.5 94.899.5 99.6 100 99.1 100 Cyaspi 2003721 GANB Leptosporangiate Monilophytes.p1 Arahal Araha.7377s0001.1 88.9 93.6 99.4 99.4 99.8 Thyele 2004957 EWXK Leptosporangiate Monilophytes.p1 Boestr Bostr.7305s0038.1 97 99.4 93.6 99.7 Culmac 2151812 PNZO Leptosporangiate Monilophytes.p1 Capgra Cagra.0094s0037.1 98.6 80.2 87.486.5 84 99.6 Plajap 2139528 UWOD Leptosporangiate Monilophytes.p1 Caprub Carub.0008s1237.1 97.5 97.2 81.5 Cyaspi 2016915 GANB Leptosporangiate Monilophytes.p1 Boestr Bostr.7305s0039.1 99.8 81.5 96.8 95.199.6 Thyele 2022640 EWXK Leptosporangiate Monilophytes.p1 Eutsal Thhalv10014551m 91.490.186.399.2 92.7 91.5 88.3 Thyele 2022641 EWXK Leptosporangiate Monilophytes.p1 Brarap Brara.B01531.1 94.5 95.1 88.2 99.7100 Pilglo 2088967 KIIX Leptosporangiate Monilophytes.p1 91.487.7 88.9 Salcuc Sacu v1.1 s0001.g000368 86.699.280.990.8 100 96.8 82.397.7 80.7 100 Salcuc Sacu v1.1 s0039.g012089 99.9 100 87.8 92.6 Azofil Azfi s0345.g065771 Helann HanXRQChr14g0462441 90.6 91.4 92.8 97.7 Nelnuc NNU 21017-RA 99.2 100100 89.9 100 Azocar 2014113 CVEG Leptosporangiate Monilophytes.p1 Tarhas lcl NW Carpap010965372.1 evm.model.supercontig XPNelnuc 010537185.1 NNU 08726-RA 13093107.50 84.492.3 Azocar 2014111 CVEG Leptosporangiate Monilophytes.p1 Bradis Bradi3g12925.1 98.9 98.9 Azofil Azfi s0345.g065770 9191.2 99.2 Azocar 2023852 CVEG Leptosporangiate Monilophytes.p1 98 94.5 89.5 Azocar 2023851 CVEG Leptosporangiate Monilophytes.p1 HorvulOrysat HORVU7Hr1G078690.1 LOC Os08g01140.1 99.5 97.8 Linmic 2008100 YIXP Leptosporangiate Monilophytes.p1 Zeamay Zm00008a017949 86.6 91.1 99.1 Linlin 2015094 NOKI Leptosporangiate Monilophytes.p1 Sorbic Sobic.K030000.1 95.4 99.498.9100 Linlin 2016472 NOKI Leptosporangiate Monilophytes.p1 Setita Seita.6G002000.1 98.998.497 100 Linmic 2009345 YIXP Leptosporangiate Monilophytes.p1 97.4 99.4 Zeamay Zm00008a006691 90.5 89 Dendav 2001844 MTGC Leptosporangiate Monilophytes.p1 Linlin 2002788 NOKI Leptosporangiate Monilophytes.p1 Sorbic Sobic.006G159600.1 Setita Seita.7G180100.1 93.8 98.2 Linlin 2002787 NOKI Leptosporangiate Monilophytes.p1 100 Cryacr 2064870 WQML Leptosporangiate Monilophytes.p1 Horvul HORVU2Hr1G091720.2Bradis Bradi5g16740.1 99 Cysuta 2030365 HNDZ Leptosporangiate Monilophytes.p1 93.2 Cysfra 2003974 LHLE Leptosporangiate Monilophytes.p1 Orysat LOC Os04g45090.2 99.8 99.7 Cysfra 2008199 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Sorbic Sobic.004G303200.1 90.1 100 100 Cysfra 2012563 XXHP Leptosporangiate Monilophytes Stewart.p1 Zeamay Zm00008a016823 98.3 Dipwic 2004959 UFJN Leptosporangiate Monilophytes.p1 Zeamay Zm00008a022446 95.8 95.6 Setita Seita.1G251100.1 95.3 Athfil 2061701 URCP Leptosporangiate Monilophytes.p1 94.7 Wooilv 2010713 YQEC Leptosporangiate Monilophytes.p1 Bradis Bradi3g50010.2 Deplob 2063420 FCHS Leptosporangiate Monilophytes crenata.p1 Horvul HORVU6Hr1G060720.1 100 Blespi 2012577 VITX Leptosporangiate Monilophytes.p1 OrysatAnacom LOC Os02g42890.1 Aco016292.1 99.3 Blespi 2044528 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 99.9 100 Plepol 2072139 UJWU Leptosporangiate Monilophytes dehydrating fronds.p1 99.6 95.6 Zeamay Zm00008a004035 96.9 Polhes 2104311 GYFU Leptosporangiate Monilophytes A type.p1 98.5 99.9 Phygro 2008221 ORJE Leptosporangiate Monilophytes.p1 SorbicSetita Sobic.001G201100.1 Seita.9G199900.1 90.7 Polacr 2070457 FQGQ Leptosporangiate Monilophytes.p1 Bradis Bradi3g30270.2 82.2 98.6 Nepexa 2032158 NWWI Leptosporangiate Monilophytes.p1 98.2 89.3 Didtru 2002204 RFRB Leptosporangiate Monilophytes.p1 98.5 91.3 100 100 94.4 Cryacr 2067117 WQML Leptosporangiate Monilophytes.p1 HorvulOrysat HORVU1Hr1G046270.2 LOC Os10g36030.1 92.2 Pteens 2001366 FLTD Leptosporangiate Monilophytes.p1 Pteens 2001365 FLTD Leptosporangiate Monilophytes.p1 Phaequ PEQU 34070 Musacu GSMUA Achr1T00250 001 100 100 99.6 Pittri 2004511 UJTT Leptosporangiate Monilophytes.p1 Phaequ PEQU 02282 92.3 99.7 Pittri 2004512 UJTT Leptosporangiate Monilophytes.p1 Musacu GSMUA Achr4T26140 001 Notmon 2064103 YCKE Leptosporangiate Monilophytes.p1 89.4 Gagari 2014641 DCDT Leptosporangiate Monilophytes.p1 98.4 100 Argniv 2073422 XDDT Leptosporangiate Monilophytes.p1 Zosmar Zosma1g00450.1 96.1 100 100 99.1 Myrruf 2008608 GSXD Leptosporangiate Monilophytes.p1 ZosmarAnacom Zosma39g00660.1 Aco010271.1 Adiale 2064818 WCLG Leptosporangiate Monilophytes.p1 85 88.1 Anacom Aco022795.1 100 100 100 86.9 100 88.7 Adirad 2060202 BMJR Leptosporangiate Monilophytes.p1 Aposhe lcl KZ451988.1 PKA53915.1 13480 93.1 100 99.5 91.1 99.8 Dencat lcl NW 021318950.1 XP 020685970.1 8654 Adirad 2011504 BMJR Leptosporangiate Monilophytes.p1 99.5 96.8 95.1 Vitapp 2013601 NDUV Leptosporangiate Monilophytes.p1 100 99.8 93.7 Vitlin 2017576 SKYV Leptosporangiate Monilophytes.p1 91.2 100 96.9 99.1 Musacu GSMUASpipol Achr1T06830 Spipo1G0033900 001 99.6 99.4 Leuimm 2073781 WGTU Leptosporangiate Monilophytes.p1 100 83.7 100 99.5 Polacr 2002360 FQGQ Leptosporangiate Monilophytes.p1 Phydru 2015632 ZZEI Lycophytes.p1 99.5 99.8 Polacr 2002359 FQGQ Leptosporangiate Monilophytes.p1 99.8 100 99.3 93.2 Marsp. 2116402 UXCS Eusporangiate Monilophytes.p2 93.7 100 99.9 93.9 81 100 Bolrep 2005174 JBLI Leptosporangiate Monilophytes.p1 95.3 99.1 95.492.7 94.8 Bolrep 2005173 JBLI Leptosporangiate Monilophytes.p1 96.1 100 100 99.6 86 84.2 99.2 Bolrep 2005172 JBLI Leptosporangiate Monilophytes.p1 Junsco 2012246 XMGP Conifers.p1 80.8 83.8 95.7 Phacar 2134302Cupdup RXRQ Hornworts 2071906 QNGJ sporophyte.p1 Conifers.p1 100 99.5 Nepexa 2005783 NWWI Leptosporangiate Monilophytes.p1 Tetsp. 2068573 CGDN Conifers.p1 96.8 99 99.5 91.8 97.4 84.8 Davfej 2005487 OQWW Leptosporangiate Monilophytes.p1 91.2 94.5 99.4 96 Ambtri evm 27.model.AmTr v1.0 scaffold00009.294 92.9 91.9 100 Davfej 2005488 OQWW Leptosporangiate Monilophytes.p1 Caldec 2058596 FRPM Conifers.p1 81.3 98.5 100 98.8 Plaori 2051308 BUWV Conifers.p1 83 91.6 98.5 82.3 100 Davfej 2005486 OQWW Leptosporangiate Monilophytes.p1 99.9 85.8 Plepol 2074068 UJWU Leptosporangiate Monilophytes dehydrating fronds.p1 Micdec 2003028 XQSG Conifers.p1 90.1 95.1 95.4 94.9 100 80.2 Phygro 2006255 ORJE Leptosporangiate Monilophytes.p1 Thupli 2039561 VFYZ Conifers.p1 100 97.2 100 93.9 90.1 99.9 87.9 100 Phygro 2006254 ORJE Leptosporangiate Monilophytes.p1 Thudol 2049842 NKIN Conifers.p1 Polamo 2071118 YLJA Leptosporangiate Monilophytes.p1 Chalaw 2008730 AIGO Conifers.p1 98.7 94.1 96.5 91 100 Polhes 2033067 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Fokhod 2059506 UEVI Conifers.p1 86.4 97.1 99.9 98.9 96.9 Polhes 2019609 GYFU Leptosporangiate Monilophytes A type.p1 98.4 93.6 Polgly 2000383 CJNT Leptosporangiate Monilophytes.p1 CalgraNeopan 2142169 2067988 IFLI Conifers JDQB Conifers.p1 March.p1 Polhes 2026251 IXLH Leptosporangiate Monilophytes B type.p1 Didtru 2034655 RFRB Leptosporangiate Monilophytes.p1 99.7 Disarc 2013677 GKCZ Conifers.p1 100 Hompyc 2008846 OCZL Leptosporangiate Monilophytes.p1 Aspnid 2057668 PSKY Leptosporangiate Monilophytes.p1 Widced 2057233 AUDE Conifers.p1 100 100 Calmac 2053884Piluvi RMMV 2059780 Conifers ETCJ March.p1 Conifers.p1 82.9 Asppla 2061146 KJZG Leptosporangiate Monilophytes.p1 Auschi 2066387 YYPE Conifers.p1 100 97.7 Gymdry 2010123 HEGQ Leptosporangiate Monilophytes.p1 87.4 97.7 Cysuta 2129514 HNDZ Leptosporangiate Monilophytes.p1 Pappap 2083397 OVIJ Conifers.p1 96.6 Cysree 2007566 RICC Leptosporangiate Monilophytes.p1 Cryjap 2072916 DSXO Conifers.p1 92.9 95.2 Cysfra 2005641 LHLE Leptosporangiate Monilophytes.p1 99.6 Cysfra 2015814 XXHP Leptosporangiate Monilophytes Stewart.p1 Cryjap 2108978 HOUF Conifers leaf.p1 Cyspro 2005744 YOWV Leptosporangiate Monilophytes.p1 97.5 Glypen 2011867 OXGJ Conifers.p1 89 Cysfra 2000994 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Taxdis 2012389 FHST Conifers.p1 100 94.8 100 Deplob 2007903 FCHS Leptosporangiate Monilophytes crenata.p1 99 86.4 Wooilv 2075104 YQEC Leptosporangiate Monilophytes.p1 99.9 84 Woosco 2076206 YJJY Leptosporangiate Monilophytes.p1 Seqsem 2048806 HBGV Conifers.p1 100 Blespi 2099841 VITX Leptosporangiate Monilophytes.p1 Metgly 2061502 NRXL Conifers.p1 82 98.7

100 Theacu 2047352 MROH Leptosporangiate Monilophytes.p1 Cryjap 2020020 SeqgigGMHZ 2006749ConifersAthcup 2QFAE samples 2062508 Conifers combined.p1 XIRK Glaucum.p1 Conifers.p1 100 Athfil 2006263 URCP Leptosporangiate Monilophytes.p1 Taicry 2066174 QSNJ Conifers.p1 98.5 100 Onosen 2040927 HTFH Leptosporangiate Monilophytes.p1 Dipwic 2009242 UFJN Leptosporangiate Monilophytes.p1 Chequi AUR62040071-RA Cunlan 2009535 OUOI Conifers.p1 Daucar DCAR 026816 Tortax 2079317 EFMS Conifers.p1 99.8 Helann HanXRQChr08g0224831 Helann HanXRQChr17g0566111 Amearg 2148670 IAJW Conifers.p1 Helann HanXRQChr16g0527291 Taxbac 2004798 WWSS Conifers.p1 Fraexc FRAEX38873 v2 000273020.1 Taxcus 2073374 ZYAX Conifers.p1 Nicben Niben101Scf01434g01015.1

100 Ausspi 2077117 BTTS Conifers.p1 100 Petaxi Peaxi162Scf00064g01323.1 Cunlan 2005517 ZQVF Conifers 2 samples combined.p1 87.7 Cunlan 2088235 ESYX Conifers branchPsechi apex 2081846with needles.p1 YLPM Conifers.p1 100 Petaxi Peaxi162Scf00086g00616.1 Cephar 2058966 GJTI Conifers.p1 Petaxi Peaxi162Scf01169g00018.1 99.4 Nicben Niben101Scf00984g08005.1 Cephar 2089446 WYAJ Conifers.p1 96.2 82.8 Capann CA08g01260 Sciver 2041622 YFZK Conifers.p1 100 Solpen Sopen01g001170.1 Sollyc Solyc01g005140.2.1 96.3 Citcle Ciclev10017511m Faltax 2058411 QHBI Conifers A.p1 100 Citsin orange1.1g036745m Faltax 2002681 ROWR Conifers.p1 Gosrai Gorai.005G153100.1 Dacbal 2072655 IZGN Conifers.p1 Thecac Thecc1EG011241t1

99.9 Carpap evm.model.supercontig 2.139 Daccom 2010412 FMWZ Conifers.p1 99 Manesc Manes.17G086900.1 Nagnag 2113775 UUJS Conifers.p1 99.8 Cephar 2109932 NVGZ Conifers 2 samples combined.p1 91.2 92.8 Riccom 29968.m000657 Retmin 2070155 VGSX Conifers.p1 Poptri Potri.008G138201.1 Faltax 2082927 PLYX Conifers Podcor2 samples 2049272 combined.p1 SCEB Conifers.p1 Poptri Potri.010G102500.1 Podrub 2057321 XLGK Conifers.p1 99.7 95.9 Pruavi Pav sc0000893.1 g750.1.mk Mornot L484 019293 Saxcon 2012280 QCGM Conifers.p1 99.9 97.3 90.9 97.6 100 Acmpan 2006516 HILW Conifers.p1 91.2 BlaspNW c380231 g1 i1 m.183515 Mictet 2005441 MHGD Conifers.p1 Distri Distr1140S12334 Mictet 2005442 MHGD Conifers.p1 Cercan Cerca554S26679 Chafas Chafa8351S27405 96.9 93.5 Sunama 2092640 KLGF Conifers.p1 98.1 Casaus Castanospermum26025-PA Pruand 2037508 EGLZ Conifers.p1 88.7 Cicari Ca 10948.1 Lepsp. 2075575 BBDD Conifers.p1 96.5 100 Medtru MtrunA17 Chr1g0161921 Phyhyp 2066578 JRNA Conifers.p1 95 Tripra Tp57577 TGAC v2 mRNA35747 Halbid 2004712 OWFC Conifers.p1 99.7 Aradur Aradu.WL0PX Lagfra 2087582 ZQWM Conifers.p1 Arahyp arahy.Tifrunner.gnm1.ann1.JLAX2L.1 99.5 99.5 Araipa Araip.WC3YE

MancolParust 2059703 2037431 CDFR JZVE Conifers.p1 Conifers.p1 99.9 94.1 Arahyp arahy.Tifrunner.gnm1.ann1.5K62BL.1 Pintae PTA00005732 99.8 100 99.6 100 Cajcaj Ccajan 37460 Agarob 2003254 MIXZ Conifers.p1 Glymax Glyma.20G012500.1 Agarob 2003253 MIXZ Conifers.p1 Phavul Phvul.003G014600.1 Vigung Vigun02g015400.1 Agamac 2012150 ACWS Conifers.p1Pinsyl PSY00013489 98.8 100 Vigang vigan.Vang0004ss00020.1 WolnobArarul 2055224 2061416 RSCE XTZO Conifers.p1 Conifers.p1Pinpin PPI00064614 Vigrad Vradi11g11610.1 93.2 Vigrad Vradi11g11650.1 Picsit PSI00006932 Alnglu Alngl54S32142 Pinrad 2052996 DZQM Conifers.p1 Jugreg g17178.t1 Pinjef 2003556 MFTM Conifers.p1 93.8 100 Casmol maker-scaffold06850-snap-gene-0.7-mRNA-1 Pinpon 2070769 JBND Conifers.p1 Casgla Casgl119S03381 Casgla Casgl13S08040 98.8 Pinpar 2076537 IIOLPicabi Conifers.p1 MA 464212g0010 Casgla Casgl13S08007 95.7 Datglo Datgl499S31343 94 Catagr 2124248 NPRL Conifers.p1 Begfuc Begfu11377S16666 93.1 Momcha lcl NW 019104551.1 XP 022150036.1 20343 86.7 Cucmax CmaCh04G000380.1 Cucmos CmoCh04G000360.1 Piceng 2004956 AWQB Conifers.p1 Cucpep Cp4.1LG01g06320.1 Notlon 2066784 AREG Conifers.p1 Citlan Cla007503 Lagsic Lsi04G011700.1 Tsuhet 2053647 GAMH Conifers.p1Psemen PME00015211 Cucmel MELO3C018298.2.1 Cedlib 2067386 GGEA Conifers.p1Psemen PME00079934 Cucsat evm.model.Chr5.138 Keteve 2090704 JUWL Conifers.p1 Zizjuj lcl NC 029688.1 XP 015895343.1 27696 Abilas 2007948 VSRH Conifers.p1 Distri Distr152S15076 Distri Distr1140S12337 Ginbil Gb 10110 Mornot L484 019294 Mongot 2112862 TFDQ Liverworts.p1 Humlup HL.SW.v1.0.G025400.1 Pseama 2078196 AQFM Conifers.p1Cycmic CMI00004830 Parand lcl JXTB01000126.1 PON60828.1 14959 Treori lcl JXTC01000409.1 PON56399.1 29650 Psewil 2055286 IOVS Conifers.p1 Rubocc Bras G00225 Roschi RchiOBHm Chr4g0442141 Larspe 2051197 WVWN Conifers.p1 Fraves FvH4 4g33090.1 Potmic 24171 t Staeri 2053888 KAWQ Cycadales.p1 Maldom MDP0000302626 Dioedu 2119466 WLIC Cycadales.p1 Pyrbre lcl NW 008988200.1 XP 009368766.1 20659 Gnemon TnS000140595t01 Pyrcom PCP041059.1 Pruavi Pav sc0000893.1 g740.1.mk Encbar 2084071 GNQG Cycadales.p1 Prudul Prudul26A030036P1 Pruper Prupe.1G336700.1 Cycmic 2010838 XZUY Cycadales.p1 Prumum lcl NC 024127.1 XP 016647009.1 5829 Pruavi Pav sc0000893.1 g730.1.mk Ginbil 2038095 SGTW Ginkgoales.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00008.190 Ambtri evm 27.model.AmTr v1.0 scaffold00008.188 Ambtri evm 27.model.AmTr v1.0 scaffold00008.189 GnemonWelmir 2056011 2007610 GTHK TOXE Gnetales.p1 Gnetales.p1 Aposhe lcl KZ452008.1 PKA52203.1 14939 Ephsin 2003159 VDAO Gnetales.p1 Phaequ PEQU 29633 Widced 2006777 AUDE Conifers.p1 Dencat lcl NW 021319552.1 XP 020698660.1 20847 Widced 2006778 AUDE Conifers.p1 Phaequ PEQU 15705 Disarc 2073081 GKCZ Conifers.p1 Anacom Aco013427.1 Orysat LOC Os10g02920.1 Bradis Bradi3g21300.2 Neopan 2069279 JDQB Conifers.p1 Horvul HORVU3Hr1G111630.1 Piluvi 2058880 ETCJ Conifers.p1 Setita Seita.9G294800.1 Sorbic Sobic.001G273800.1 Auschi 2066906 YYPE Conifers.p1 Zeamay Zm00008a020263 Zosmar Zosma80g00180.1 Calmac 2053529Calgra 2000619RMMVPappap Conifers IFLIThupli Conifers 2082775 2038979March.p1 March.p1 OVIJ VFYZ Conifers.p1 Conifers.p1 Musacu GSMUA Achr10T17880 001 Anacom Aco020948.1 Thudol 2048764 NKIN Conifers.p1 100 Aposhe lcl KZ452008.1 PKA52202.1 14938 Dencat lcl NW 021319552.1 XP 020698680.1 20846 Fokhod 2058052 UEVI Conifers.p1 Phaequ PEQU 39883 Chalaw 2066604 AIGO Conifers.p1 Spipol Spipo15G0036500 Setita Seita.9G115700.1 Cupdup 2007519 QNGJ Conifers.p1 Sorbic Sobic.001G113700.1 Junsco 2006307 XMGP Conifers.p1 Zeamay Zm00008a005004 Tetsp. 2069048 CGDN Conifers.p1 Orysat LOC Os03g50820.1 Plaori 2049924 BUWV Conifers.p1 Bradis Bradi1g10670.1 Horvul HORVU4Hr1G008200.8 Nelnuc NNU 14882-RA Micdec 2052665 XQSG Conifers.p1 Betvul Bv7 157680 yznn.t1 Caldec 2059232 FRPM Conifers.p1 Diacar Dca33069.1 Cryjap 2008374 DSXO Conifers.p1 Chequi AUR62038492-RA Helann HanXRQChr08g0224841 Utrgib Utricularia gibba unitig 52 2094874 2098308 unitig 52.g17290.t1 1 CDS 875823989 19230 Daucar DCAR 023546 GlypenTaxdis 2043465 2000082 OXGJ FHST Conifers.p1 Conifers.p1 Daucar DCAR 026817 Fraexc FRAEX38873 v2 000273010.1 Taxdis 2000083 FHST Conifers.p1 Petaxi Peaxi162Scf01169g00017.1 Cryjap 2107958 HOUFTaxdis Conifers 2000081 leaf.p1 FHST Conifers.p1 Nicben Niben101Scf00927g08011.1 Nicben Niben101Scf00984g09008.1 Athcup 2060996 XIRK Conifers.p1 Sollyc Solyc01g005150.2.1 Solpen Sopen01g001180.1 Datglo Datgl499S31342 Begfuc Begfu1793S22828 Metgly 2061085 NRXL Conifers.p1 Cucsat evm.model.Chr5.1868 Taicry 2007068 QSNJ Conifers.p1 Cucmel MELO3C005246.2.1 Citlan Cla005812 Lagsic Lsi09G007110.1 Momcha lcl NW 019104528.1 XP 022146393.1 17053 Cucmax CmaCh04G021470.1 Cucmos CmoCh04G022390.1 Cucpep Cp4.1LG00g04930.1 Cucpep Cp4.1LG01g18650.1 Nissch Nissc524481S26695 Seqgig 2000077 QFAE Conifers Glaucum.p1Cunlan 2002476 OUOI Conifers.p1 82.1 Aradur Aradu.J0689 Arahyp arahy.Tifrunner.gnm1.ann1.XHAH6Y.1 Seqgig 2000078 QFAE Conifers Glaucum.p1Cunlan 2002477 OUOI Conifers.p1 Arahyp arahy.Tifrunner.gnm1.ann1.IRYV2C.1 Cryjap 2012702 GMHZ Conifers 2 samples combined.p1 Araipa Araip.R8A8Y Taxcus 2011711 ZYAX Conifers.p1 98.5 Lotjap Lj0g3v0041159.1 Taxbac 2010352 WWSS Conifers.p1 Medtru MtrunA17 Chr1g0161941 Ausspi 2005770 BTTS Conifers.p1 99.5 Tripra Tp57577 TGAC v2 mRNA35737 Trisub lcl DF973212.1 GAU20431.1 9489 Psechi 2005092 YLPM Conifers.p1 Cajcaj Ccajan 37461 Cephar 2004075 GJTI Conifers.p1 Glymax Glyma.07G174600.1 100 Glymax Glyma.20G012400.1 Cephar 2004076 GJTI Conifers.p1 Phavul Phvul.003G014500.1 95.4 Vigung Vigun02g015500.1 Vigang vigan.Vang0004ss00080.1 97.7 Vigrad Vradi11g11640.1 CepharTortax 2007322 2010938 WYAJ EFMS Conifers.p1 Conifers.p1 Cercan Cerca554S26678 89.6 Casaus Castanospermum18293-PA Chafas Chafa8351S27406 Lupang Lup019303.2 Tornuc 2015797 HQOM Conifers.p1 Nissch Nissc524369S26104 Amearg 2023819 IAJW Conifers.p1 Araipa Araip.VBB34 Arahyp arahy.Tifrunner.gnm1.ann1.DWJ5NI.1 Arahyp arahy.Tifrunner.gnm1.ann1.2QAD3K.1 Micdec 2048777 XQSG Conifers.p1 Aradur Aradu.8X6B9 Caldec 2054648 FRPM Conifers.p1 Cicari Ca 26483.1 Fokhod 2051994 UEVI Conifers.p1 98.4 Medtru MtrunA17 Chr8g0375991 Piluvi 2057332 ETCJ Conifers.p1 Tripra Tp57577 TGAC v2 mRNA5273 Cunlan 2004885 ZQVF Conifers 2 samples combined.p1 Trisub lcl DF973563.1 GAU34664.1 23722 Chalaw 2064912 AIGO Conifers.p1 Lotjap Lj4g3v2409490.1 Cajcaj Ccajan 22991 Cunlan 2004887 ZQVF Conifers 2 samples combined.p1 Glymax Glyma.08G094000.1 Glymax Glyma.05G138800.1 Pappap 2081786 OVIJ Conifers.p1 Phavul Phvul.002G182100.1 Vigung Vigun03g160500.1 Auschi 2063546 YYPE Conifers.p1 Vigrad Vradi07g08680.1 Vigang vigan.Vang0062ss00220.1 Cunlan 2004886 ZQVF Conifers 2 samples combined.p1 Citsin orange1.1g027354m Citcle Ciclev10016590m Cepfol Cfol v3 00779 Poptri Potri.010G102400.1 Taxdis 2011801 FHST Conifers.p1 Poptri Potri.008G138300.1 Riccom 29968.m000658 Manesc Manes.17G087000.1 Gosrai Gorai.013G031900.1 Thecac Thecc1EG011240t1 Carpap evm.model.supercontig 2.138 Tarhas lcl NW 010960187.1 XP 010553517.1 3163 Cunlan 2004581 ESYX Conifers branch apex with needles.p1 GlypenAthcup 2042933 2057644 OXGJ XIRK Conifers.p1 Conifers.p1 Eutsal Thhalv10008705m Braolecap Bol031517 Brarap Brara.I04969.1 Braolecap Bol038068 Brarap Brara.F00996.1 ArathaAT1G14730.1 AralyrAL1G26740.t1 ArahalAraha.16488s0014.1 Boestr Bostr.0124s0187.1 Cryjap 2106228 HOUF ConifersMetgly leaf.p1 2058917 NRXL Conifers.p1 Caprub Carub.0001s1451.1 Capgra Cagra.3501s0021.1 Jugreg g38385.t1 AlngluAlngl2700S22385 Querob Qrob P0320670.2 Casmol maker-scaffold13938-augustus-gene-0.7-mRNA-1 Zizjuj lcl NC 029688.1 XP 015895346.1 27707 Distri Distr1140S12333 Mornot L484 019292 Humlup HL.SW.v1.0.G025399.1 Treori lcl JXTC01000409.1 PON56401.1 29652 Cunlan 2007250 OUOI Conifers.p1 Parand lcl JXTB01000126.1 PON60829.1 14960 Roschi RchiOBHm Chr4g0442131 Potmic 24172 t Fraves FvH4 4g33080.1 Fraana iscf00260433.1.g00001.1 FAN Prumum lcl NC 024127.1 XP 008220939.1 5830 Pruavi Pav sc0000893.1 g760.1.mk Pruper Prupe.1G336800.1

Amearg 2146591 IAJW Conifers.p1 Agarob 2074863 MIXZ Conifers.p1 Agamac 2068441 ACWSArarul Conifers.p12005133 XTZO Conifers.p1 Wolnob 2054602Ararul RSCE 2005132 Conifers.p1 XTZO Conifers.p1 Sciver 2042656 YFZK Conifers.p1

Seqgig 2052840 QFAE Conifers Glaucum.p1 Faltax 2057576 ROWR Conifers.p1 Dacbal 2070913 IZGN Conifers.p1 Faltax 2004809 QHBI Conifers A.p1

Daccom 2000624Retmin FMWZ 2001858 Conifers.p1 VGSX Conifers.p1 Daccom 2000621Retmin FMWZ 2001857 Conifers.p1 VGSX Conifers.p1 NagnagPodcor 2113872 2048993 UUJS SCEB Conifers.p1 Conifers.p1 Pintae PTA00071208 Cryjap 2013565 GMHZ Conifers 2 samples combined.p1 Pinpin PPI00070899 Podrub 2055712 XLGK Conifers.p1 Pinsyl PSY00024721 Pinpin PPI00018818 Acmpan 2005790 HILW Conifers.p1 Pintae PTA00043479 Acmpan 2005791 HILW Conifers.p1 Pintae PTA00031530 Ginbil Gb 02831 Pintae PTA00002565 Picsit PSI00004564 Acmpan 2005789 HILW Conifers.p1 Pintae PTA00038975 Pinpin PPI00035792 Mictet 2070252 MHGD Conifers.p1 Pintae PTA00080832 Saxcon 2011788 QCGM Conifers.p1 Dacbal 2010039 IZGN Conifers.p1

Daccom 2000623 FMWZRetmin Conifers.p1 2061419 VGSX Conifers.p1 Daccom 2000622 FMWZ PodcorConifers.p1 2047790 SCEBParust Conifers.p1 2005642 JZVE Conifers.p1 Cunlan 2013618 ZQVF Conifers 2 samples combined.p1 Phyhyp 2007417 JRNA Conifers.p1 Picabi MA 831591g0010 Pruand 2007843 EGLZ Conifers.p1 Cycmic CMI00008774 Sunama 2091785 KLGFHalbid Conifers.p12051653 OWFC Conifers.p1 Pyrcom PCP044141.1 Lagfra 2002661 ZQWM Conifers.p1 Lagfra 2002660 ZQWM Conifers.p1 Lagfra 2002662 ZQWM Conifers.p1 Mancol 2059183Lepsp. CDFR2001864 Conifers.p1 BBDD Conifers.p1 Lepsp. 2001863 BBDD Conifers.p1 Pinjef 2081023 MFTM Conifers.p1 Faltax 2078946 PLYX Conifers 2 samples combined.p1 Phyhyp 2003823Pinpon JRNA 2011535 Conifers.p1 JBND Conifers.p1

Maldom MDP0000254890 Maldom MDP0000270565 Pinpar 2076483 IIOL Conifers.p1 Gnemon TnS000180163t02 Maldom MDP0000302625

Pinrad 2012081 DZQM Conifers.p1

Prudul Prudul26A002450P1

Catagr 2015927 NPRL Conifers.p1

Piceng 2049007 AWQB Conifers.p1 Psewil 2011623 IOVS Conifers.p1 Notlon 2066582 AREG Conifers.p1

Keteve 2011234 JUWLCedlib Conifers.p1 2013119 GGEA Conifers.p1 Tsuhet 2006792 GAMH Conifers.p1

Pseama 2075262 AQFM Conifers.p1

Mongot 2116771 TFDQ Liverworts.p1 Welmir 2001186 TOXE Gnetales.p1 Larspe 2005069 WVWN Conifers.p1 Welmir 2001185 TOXE Gnetales.p1 Ephsin 2003351 VDAO Gnetales.p1

Gnemon 2056002 GTHK Gnetales.p1 Dioedu 2008185 WLIC Cycadales.p1 Dioedu 2008184 WLIC Cycadales.p1 Staeri 2005274 KAWQ Cycadales.p1

Cycmic 2047212 XZUY Cycadales.p1

Encbar 2083134 GNQG Cycadales.p1

Encbar 2003096 GNQG Cycadales.p1

Pyrbre lcl NW 008988058.1 XP 009351583.1 5026

Tree scale: 0.1 Supplementary Figure 30: Maximum likelihood tree of GRAS.

Anetom 2097047 CQPW Leptosporangiate Monilophytes.p1 Anetom 2097624 CQPW Leptosporangiate Monilophytes.p1

Azocar 2001983 CVEG Leptosporangiate Monilophytes.p1

Plajap 2003119 UWOD Leptosporangiate Monilophytes.p1 Osmsp. 2080621 UOMY Leptosporangiate Monilophytes gametophyte.p1

Angeve 2012959 NHCM Eusporangiate Monilophytes.p1

Pilglo 2091467 KIIX Leptosporangiate Monilophytes.p1

Osmjav 2075755 VIBO Leptosporangiate Monilophytes.p1

Calmac 2057102 RMMV Conifers March.p1

Pinrad 2055825 DZQM PinponConifers.p1 2073191 JBND Conifers.p1 Salcuc Sacu v1.1 s0014.g006404 Salcuc Sacu v1.1 s0123.g021525 Pinjef 2083348 MFTM Conifers.p1 Piceng 2010696AWQB Conifers.p1 Pseama 2014587AQFM Conifers.p1 Tsuhet 2001921 GAMH Conifers.p1 Encbar 2008689 GNQG Cycadales.p1Staeri 2012139 KAWQ Cycadales.p1 Dioedu 2013763 WLIC Cycadales.p1 Abilas 2058507 VSRH Conifers.p1

Ginbil 2004852 SGTW Ginkgoales.p1Mancol 2059394 CDFR Conifers.p1 Encbar 2087400 GNQG Cycadales.p1 Ararul 2066103 XTZO Conifers.p1

AzofilAzfi s0807.g087717

Staeri 2012482 KAWQ Cycadales.p1

Isoesp. 2070708 PYHZ Lycophytes.p1 Picabi MA 140003g0010

Isoteg 2098095 PKOX Lycophytes.p1

Psemen PME00014636

Pinpin PPI00012154 Selsta 2006311 ZZOL Lycophytes.p1

Sellep 2008188 ABIJ Lycophytes.p1 Selkra Selwil2009277 2013142 ZFGK KJYCLycophytes.p1 Lycophytes.p1 Phacar 2120037 WCZB Hornworts gametophyte.p1 Selsel 2009021 KUXM Lycophytes.p1 Selapo 2001395 LGDQ Lycophytes.p1

Selwil 2010616 KJYC Lycophytes.p1 Selsel 2009893 KUXM Lycophytes.p1 Cycmic CMI00007722 DenobsSelwal 2013504 2000396 XNXF JKAA Lycophytes.p2 Lycophytes.p1 Ginbil Gb 12802 Ginbil Gb 10920

Psecar 2082470 UPMJ Lycophytes.p1 Ginbil Gb 04650 Lycdeu 2078846 PQTO Lycophytes.p1

Parhal 2057651 FAJB Hornworts.p1

Pittri 2025478 UJTT Leptosporangiate Monilophytes.p1 Megfla 2053960 UCRN Hornworts.p1 Pteens 2002569 FLTD Leptosporangiate Monilophytes.p1 Ptevit 2013049 POPJ Leptosporangiate Monilophytes.p1 Cryacr 2010136 WQML Leptosporangiate Monilophytes.p1 Vitlin 2015301 SKYV Leptosporangiate Monilophytes.p1 Vitapp 2014552 NDUV Leptosporangiate Monilophytes.p1 Adirad 2006396 BMJR Leptosporangiate Monilophytes.p1 Adiale 2010610 WCLG Leptosporangiate Monilophytes.p1 Argniv 2006776 XDDT Leptosporangiate Monilophytes.p1 Parcor 2016482 ZXJO Leptosporangiate Monilophytes.p1 Gagari 2076699 DCDT Leptosporangiate Monilophytes.p1 Leuimm 2010359 WGTU Leptosporangiate Monilophytes.p1 Notvin 2010794 TCBC Hornworts.p1 Selmoe 85562 Nepexa 2129121 NWWI Leptosporangiate Monilophytes.p1 Davfej 2018343 OQWW Leptosporangiate Monilophytes.p1 Polgly 2081200 CJNT Leptosporangiate Monilophytes.p1 Polhes 2024002 IXLH Leptosporangiate Monilophytes B type.p1 Polhes 2031721 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Polhes 2031720 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Phlpse 2026498 ZQYU Leptosporangiate Monilophytes.p1 Polamo 2003122 YLJA Leptosporangiate Monilophytes.p1 Dipwic 2004193 UFJN Leptosporangiate Monilophytes.p1 Anocla 2054585 VBMM Mosses.p1 Blespi 2034902 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Wooilv 2008562 YQEC Leptosporangiate Monilophytes.p1 Gymdry 2014260 HEGQ Leptosporangiate Monilophytes.p1 Marpal scaff10060 FGenesh4.1 Cysuta 2013505 HNDZ Leptosporangiate Monilophytes.p1 Rhyser 2008526 JADL Mosses.p1 Selmoe 84762 Cysfra 2016862 LHLE Leptosporangiate Monilophytes.p1 Necdou 2019683 TMAJ Mosses.p1 Cyspro 2068947 YOWV Leptosporangiate Monilophytes.p1 Cysfra 2029823 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Cysfra 2015772 XXHP Leptosporangiate Monilophytes Stewart.p1 Encbar 2087382 GNQG Cycadales.p1 Cliden 2087272 MIRS Mosses.p1 Staeri 2012577 KAWQ Cycadales.p1 Ginbil 2005977 SGTW Ginkgoales.p1 Thudel 2006932 EEMJ Mosses.p1 Ginbil Gb 19167 Pseama 2083246 AQFM Conifers.p1 Abilas 2058701 VSRH Conifers.p1 LeubraLeujul 2014028 2167979 ZACW IGUH Mosses.p1 Mosses.p1 Tsuhet 2052573 GAMH Conifers.p1 Psemen PME00060716 Stesub 2066730 LNSF Mosses.p1 Piceng 2054919 AWQB Conifers.p1 Loebre 2007969 WSPM Mosses.p1 Picabi MA 1793g0010 Pinpon 2073362 JBND Conifers.p1 Anoatt 2062049 QMWB Mosses.p1 Pinrad 2011919 DZQM Conifers.p1 Pintae PTA00034058 Pseele 2051606 QKQO Mosses.p1 Pinjef 2083243 MFTM Conifers.p1 Fonant 2074449 DHWX Mosses.p1 Pinpin PPI00011686 Pinsyl PSY00000342 Aulhet 2090444 WNGH Mosses.p1 Ararul 2066512 XTZO Conifers.p1 Halbid 2012330 OWFC Conifers.p1 Ortlye 2016380 CMEQ Mosses.p1 Parust 2006950 JZVE Conifers.p1 Acmpan 2114032 HILW Conifers.p1 Hedcil 2003509 YWNF Mosses.p1 Podcor 2011452 SCEB Conifers.p1 Phifon 2058968 ORKS Mosses.p1 Podrub 2012652 XLGK Conifers.p1 Dacbal 2014091 IZGN Conifers.p1 Synpri 2020257 GRKU Mosses.p1 Faltax 2011021 ROWR Conifers.p1 Encstr 2003163 KEFD Mosses.p1 Faltax 2083552 PLYX Conifers 2 samples combined.p1 Racvar 2018679 RDOO Mosses.p1 Faltax 2013021 QHBI Conifers A.p1 Cephar 2012963 GJTI Conifers.p1 Leugla 2065341 RGKI Mosses.p1 Cephar 2022445 NVGZ Conifers 2 samples combined.p1 Taxbac 2010631 WWSS Conifers.p1 Leualb 2132633 VMXJ Mosses.p1 Amearg 2025637 IAJW Conifers.p1 Dicsco 2100705 NGTD Mosses.p1 Tortax 2081708 EFMS Conifers.p1 Cerpur 2005320 FFPD Mosses.p1 Taicry 2068094 QSNJ Conifers.p1 Scoaqu 2022667 BPSG Mosses.p1 Metgly 2064080 NRXL Conifers.p1 Taxdis 2064817 FHST Conifers.p1 Timaus 2018160 ZQRI Mosses.p1 Cryjap 2012943 HOUF Conifers leaf.p1 Racvar 2008949 RDOO Mosses.p1 Cryjap 2147869 GMHZ Conifers 2 samples combined.p1 Racvar 2008950 RDOO Mosses.p1 Auschi 2071826 YYPE Conifers.p1 Calmac 2007604 RMMV Conifers March.p1 Racelo 2000972 ABCD Mosses.p1 Widced 2058005 AUDE Conifers.p1 Dicsco 2005707 NGTD Mosses.p1 Plaori 2012618 BUWV Conifers.p1 Caldec 2013448 FRPM Conifers.p1 Cerpur 2012269 FFPD Mosses.p1 Cupdup 2013068 QNGJ Conifers.p1 Scoaqu 2090713 BPSG Mosses.p1 Thupli 2011421 VFYZ Conifers.p1 Thudol 2012890 NKIN Conifers.p1 Physsp. 2082312 YEPO Mosses.p1 Chalaw 2067544 AIGO Conifers.p1 Fokhod 2010556 UEVI Conifers.p1 Phypat Pp3c19 18560V3.1 Ginbil Gb 17596 Cycmic 2001932 XZUY Cycadales.p1 Physsp. 2078691 YEPO Mosses.p1 Staeri 2053088 KAWQ Cycadales.p1 Phypat Pp3c22 13060V3.1 Encbar 2013579 GNQG Cycadales.p1 Dipfol 2073555Phypat AWOI Pp3c21 Mosses.p1 17650V3.1 Welmir 2002218 TOXE Gnetales.p1 Atrang 2015418 ZTHV Mosses.p1 Welmir 2002217 TOXE Gnetales.p1 Andrup 2095725 WOGB Mosses.p1 Larspe 2055427 WVWN Conifers.p1 Psemen PME00092940 Pseama 2010757 AQFM Conifers.p1 Sphrec 2010771 UHLI Mosses.p1 Tsuhet 2057618 GAMH Conifers.p1 Sphpal 2018791Sphfal RCBTSphfalx0006s0122.1 Mosses.p1 Keteve 2012911 JUWL Conifers.p1 Sphles 2081463 GOWD Mosses.p1 Abilas 2058402 VSRH Conifers.p1 Piceng 2011934 AWQB Conifers.p1 Picabi MA 18234g0010 Pinpar 2015951 IIOL Conifers.p1 Sphfal Sphfalx0105s0005.1 Sphrec 2022206 UHLI Mosses.p1 Pinpin PPI00070194 Sphpal 2008387Sphfal RCBTSphfalx0262s0012.1 Mosses.p1 Pinjef 2011802 MFTM Conifers.p1 Pinjef 2011803 MFTM Conifers.p1 Pinpon 2011477 JBND Conifers.p1 Sphfal Sphfalx0197s0015.1 Pinpon 2011478 JBND Conifers.p1 Pinrad 2011575 DZQM Conifers.p1 Pintae PTA00042936 Sciver 2010395 YFZK Conifers.p1 Ararul 2065838 XTZO Conifers.p1 Wolnob 2058518 RSCE Conifers.p1 Agarob 2011836 MIXZ Conifers.p1 Agamac 2070334 ACWS Conifers.p1 Pruand 2007103 EGLZ Conifers.p1 Sunama 2013238 KLGF Conifers.p1 Phyhyp 2069396 JRNA Conifers.p1 Lepsp. 2003403 BBDD Conifers.p1 Halbid 2055883 OWFC Conifers.p1 Parust 2007798 JZVE Conifers.p1 Lagfra 2091004 ZQWM Conifers.p1 Mancol 2064062 CDFR Conifers.p1 Acmpan 2114118 HILW Conifers.p1

91.3 100 Mictet 2073981 MHGD Conifers.p1 100 Saxcon 2075299 QCGM Conifers.p1 100

99

99.6 99.9 Retmin 2072309 VGSX Conifers.p1

95.2 99 95.3 Nagnag 2116516 UUJS Conifers.p1 94.4 96.1 Sollyc Solyc07g043330.1.1 99.9 99.9 Podcor 2054503 SCEB Conifers.p1

80.7 Solpen Sopen07g022890.1 92.2 Podrub 2012715 XLGK Conifers.p1 100 97.7 94.886.7 Daccom 2058804 FMWZ Conifers.p1 91 95.4 Nicben Niben101Scf21026g00010.1 95.4 99.9 95.6 Dacbal 2074288 IZGN Conifers.p1 Nicben Niben101Scf02807g11019.1Capann CA07g08560 100 Faltax 2012672 ROWR Conifers.p1 96.4 Petaxi Peaxi162Scf00393g00042.1 Faltax 2083751 PLYX Conifers 2 samples combined.p1

98.8

99.5 Fraexc FRAEX38873 v2 000387000.1 86.1 Faltax 2013573 QHBI Conifers A.p1 83.9 97.8 Fraexc FRAEX38873 v2 000260500.1 100 Cephar 2012964 GJTI Conifers.p1 83.583.7 100 Cephar 2091668 WYAJ Conifers.p1

Chequi AUR62044774-RA 96.1 Cephar 2016663 NVGZ Conifers 2 samples combined.p1 100 86.7 Cephar 2016662 NVGZ Conifers 2 samples combined.p1 Chequi AUR62039155-RA 100 Cephar 2012965 GJTI Conifers.p1 Chequi AUR62009109-RA 98.5 97.7 98.3 93.9 Amearg 2026173 IAJW Conifers.p1 100 Spiole Sp 107360 xjej.t1 100 100 Tortax 2013451 EFMS Conifers.p1 98.8 97.9 93.7 100 Betvul Bv2 034300 dzwp.t1 99.8 94.2 Ausspi 2078003 BTTS Conifers.p1 89.7 87.8 80.6 99.8 83.2 Taxbac 2043759 WWSS Conifers.p1 Nelnuc NNU 01236-RA 100 97.8 99.9 100 93.1 99.9 100 100 96.6 Taxcus 2006787 ZYAX Conifers.p1 Daucar DCAR 009840 82.3 92.6 99.9 86.7 100 98.4100 Poptri Potri.016G018900.1 100 97.7 100 99.6 100 Cunlan 2019658 ZQVF Conifers 2 samples combined.p1 100 90 85.598.188.7 Cunlan 2013077 OUOI Conifers.p1 99.9 100 95.1 Poptri Potri.006G021400.1 86.1 98.1 100 100 98.9 100 87.5 100 100 Cunlan 2016303 ESYX Conifers branch apex with needles.p1 Riccom 29872.m000537 94.2 100 99.9 Manesc Manes.08G071100.1 100 99.4 99.6 94.6 Taicry 2068393 QSNJ Conifers.p1 99.8 100 84.594.9 95.4 99.8 99.8 100 100 100 Athcup 2065395 XIRK Conifers.p1 100 96 82.8 Cepfol Cfol v3 23139 93.7 94.7 99.696.393.985.4 100 Seqgig 2062501 QFAE Conifers Glaucum.p1 Gosrai Gorai.004G063200.1 96.4 93.7 95.5 99.9 99.7 91.4 84.3 Metgly 2065473 NRXL Conifers.p1 99 99.9 92.2 80.489.5 Thecac Thecc1EG002021t1 100 100 95.7 92.8 95.3 92.7 95.4 Taxdis 2014129 FHST Conifers.p1 93.8 100 Citsin orange1.1g013903m 97.4 98.38899.397.9 Glypen 2047596 OXGJ Conifers.p1 100 100 91.3 Citcle Ciclev10011732m 100 100 97.6 96.598.510093.7 Cryjap 2011247 HOUF Conifers leaf.p1 Carpap evm.model.supercontig 8.295 86.4 Cryjap 2015986 GMHZ Conifers 2 samples combined.p1 95.5 99.9 Cucmel MELO3C016202.2.1 86.5 97 100 Cryjap 2075755 DSXO Conifers.p1 99.9 100 100 83.8 99.596.1 Auschi 2070670 YYPE Conifers.p1 Cucsat evm.model.Chr4.712 96.3 100 91.1 93.3 Pappap 2006082 OVIJ Conifers.p1 87.1 98.7 99.6 100 Citlan Cla005438 100 100 93.4 100 99.9 Piluvi 2063881 ETCJ Conifers.p1 Lagsic Lsi07G008000.1 100 100 Disarc 2076050 GKCZ Conifers.p1 Cucmos CmoCh04G006610.1 89.3 97 100 96.4 Widced 2060958 AUDE Conifers.p1 99.9 91.189.2 Cucpep Cp4.1LG01g00980.1 100 99.797.7 Calgra 2008428 IFLI Conifers March.p1 87.3 88 Cucmax CmaCh04G006140.1 100 Neopan 2070529 JDQB Conifers.p1 99.8 93.5 100 Begfuc Begfu383S03930 99.8 94.9 98.5 Calmac 2056319 RMMV Conifers March.p1 98.6 97.7100 Begfuc Begfu4057S49422 100 100 92 Fokhod 2061039 UEVI Conifers.p1 97.8 97.7 Datglo Datgl27371S06819 85.8 Chalaw 2071404 AIGO Conifers.p1 85.799.3 Thupli 2041238 VFYZ Conifers.p1 Alnglu Alngl1708S39262 99.9 87.7 81.2 100 99.9 Thudol 2014677 NKIN Conifers.p1 Casgla Casgl89S06178 85.5 100 99.9 85.2 99.794.5 Caldec 2013860 FRPM Conifers.p1 Jugreg g12238.t1 99.7 Tetsp. 2005575 CGDN Conifers.p1 Jugreg g33773.t1 99.5 99.8 98.4 Cupdup 2074659 QNGJ Conifers.p1 99.6 100 Junsco 2014512 XMGP Conifers.p1 100 89.3 95.2 99.4 Casmol augustus masked-scaffold00731-abinit-gene-0.3-mRNA-1Pyrcom PCP028176.1 92.9 Plaori 2054253 BUWV Conifers.p1 92.1 99.9 99.6 Pyrcom PCP043201.1 100 98.6 93.8 95.9 99.8 Micdec 2003805 XQSG Conifers.p1 89.1 91 Micdec 2003804 XQSG Conifers.p1 99.7 Welmir 2011529 TOXE Gnetales.p1 Pyrbre lcl NW 008988299.1Maldom XP 009375331.1 MDP0000287321 26811 100 100 99.8 85.5 93.198.1 Ambtri evm 27.model.AmTr v1.0 scaffold00077.226 Maldom MDP0000289554 87.8 94.1 Zosmar Zosma113g00340.1 Maldom MDP0000269044 100 99.9 100 10089.2 85.1 93.3 Zosmar Zosma74g00100.1 Pyrcom PCP027684.1 99.199.8 91.7 99.8 Mornot L484 022753 93.7 99.9 Pruper Prupe.3G187000.1 100 99.8 Utrgib Utricularia gibba unitig 699 103798 104992 unitig 699.g19017.t1 1 CDS 875833449 9281 97.2 Drydru Drydr291S19868 Prudul Prudul26A030794P1 83.2 100 100 100 98.999.6 Rubocc Bras G11033 95 Roschi RchiOBHm Chr3g0459291 Prumum lcl NC 024129.1 XP 008229662.1 14075 Pruavi Pav sc0001543.1Drydru Drydr258S09242 g140.1.mk 99.9 Potmic 17240 t 99.8 Fraana FAN iscf00245703.1.g00001.1 99.696.699.2 100 98.2 Fraves FvH4 6g09040.1 Fraana FAN iscf00092346.1.g00001.1Fraves FvH4 6g39610.1 97.8 100 89.8100 92.8 93.7 91.3 Fraana FAN iscf00064378.1.g00001.1 99.6 92.6 94.7 Potmic 30490 t 90.7 91.9100 Prumum lcl NC 024126.1 XP 008244193.1 2680 96.4 100 Fraana FAN iscf00091513.1.g00001.1 99.9 98.7 80.1 98.4 99.6 Pruavi Pav sc0001699.1 g490.1.mk 100 97 97.3 87.6 99.4 86.3 89 Pruper Prupe.6G300900.1 Rubocc Bras G08433 87.5 86 100 Roschi RchiOBHm Chr2g0153661 82.9 Prudul Prudul26A008076P1 98.5 91.3 100 100 92.6 Diacar Dca30033.1 99.9 99.4 Distri Distr200S06448 99.8 99.5 98.5 90.2 88 99.8 Spiole Sp 058490 wiju.t1 97.7 99.9 99.4 94.6 96.9 100 Betvul Bv9 221600 fznw.t1 93.3 88.2 Zizjuj lcl NW 015453766.1 XP 015867058.1 37551 91.3 100 Chequi AUR62012891-RA 100 99.7 100 96.7 Chequi AUR62027115-RA 100 86.3 99.7 100 99.8 Treori lcl JXTC01000245.1 PON77617.1Mornot L484 23991 009332 100 99.2 Maldom MDP0000419045 Humlup HL.SW.v1.0.G029557.1 100 99.9 99 Pyrbre lcl NW 008988226.1 XP 018506120.1 22703 87.1 94.6 Parand lcl JXTB01000454.1 PON39855.1 30209 99.9 82.9 98.9 Vigrad Vradi02g01980.1 100 100 100 Pyrcom PCP006564.1 99.6 99.9 82.4 100 100 100 Maldom MDP0000397638 Vigang vigan.Vang05g05690.1 100 94 Vigung Vigun11g199500.1 98.380.9 99.9 Pyrbre lcl NW 008988505.1 XP 009337846.1 34744 Pyrcom PCP019633.1 100 100 Phavul Phvul.011G024600.2Cajcaj Ccajan 21058 100 100 87.9 99.9 88.4 Humlup HL.SW.v1.0.G001247.1 100 Treori lcl JXTC01000324.1 PON64996.1 27200 GRAS 96.8 100 Parand lcl JXTB01000738.1 PON33318.1 35388 Glymax Glyma.12G022600.1 Glymax Glyma.11G096500.1Aradur Aradu.2376Y 100 100 Distri Distr923S29289 100 99.9 100 Zizjuj lcl NC 029689.1 XP 015897596.1 30115 Zizjuj lcl NC 029689.1 XP 015897583.2 30114 96.5 Nissch Nissc671S10960 99.6 Begfuc Begfu1465S19687 99.6 Begfuc Begfu3842S33237 94.6 Begfuc Begfu1165S07211 Arahyp arahy.Tifrunner.gnm1.ann1.M96WLV.1Cicari Ca 17271.1 99.8 Momcha lcl NW 019104646.1 XP 022156207.1 25857 Tripra Tp57577 TGAC v2 mRNA21992 Cucmax CmaCh07G011780.1

94.4 Medtru MtrunA17Lupang Chr4g0038761 Lup017421.1 100 Cucpep Cp4.1LG19g01780.1 Trisub lcl DF973666.1 GAU37323.1 26381 Cucmos CmoCh07G012270.1

100 100 Cucmax CmaCh03G002590.1 Chafas Chafa54S10619 Cucmos CmoCh03G002750.1 81.8 Cucpep Cp4.1LG10g07230.1 Casaus Castanospermum24193-PACercanAralyr Cerca228S01770 AL7G47290.t1 85.3 Cucmel MELO3C025282.2.1 99.5 Aratha AT5G41920.1 Cucsat evm.model.Chr4.1150 99.8 Lagsic Lsi01G016490.1 Caprub Carub.0007s3345.1 Citlan Cla012151 Cepfol Cfol v3 20966 Capgra Cagra.6263s0002.1 Carpap evm.model.supercontig 1018.1 Boestr Bostr.25375s0003.1 Citsin orange1.1g014896m Boestr Bostr.17016s0016.1 Eutsal Thhalv10027784m 81.3 Citcle Ciclev10011085m

Brarap Brara.D01210.1 91.2 Tarhas lcl NW 010962392.1 XP 010529957.1 6580 100 95.9 Tarhas lcl NW 010960187.1 XP 010529432.1 660 97.7 98.5 99.9 Brarap Brara.I03694.1 96.8 97.8 Braolecap Bol025184 93 97.5 Eutsal Thhalv10010179m

97.2

98.7 99.6 99.3 100 Eutsal Thhalv10023455m 99.5 Caprub Carub.0005s2081.1 99.2 Mimpud Mimpu20058S02054 99.6 Capgra Cagra.0562s0013.1 99.9 100 95.4 Boestr Bostr.0697s0034.1 99.7

91.9 Phaequ PEQU 05614 100 Aratha AT3G54220.1 Tarhas lcl NW 010960187.1 XP 010544911.1Zosmar Zosma224g00050.1 2272 Arahal Araha.23770s0001.1 Tarhas lcl NW 010960187.1 XP 019059486.1 2270 100 Aralyr AL5G35260.t1 Phaequ PEQU 04461 100 99.1 Gosrai Gorai.006G236200.1 Tarhas lcl NW 010960187.1 XP 019059489.1 2271 99.8 95.8 Thecac Thecc1EG017746t1 82.1 Gosrai Gorai.005G001300.1 100 Anacom Aco031731.1 97.9 100 97.7 Riccom 30073.m002204 Anacom Aco002115.1 100 Manesc Manes.09G119400.1 100 99.9 100 100 100 Manesc Manes.08G165800.1 95.5 94.9 96.9 93.6 90.8 Poptri Potri.006G114200.1 100 96.7 Zeamay Zm00008a029122 Poptri Potri.016G143900.1 Poptri Potri.T138100.1 SorbicSetita Sobic.002G342800.1 Seita.2G356700.1 100 Nelnuc NNU 16619-RA Dencat lcl NW 021319089.1 XP 020677583.1 11419 Helann HanXRQChr01g0000691 Aposhe lcl KZ454830.1 PKA45610.1 21598 100 98.1 Helann HanXRQChr11g0329331 Orysat LOCBradis Os07g38030.1 Bradi1g24310.1 100 Daucar DCAR 028933 Dencat lcl NW 021319594.1 XP 020698345.1 21691 99.9 Daucar DCAR 031212 Horvul HORVU0Hr1G003230.1 Fraexc FRAEX38873 v2 000087300.1 Spipol Spipo8G0021400 Fraexc FRAEX38873 v2 000087300.2 Petaxi Peaxi162Scf00374g00723.1 Nicben Niben101Scf12516g02006.1 Nicben Niben101Scf00199g05004.1 Musacu GSMUA Achr4T23590 001 Capann CA10g10180 Vigrad Vradi08g07630.1 Solpen Sopen10g027150.1 Gnemon TnS000552883t03 Sollyc Solyc10g074680.1.1 Jugreg g33634.t1 85.9 Utrgib UtriculariaUtrgib Utricularia gibba unitig gibba 699 unitig 2186576 85 454648 2187763 457680 unitig unitig 699.g19630.t1 85.g27315.t1 -1 -1 CDS CDS 875834481 875852067 15754 19369 Jugreg g17431.t1 Vigung Vigun07g094300.1 Jugreg g15952.t1 Vigang vigan.Vang06g14650.1 Casmol maker-scaffold08547-augustus-gene-0.10-mRNA-1 Cajcaj Ccajan 06634 Querob Qrob P0240710.2 99.6 Phavul Phvul.007G191300.1 Casgla Casgl671S21042 Glymax Glyma.10G038500.1 100 Alnglu Alngl424639S03879 Cicari Ca 08969.1 87.4 Datglo Datgl191S23480 Glymax Glyma.13G124900.1 Mimpud Mimpu24440S20648 100 Cercan Cerca556S26696 Ambtri evm 27.model.AmTr v1.0 scaffold00036.135 Casaus Castanospermum22967-PA Lupang Lup011148.1 Ambtri evm 27.model.AmTr v1.0 scaffold00032.155 Lupang Lup012111.1 Cajcaj Ccajan 34953 Nissch Nissc3112S01980 Glymax Glyma.18G220100.1 Lotjap Lj6g3v0886420.1 Glymax Glyma.09G270000.1 Phavul Phvul.008G077000.1 Vigung Vigun05g080600.1 Medtru MtrunA17 Chr1g0183641Cercan Cerca54S09750 Vigang vigan.Vang04g07780.1 Jugreg g33636.t1 Vigrad Vradi0360s00120.1 Lotjap Lj1g3v2580600.1 Tripra Tp57577 TGAC v2 mRNA36927 Cicari Ca 06305.1 Medtru MtrunA17 Chr7g0245601 Trisub lcl DF973996.1 GAU43822.1 32880 Tripra Tp57577 TGAC v2 mRNA3260 MimpudChafas Mimpu3632S31515 Chafa3674S21657 Trisub lcl DF973664.1 GAU37280.1 26338 Alnglu Alngl45849S10780 Nissch Nissc1274S05378 Casgla Casgl128S00246 Aradur Aradu.J7N5K Arahyp arahy.Tifrunner.gnm1.ann1.9H4MHS.1 Araipa Araip.LR314 Casaus Castanospermum04646-PA Arahyp arahy.Tifrunner.gnm1.ann1.VUGA5D.1 Spipol Spipo3G0011100 Querob Qrob P0658450.2 Aposhe lcl KZ452012.1 PKA51827.1 15355 Dencat lcl NW 021415225.1 XP 020695561.2 31669 Capann CA00g42950 Phaequ PEQU 38872 Musacu GSMUA Achr8T09400 001 Musacu GSMUA Achr11T20070 001 Musacu GSMUA Achr5T21440 001 Anacom Aco012593.1 Solpen Sopen09g028180.1 Horvul HORVU5Hr1G045920.2 Bradis Bradi4g44093.1 Orysat LOC Os11g03110.1 Sollyc Solyc09g066450.1.1 Orysat LOC Os12g02870.1 Setita Seita.8G008700.1 Setita Seita.7G305500.1 Sorbic Sobic.008G023401.1 Sorbic Sobic.005G017500.2 Zeamay Zm00008a017706 Zeamay Zm00008a008389 Zeamay Zm00008a034587 Gnemon TnS000140939t02 Orysat LOC Os05g40710.1 Bradis Bradi2g22010.1 Setita Seita.3G200500.1 Sorbic Sobic.009G177100.1 Zeamay Zm00008a026055 Ambtri evm 27.model.AmTr v1.0 scaffold04794.1 Anacom Aco010118.1 Anacom

Daucar DCAR 005683

Riccom 28492.m000479 Nicben Niben101Scf02243g01001.1 NicbenPetaxi Niben101Scf05997g00036.1 Peaxi162Scf00624g00051.1 Poptri Potri.005G226800.1 Manesc Manes.12G034000.1Poptri Potri.002G036100.1Citcle Ciclev10019735m Helann HanXRQChr09g0254241 Citsin orange1.1g045494m Pyrcom PCP016225.1 Potmic 10795 t Fraexc FRAEX38873 v2 000297880.1 Fraexc FRAEX38873 v2 000297020.1 Gosrai Gorai.004G221600.1 Pyrcom PCP006757.1 Gosrai Gorai.001G254600.1

Thecac Thecc1EG003984t1 Citlan Cla014874 Maldom MDP0000230994

Rubocc Bras G13775 Maldom MDP0000307619 Pruper Prupe.8G220900.1 Fraves FvH4 2g21170.1

Mornot L484 005640

Prudul Prudul26A000263P1 Lagsic Lsi02G021610.1 Distri Distr211S06632

Distri Distr1125S00248

Begfuc Begfu234S09777

Cucmel MELO3C012729.2.1 Carpap evm.model.supercontig 165.22

Cucsat evm.model.Chr7.1468 Casmol augustus masked-scaffold05068-abinit-gene-0.0-mRNA-1 Cucpep Cp4.1LG17g11330.1 Cucmax CmaCh08G002610.1

Cucmos CmoCh08G002570.1

Pruavi Pav sc0000583.1 g990.1.mkRoschi RchiOBHm Chr6g0287671

Humlup HL.SW.v1.0.G002126.1

Pyrbre lcl NW 008988461.1 XP 009336159.1 33237

Pyrbre lcl NW 008988207.1 XP 009369454.1 21426 Prumum lcl NC 024131.1 XP 008235644.2 19758

Zizjuj lcl NC 029687.1 XP 015891260.1 23384

Treori lcl JXTC01000209.1 PON81762.1 22482

Parand lcl JXTB01000111.1 PON62657.1 13774

Momcha lcl NW 019104643.1 XP 022156094.1 25759

Tree scale: 0.1 Supplementary Figure 31: Maximum likelihood tree of HEP.

Utrgib Utricularia gibba unitig 699 2312371 2315125 unitig 699.g19673.t1 1 CDS 875834565 10757

Casmol maker-scaffold00479-augustus-gene-0.29-mRNA-1 Casmol maker-scaffold00479-augustus-gene-0.29-mRNA-2

Cysfra 2025804 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Tarhas lcl NW 010966177.1 XP 010546726.1 21618 Tarhas lcl NW 010966177.1 XP 010546725.1 21616 Tarhas lcl NW 010966177.1 XP 010546727.1 21617

Blespi 2218903 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1

Fraexc FRAEX38873 v2 000117690.1 Fraexc FRAEX38873 v2 000117690.3 Fraexc FRAEX38873 v2 000117690.2

Nicben Niben101Scf00369g09016.1 Nicben Niben101Scf03643g09016.1

Petaxi Peaxi162Scf00037g01225.1

Helann HanXRQChr03g0074711

Carpap evm.model.supercontig 327.1 Cysfra 2086476 XXHP Leptosporangiate Monilophytes Stewart.p1Cysfra 2003131 LHLE Leptosporangiate Monilophytes.p1 Cysfra 2003134 LHLE Leptosporangiate Monilophytes.p1Dencat lcl NW 021320106.1 XP 020696240.1 29357 Alngl424681S27989Alnglu Solpen Sopen01g043270.1 Sollyc Solyc01g099750.2.1

Cysfra 2003133 LHLE Leptosporangiate Monilophytes.p1 Querob Qrob P0474070.2 Capgra Cagra.14151s0003.1 Cysfra 2003132 LHLE Leptosporangiate Monilophytes.p1 Caprub Carub.0006s2483.1 Cysuta 2002841 HNDZ Leptosporangiate Monilophytes.p1

Casgla Casgl72S21518 Cysuta 2002844 HNDZ Leptosporangiate Monilophytes.p1Ambtri evm 27.model.AmTr v1.0 scaffold00045.306 Boestr Bostr.29827s0095.1 ArahalAraha.2427s0001.1 Cysuta 2002843 HNDZ Leptosporangiate Monilophytes.p1

Capann CA01g23920 Capann CA12g01510 Capann CA11g08160 Capann CA00g66960

Daucar DCAR 022144 Eutsal Thhalv10004288m Citsin orange1.1g012127m Thecac Thecc1EG026658t1 Gosrai Gorai.007G300200.1 Manesc Manes.08G117300.1 Brarap Brara.B03553.1 Dipwic 2012841Blespi 2099757 UFJN Leptosporangiate VITX Leptosporangiate Monilophytes.p1 Monilophytes.p1 Jugreg g48110.t1 Poptri Potri.005G025200.2 Braolecap Bol012770 AralyrAL6G39220.t1 ArathaAT5G27730.1 Poptri Potri.013G016900.2 Citcle Ciclev10001045m PolamoPolgly 2008942 2012260 YLJA CJNTLeptosporangiate Leptosporangiate Monilophytes.p1 Monilophytes.p1 Aposhe lcl KZ451953.1 PKA58430.1 8946

Polamo 2008941 YLJA Leptosporangiate Monilophytes.p1 Begfuc Begfu4076S33875 Davfej 2001466Phlpse 2011016 OQWW ZQYU Leptosporangiate Leptosporangiate Monilophytes.p1 Monilophytes.p1 Davfej 2001467 OQWW Leptosporangiate Monilophytes.p1 Betvul Bv4 075840 jjsk.t3 Chequi AUR62000759-RABetvul Bv4 075840 jjsk.t1 Leuimm 2073750 WGTU Leptosporangiate Monilophytes.p1 Musacu GSMUA Achr3T08090 001 Betvul Bv4 075840 jjsk.t2 Chequi AUR62005209-RA

Cryacr 2002775 WQML Leptosporangiate Monilophytes.p1 Spiole Sp 186580 cetq.t1 Cepfol Cfol v3 14137 Sorbic Sobic.003G414300.1 Cryacr 2002774 WQML Leptosporangiate Monilophytes.p1 Zeamay Zm00008a032563

Orysat LOC Os01g70550.1 Nelnuc NNU 05718-RA Setita Seita.5G440300.1 Argniv Ptevit2004884 2012231Pittri XDDT 2091750 POPJ Leptosporangiate UJTT Leptosporangiate Leptosporangiate Monilophytes.p1 Monilophytes.p1 Monilophytes.p1 Diacar Dca50215.1 NotmonArgniv 2062365 2004883 YCKE XDDT Leptosporangiate Leptosporangiate Monilophytes.p1 Monilophytes.p1 Bradis Bradi2g59690.1 Diacar Dca55479.1

Jugreg g31057.t1 Zizjuj lcl NC 029680.1 XP 015875090.1 6467 Distri Distr429S24317 Mornot L484 000992 Humlup HL.SW.v1.0.G009440.1 Treori lcl JXTC01000464.1 PON52090.1 30935 Parand lcl JXTB01000657.1 PON34486.1 34412 Rubocc Bras G18540 Roschi RchiOBHm Chr3g0455771 Anacom Aco002457.1 Potmic 22897 t Osmsp. 2078446 UOMY Leptosporangiate Monilophytes Culmacgametophyte.p1 2152156 PNZO Leptosporangiate Monilophytes.p1 Fraana FAN iscf00261701.1.g00001.1 Fraana FAN iscf00072626.1.g00001.1 Fraana FAN iscf00119199.1.g00001.1 Fraana FAN iscf00232559.1.g00001.1 Fraves FvH4 6g06580.1 Fraana FAN iscf00023956.1.g00001.1 Drydru Drydr291S09941 Linlin 2005635 NOKI Leptosporangiate Monilophytes.p1 Maldom MDP0000304297 Plajap 2139658 UWOD Leptosporangiate Monilophytes.p1 Pyrbre lcl NW 008988328.1 XP 009376612.1 27989 Pyrcom PCP027403.1 Pruavi Pav sc0000671.1 g110.1.mk Prudul Prudul26A025297P1 Phaequ PEQU 04057 Pruper Prupe.6G320400.1 Thyele 2023622 EWXK Leptosporangiate Monilophytes.p1 Prumum lcl NC 024126.1 XP 016651648.1 3079 Prumum lcl NC 024126.1 XP 016651645.1 3080 Prumum lcl NC 024126.1 XP 008246429.1 3078 Datglo Datgl750S34375 Momcha lcl NW 019104651.1 XP 022156389.1 25972 Cucmax CmaCh05G010990.1 Cucmos CmoCh05G011140.1 Cucpep Cp4.1LG11g09000.1 Citlan Cla019935 Lygjap 2015114 PBUU Leptosporangiate Monilophytes.p1 Lagsic Lsi11G006030.1 Cucsat evm.model.Chr2.431 Dipcon 2107996 MEKP Leptosporangiate Monilophytes.p1 Cucmel MELO3C004217.2.1 Pilglo 2088804 KIIX Leptosporangiate Monilophytes.p1 Cercan Cerca14S14948 Chafas Chafa95604S30187 Hymbiv 2000638 QIAD Leptosporangiate Monilophytes.p1 Mimpud Mimpu1699S18330 Casaus Castanospermum13597-PA Lupang Lup001057.1 Osmjav 2007005 VIBO Leptosporangiate Monilophytes.p1 Nissch Nissc266120S19703 Aradur Aradu.M1IA1 Osmjav 2007004 VIBO Leptosporangiate Monilophytes.p1 Aradur Aradu.MM4KN Arahyp arahy.Tifrunner.gnm1.ann1.09ZXWH.2 Araipa Araip.QSJ05 Arahyp arahy.Tifrunner.gnm1.ann1.Z3D6FW.1 Arahyp arahy.Tifrunner.gnm1.ann1.653B24.5 Arahyp arahy.Tifrunner.gnm1.ann1.FNRX56.1 Cicari Ca 07727.1 Medtru MtrunA17 Chr7g0272261 Tripra Tp57577 TGAC v2 mRNA30181 Trisub lcl DF973114.1 GAU11485.1 543 Botvir 2023762 BEGM Eusporangiate Monilophytes.p1 Tripra Tp57577 TGAC v2 mRNA34313 Scedis 2018028 EEAQ Eusporangiate Monilophytes.p1 Cajcaj Ccajan 10158 Tmepar 2103042 ALVQ Eusporangiate Monilophytes.p1 Glymax Glyma.19G233000.1 Glymax Glyma.03G235300.1 Marsp. 2017058 UXCS Eusporangiate Monilophytes.p1 Phavul Phvul.006G089300.1 Hupsel 2169178Angeve YHZW 2013497 Lycophytes NHCM 2Eusporangiate samples combined.p1 Monilophytes.p1 Vigung Vigun06g099500.1 Vigang vigan.Vang03g11600.1 Vigrad Vradi10g04660.1 Sciver 2006981 YFZK Conifers.p1 Wolnob 2057342 RSCE Conifers.p1 Ararul 2063929 XTZO Conifers.p1 Agarob 2074191 MIXZ Conifers.p1 Halbid 2054328 OWFC Conifers.p1 Lepsp. 2013690 BBDD Conifers.p1 Pruand 2003439 EGLZ Conifers.p1 Pruand 2003440 EGLZ Conifers.p1 Pruand 2003441 EGLZ Conifers.p1 Parust 2039291 JZVE Conifers.p1 Mancol 2062395 CDFR Conifers.p1 Lagfra 2008007 ZQWM Conifers.p1 Lagfra 2008006 ZQWM Conifers.p1 Phyhyp 2014068 JRNA Conifers.p1 Mictet 2073388 MHGD Conifers.p1 Saxcon 2074094 QCGM Conifers.p1 Hupluc 2097679 GKAG Lycophytes.p1 Daccom 2003627 FMWZ Conifers.p1 Podrub 2001520 XLGK Conifers.p1 Podrub 2001521 XLGK Conifers.p1 Welmir 2001692 TOXE Gnetales.p1 HupsquPhydru 2015003 2127386 GAON ZZEI Lycophytes.p1 Lycophytes.p1 Welmir 2001690 TOXE Gnetales.p1 Gnemon TnS000984855t07 Hupmyr 2061012 CBAE Lycophytes.p1 Gnemon 2006047 GTHK Gnetales.p1 Lycdeu 2003082 PQTO Lycophytes.p1 Gnemon 2006046 GTHK Gnetales.p1 Psemen PME00053360 Denobs 2012345 XNXF Lycophytes.p1 Psemen PME00018276 Psemen PME00053354 Dipdig 2010114 WAFT Lycophytes.p1 Psemen PME00053358 Dipdig 2010113 WAFT Lycophytes.p1 Psemen PME00053362 Psecar 2015908 UPMJ Lycophytes.p1 Picabi MA 10435913g0010 Psecar 2015907 UPMJ Lycophytes.p1 Picsit PSI00001651 Pinpin PPI00065727 Lycann 2084726 ENQF Lycophytes.p1 Pinpin PPI00014714 Pinsyl PSY00006817 Selapo 2011847 LGDQ Lycophytes.p1 Pinrad 2006758 DZQM Conifers.p1 Sellep 2006703 ABIJ Lycophytes.p1 Pinpon 2006197 JBND Conifers.p1 Pinjef 2007306 MFTM Conifers.p1 Psemen PME00017352 Selsta 2011531 ZZOL Lycophytes.p1 Notlon 2005727 AREG Conifers.p1 Phacar 2117816 WCZB Hornworts gametophyte.p1Selwil 2048923 KJYC Lycophytes.p1 Keteve 2015614 JUWL Conifers.p1 Selkra 2000768 ZFGK Lycophytes.p1 Picsit PSI00008279 Selkra 2000767 ZFGK Lycophytes.p1 Pinpar 2078211 IIOL Conifers.p1 Isoteg 2010446 PKOX Lycophytes.p1 Pinjef 2011324 MFTM Conifers.p1 Isoesp. 2070284 PYHZ Lycophytes.p1 Pinrad 2009780 DZQM Conifers.p1 Pinpon 2014938 JBND Conifers.p1 Isoteg 2010445 PKOX Lycophytes.p1 Pintae PTA00083256 Picsit PSI00017886 Parhal 2009249 FAJB Hornworts.p1 Picsit PSI00000486 Picabi MA 10428165g0010 Psemen PME00053357 Selmoe 75452 Larspe 2005987 WVWN Conifers.p1 Leualb 2013883 VMXJ Mosses.p2 Larspe 2005985 WVWN Conifers.p1 Leualb 2013881 VMXJ Mosses.p1 Psewil 2056381 IOVS Conifers.p1 Leugla 2010764 RGKI Mosses.p1 Psemen PME00016658 Leualb 2013882 VMXJ Mosses.p1 Ginbil Gb 06559 Dicsco 2009895 NGTD Mosses.p1 Cycmic CMI00022600 Racelo 2006364 ABCD Mosses.p1 Cycmic CMI00025534 Racvar 2002635 RDOO Mosses.p2 Dioedu 2010986 WLIC Cycadales.p1 Dioedu 2010987 WLIC Cycadales.p1 Cerpur 2012691 FFPD Mosses.p1 Ginbil Gb 07710 Synpri 2078350 GRKU Mosses.p1 Wolnob 2057118 RSCE Conifers.p1 Agarob 2076545 MIXZ Conifers.p1 Cliden 2009636 MIRS Mosses.p1 Agamac 2010938 ACWS Conifers.p1 PseeleLeujul 2047270 2165541 QKQO IGUH Mosses.p1 Mosses.p1 Mictet 2010210 MHGD Conifers.p1 Lepsp. 2077547 BBDD Conifers.p1 Aulhet 2009484 WNGH Mosses.p1 Phyhyp 2006411 JRNA Conifers.p1 Phifon 2007561 ORKS Mosses.p1 Phyhyp 2006412 JRNA Conifers.p1 Parust 2040083 JZVE Conifers.p1 Encstr 2004626 KEFD Mosses.p1 Lagfra 2012360 ZQWM Conifers.p1 Encstr 2004625 KEFD Mosses.p1 Mancol 2062834 CDFR Conifers.p1 Encstr 2004628 KEFD Mosses.p1 Neopan 2068056 JDQB Conifers.p1 Encstr 2004627 KEFD Mosses.p1 Calmac 2004618 RMMV Conifers March.p1 Chalaw 2011124 AIGO Conifers.p1 Physsp. 2081135 YEPO Mosses.p1 Plaori 2012136 BUWV Conifers.p1 Cerpur 2057275 FFPD Mosses.p1 Plaori 2012135 BUWV Conifers.p1 Ausspi 2002981 BTTS Conifers.p1 Synpri 2018117 PhypatGRKU Mosses.p1Pp3c14 3250V3.1 Cephar 2010540 WYAJ Conifers.p1 Leugla 2065209 RGKI Mosses.p1 Cephar 2019870 NVGZ Conifers 2 samples combined.p1 Leualb 2132039 VMXJ Mosses.p1 Cephar 2060889 GJTI Conifers.p1 Scoaqu 2089934 BPSG Mosses.p1 Cunlan 2101591 ZQVF Conifers 2 samples combined.p1 Timaus 2018575 ZQRI Mosses.p1 Cunlan 2016663 ESYX Conifers branch apex with needles.p1 Aulhet 2086412 WNGH Mosses.p1 Taicry 2004362 QSNJ Conifers.p1 Athcup 2064893 XIRK Conifers.p1 Physsp. 2019208 YEPO Mosses.p1 Metgly 2064050 NRXL Conifers.p1 Taxdis 2000028 FHST Conifers.p1 Encstr 2060932 KEFD Mosses.p1 Glypen 2047380 OXGJ Conifers.p1 Phypat Pp3c1 27830V3.1 Dipfol 2011702 AWOI Mosses.p1 Cryjap 2108251 HOUF Conifers leaf.p1 Atrang 2006061 ZTHV Mosses.p1 Cryjap 2019606 GMHZ Conifers 2 samples combined.p1 Atrang 2006062 ZTHV Mosses.p1 Cryjap 2014016 DSXO Conifers.p1 Atrang 2010947 ZTHV Mosses.p1 Thupli 2041766 VFYZ Conifers.p1 Andrup 2005352 WOGB Mosses.p1 Fokhod 2013443 UEVI Conifers.p1 Andrup 2005351 WOGB Mosses.p1 Tetsp. 2071611 CGDN Conifers.p1 Micdec 2057244 XQSG Conifers.p1 Plaori 2008660 BUWV Conifers.p1 Piluvi 2011011 ETCJ Conifers.p1 Sphfal Sphfalx0057s0124.1 Auschi 2011524 YYPE Conifers.p1 Taklep 2002675Sphfal SKQD Sphfalx0070s0077.1 Mosses.p1 Pappap 2008143 OVIJ Conifers.p1 Pornav 2007507Sphfal KRUQ Sphfalx0174s0012.1 Liverworts.p1 Calmac 2004108 RMMV Conifers March.p1 Pornav 2007506 KRUQ Liverworts.p1 Disarc 2009213 GKCZ Conifers.p1 Disarc 2009214 GKCZ Conifers.p1 Pornav 2112730Sphfal KRUQ Sphfalx0028s0103.1 Liverworts.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00131.15 Schisp. 2103585 LGOW Liverworts.p1 Aposhe lcl KZ451917.1 PKA62395.1 4834 Dencat lcl NW 021319484.1 XP 020697300.1 19272 OdoproPtipul 2009069 2136811 YBQN HPXA Liverworts.p1 Liverworts.p1 Dencat lcl NW 021319484.1 XP 020697299.1 19271 Odopro 2009070 YBQN Liverworts.p1 Phaequ PEQU 02543 Mixspe 2156914 NWQC Liverworts.p1 Phaequ PEQU 39145 Anacom Aco003413.1 Pallye 2003554 YFGP Liverworts.p1 Musacu GSMUA Achr6T06950 001 Pallye 2003551 YFGP Liverworts.p1 Orysat LOC Os11g14080.1 Pelnee 2010517 JHFI Liverworts.p1 Horvul HORVU4Hr1G015020.3 Pelnee 2010518 JHFI Liverworts.p1 Bradis Bradi4g21010.1 100 Setita Seita.8G078700.1 Marpal 2001945 IHWO Liverworts mycorrizal.p1 Pelepi 2005747 PIUF Liverworts.p1 Setita Seita.8G229400.1 Marpal Marpal2000368Marpal 2004005 LFVP 2001942 Liverworts HMHL IHWO PelepiLiverworts 2 samples Liverworts 2005745 non combined.p1 mycorrizal.p1 PIUF mycorrizal.p1 Liverworts.p1 99.9 100 Sorbic Sobic.005G085700.2 89.1 Zeamay Zm00008a015163 Helann HanXRQChr06g0184411 Marpal scaff3936 FGenesh1.1 96.8 Helann HanXRQChr14g0430021 84.2 Daucar DCAR 017668 Daucar DCAR 015007 Fraexc FRAEX38873 v2 000279550.1

Luncru 2011929 TXVB Liverworts.p1 100 Fraexc FRAEX38873 v2 000253760.1 Ricnat 2004483Marpol WJLO Mapoly0245s0003.1 Liverworts.p1 100 Fraexc FRAEX38873 v2 000394530.1 Fraexc FRAEX38873 v2 000057730.1 BlaspNW c332005 g2 i3 m.117060 Capann CA09g01890 BlaspNW c332005 g2 i7 m.117065 Solpen Sopen09g003180.1 99.7 97.8 BlaspNW c332005 g2 i5 m.117063 Sollyc Solyc09g008360.2.1 Nicben Niben101Scf00457g11001.1 Nicben Niben101Scf06999g00010.1 99.9 98.8 Petaxi Peaxi162Scf00722g00419.1 98 Petaxi Peaxi162Scf63023g00004.1 98.9 Poptri Potri.006G122500.2 84.4 80.1 Riccom 30078.m002265 89.3 98.1 Manesc Manes.09G064400.1 Cepfol Cfol v3 01694 Citcle Ciclev10011557m 100 92.5 99.6 Citsin orange1.1g010791m 100 Carpap evm.model.supercontig 92.103 93.7 100 95.9 98.4 100 98.4 100 97.5 Gosrai Gorai.006G161700.1 100 100 Thecac Thecc1EG022282t1 95.7 99 100 100 Thecac Thecc1EG022283t1 100 100 100 86.5 100 98.7 94.5 85.3 98.1 Gosrai Gorai.N011600.1 99.8 97.8 92.5 100 99.4 Gosrai Gorai.002G161600.1 99.7 100 94.4 99 Querob Qrob P0381380.2 92.9 97.7 95.4 100 99.4 Casmol maker-scaffold01073-snap-gene-0.35-mRNA-1 100 99.8 90 100 100 84.5 Alnglu Alngl5608S32382 98.5 95.9 99.1 Casgla Casgl43S17799 90.3 100

99.5 97.9 Jugreg g13775.t1

99.9 86.5 Zizjuj lcl NC 029690.1 XP 024922367.1 31022 98.8 100

99 Distri Distr625S26468 99.4 99.1 100 Mornot L484 022563 100 99.4 94.2 Humlup HL.SW.v1.0.G029495.1 91.3 84.5 Treori lcl JXTC01000007.1 POO01767.1 2545 97.3 93.1 100 94.6 98.9 Parand lcl JXTB01000268.1 PON49032.1 23300 100 100 80.7 100 100 81.1 Drydru Drydr270S09444 100 99.9 88.7 80.5 Rubocc Bras G13231 96.6 95.6 94.2 Roschi RchiOBHm Chr3g0470581 95.6 Fraves FvH4 6g16620.1 94.7 Potmic 17565 t Fraves FvH4 6g16610.1 99.9 100 Pruavi Pav sc0000683.1 g140.1.mk 100 88.7 Pruavi Pav sc0003839.1 g010.1.mk 100 Prumum lcl NC 024133.1 XP 008241451.1 25077 Plaori 2005293 BUWV Conifers.p1 100 Pruper Prupe.7G127200.1 Micdec 2057508 XQSG Conifers.p1 97.1 86.7 Prudul Prudul26A003739P1 Tetsp. 2070634 CGDN Conifers.p1 98.499.9 91.1 99.2 99.6 Pyrcom PCP023712.1 Caldec 2061790 FRPM Conifers.p1 99.9 Maldom MDP0000315326 Junsco 2013802 XMGP Conifers.p1 100 99.9 Maldom MDP0000800684 Cupdup 2012862 QNGJ Conifers.p1 Pyrcom PCP025504.1 99.1 Fokhod 2012034 UEVI Conifers.p1 99.4 100 91.9 Pyrbre lcl NW 008988337.1 XP 009377044.1 28397 Chalaw 2008464 AIGO Conifers.p1 100 Pyrcom PCP013952.1 100 100 85.6 98.596.3 Datglo Datgl208S24294 Thudol 2009676 NKIN Conifers.p1 97 99.6 99.694.2 100 100 100 100 Begfuc Begfu300S29669 CalgraThupli 2145497 2007001 IFLI Conifers VFYZ Conifers.p1 March.p1 95.6 100 Momcha lcl NW 019104520.1 XP 022144688.1 15627 91.9 97.2 100 100 98.7 85.1 100 91 Cucmax CmaCh14G002320.1 Calmac 2058295Neopan 2071707 RMMV Conifers JDQB Conifers.p1 March.p1 100 93.3 100 98 88.2 94 100 Cucmos CmoCh14G002220.1 100 83.7 99.9 99.9 Cucpep Cp4.1LG03g01450.1 Widced 2010112 AUDE Conifers.p1 97.496 99.2 81.2 96.3 98.9 98.3 99.8 97.699.9 99.780.7 90.4100 Citlan Cla017790 Widced 2010111 AUDE Conifers.p1 99.9 97.6 99.2 96.8 Lagsic Lsi03G019950.1 97.3 81.2 98.7 98.8 88.896.794.391.3 95.3 100 Disarc 2016844 GKCZ Conifers.p1 88 96.991 99.3 91.510099.3 100 Cucsat evm.model.Chr3.3296 Auschi 2069804 YYPE Conifers.p1 10099.8 80.489.5 Cucmel MELO3C009371.2.1 100 99.9 99.7 99.6 100 Cercan Cerca56S26847 Piluvi 2064104 ETCJ Conifers.p1 100 100 84.4 Cryjap 2016489 GMHZPappap Conifers 2011475 2 samples OVIJ combined.p1 Conifers.p1 97.7 97.9 92.9 100 Chafas Chafa95182S28729 Cryjap 2011863 DSXO Conifers.p1 98 95.4 100 100 Chafas Chafa1432S06779 99.8 Casaus Castanospermum02553-PA 100 87.8 Cryjap 2111369 HOUF Conifers leaf.p1 93.6 Casaus Castanospermum09604-PA 100 99.9 Nissch Nissc2738S20000 Glypen 2047500 OXGJ Conifers.p1 97.5 98.2 87.4 100 94.1 95.6 99.6 98.8 Aradur Aradu.NVN7I Taxdis 2065343 FHST Conifers.p1 100 99.5 Arahyp arahy.Tifrunner.gnm1.ann1.NKEM9Y.1 Athcup 2065104 XIRK Conifers.p1 100 99.9 99.3 Arahyp arahy.Tifrunner.gnm1.ann1.GZ339Q.1 Metgly 2065560 NRXL Conifers.p1 99.5 97.5 Arahyp arahy.Tifrunner.gnm1.ann1.B2B9U5.1 Seqsem 2003655 HBGV Conifers.p1 100 100 81.8 100 99.2 96.9 Cunlan 2018102 ZQVF Conifers 2 samples combined.p1 92.2 96.9 100 Araipa Araip.397T1 Cunlan 2053213 OUOI Conifers.p1 95.3 84.2 100 80.4 Arahyp arahy.Tifrunner.gnm1.ann1.72Y1KB.1 100 100 Tripra Tp57577 TGAC v2 mRNA35551 Cephar 2021124 NVGZ Conifers 2 samples combined.p1 91.6 100 Cicari Ca 11315.1 Taicry 2068463 QSNJ Conifers.p1 99.8 100 98.6 93.2 96.2 98.989.4 100 99.293.9100 Cicari Ca 11066.1 Cephar 2012064 GJTI Conifers.p1 100 Trisub lcl DF973977.1 GAU43512.1 32570 99.6 97.5 99.8 100 Cephar 2017370 WYAJ Conifers.p1 100 99.9 92.4100 82.7 100 Tripra Tp57577 TGAC v2 mRNA41197 100 Medtru MtrunA17 Chr1g0180411 Tornuc 2011640 HQOM Conifers.p1 98.3 100 99.6 HEP Tripra Tp57577 TGAC v2 mRNA21723 Amearg 2026046 IAJW Conifers.p1 98.8 99.8 87.799.5 100 80.7 99.3 Cajcaj Ccajan 35993 Psechi 2004747 YLPM Conifers.p1 92.7 100 100 Glymax Glyma.13G145500.1 Ausspi 2009639 BTTS Conifers.p1 100 Glymax Glyma.10G058700.1 Taxbac 2011577 WWSS Conifers.p1 97.8 98.6 98.8 Phavul Phvul.007G150900.1 Taxcus 2075487 ZYAX Conifers.p1 100 Vigung Vigun07g076400.1 Sciver 2011642 YFZK Conifers.p1 94.6 Vigrad Vradi08g17940.1 100 95.8 88.5 85.3 Faltax 2083296 PLYXFaltax Conifers 2062283 2 samples ROWR combined.p1 Conifers.p1 89.8 92 100 Vigang vigan.Vang06g19530.1 92.9 100 99.9 Nissch Nissc37923S22503 Faltax 2013565 QHBI Conifers A.p1 99.794.9100 100 Araipa Araip.RKI4J Daccom 2058349 FMWZ Conifers.p1 99.1 100 98.3 Arahyp arahy.Tifrunner.gnm1.ann1.N44J0V.1 81.4 Arahyp arahy.Tifrunner.gnm1.ann1.HETY6C.1 Podcor 2010461 SCEB Conifers.p1 95.2 93.9 92.5 100 Podrub 2009774 XLGK Conifers.p1 100100 100 Aradur Aradu.RA4QX Retmin 2072007 VGSX Conifers.p1 81.689.5 Arahyp arahy.Tifrunner.gnm1.ann1.10V25C.1 100 Aradur Aradu.99PSH Nagnag 2116124 UUJS Conifers.p1 86.284.7 94.399.5 Cajcaj Ccajan 09871 Acmpan 2015235 HILW Conifers.p1 97 90.3 Glymax Glyma.03G184900.1 Mictet 2072875 MHGD Conifers.p1 100 95.787.2 99.9 100 99.3 98.7 10096.7 81.210099.683.5 Glymax Glyma.19G185400.1 Phyhyp 2011575 JRNA Conifers.p1 97.7 97.6 Phavul Phvul.001G180300.1 Lepsp. 2010879 BBDD Conifers.p1 100 100 Vigung Vigun01g163200.1 96.2 99.7 100 95.1 Mancol 2003263 CDFR Conifers.p1 96.2 97.1 Vigang vigan.Vang0134s00130.1 Mancol 2003264 CDFR Conifers.p1 94.599.986.4 81.4 100 93.1 Vigrad Vradi03g03760.1 Lagfra 2090483 ZQWM Conifers.p1 97.991.8 Lotjap Lj1g3v4626570.1 Parust 2039215 JZVE Conifers.p1 100 100 Medtru MtrunA17 Chr7g0264851 Pruand 2005484 EGLZ Conifers.p1 85 93.3 90 Tripra Tp57577 TGAC v2 mRNA33943 100 98.2 100 Trisub lcl DF973211.1 GAU20333.1 9391 Halbid 2005394 OWFC Conifers.p1 10094.697.8 99.8 Agarob 2075738 MIXZ Conifers.p1 100 99.499.8 85.8 100 99.698.2 Medtru MtrunA17 Chr7g0264821 Agamac 2013215 ACWS Conifers.p1 86.8 Medtru MtrunA17 Chr7g0264831 93.9 Cicari Ca 07977.1 Agamac 2013214 ACWS Conifers.p1 88.398.9 99.8 86.2 91.8 99.999.9 Trisub lcl DF973211.1 GAU20332.1 9390 Wolnob 2001783 RSCE Conifers.p1 84.2 99.6 10095.283.7 91.8 Tripra Tp57577 TGAC v2 mRNA33921 Ararul 2064297 XTZO Conifers.p1 100 100 95.590.6 Phacar 2014546 WCZB Hornworts gametophyte.p1 Pinpin PPI00006521 100 100 Fonant 2010775 DHWX Mosses.p1 Pinpin PPI00068678 90.7100 99.1 100 Fonant 2010774 DHWX Mosses.p1 Pinsyl PSY00018266 87.793.5100 92.4 82.9 100 97.296.2 100 Hupluc 2006916 GKAG Lycophytes.p1 Pinrad 2009478 DZQM Conifers.p1 99.7 99.8 100 96.9 Hupmyr 2058224 CBAE Lycophytes.p1 Pinpon 2070924 JBND Conifers.p1 94.884 96.697.3 99.7 100 91.4 93.3 Psecar 2008853 UPMJ Lycophytes.p1 Pinpar 2079191 IIOL Conifers.p1 94.7 100 100 97.5 99.9 99.6100 Psecar 2008852 UPMJ Lycophytes.p1 Psemen PME00001937 100 100 100 Lycdeu 2004899 PQTO Lycophytes.p1 Tsuhet 2054688 GAMH Conifers.p1 84.9 98.7 Denobs 2011009 XNXF Lycophytes.p1 Notlon 2067672 AREG Conifers.p1 96.5 Isoteg 2098574 PKOX Lycophytes.p1 94.9 100 Trelac 2012182 FITN Liverworts.p1 Abilas 2056252 VSRH Conifers.p1 89.490.2 88.186.9 95.3 Isoesp. 2009893 PYHZ Lycophytes.p1 Pseama 2082467 AQFM Conifers.p1 100 97.7 100 Picsit PSI00004304 Isoesp. 2009894 PYHZ Lycophytes.p1 92.9 98.499.6 99.3 99.8 Trelac 2012181 FITN Liverworts.p1 Gnemon TnS000703067t01 99.6 98.7 100 100 Selaca 2009569 ZYCD Lycophytes.p1 Gnemon 2014361 GTHK Gnetales.p1 81 91.1 100 100 92.6 84.799.998.2 100 88.6 Selkra 2039312 ZFGK Lycophytes.p1 Welmir 2012620 TOXE Gnetales.p1 99.188.9 100 99.5 100 Selsel 2010180 KUXM Lycophytes.p1 Ephsin 2002959 VDAOGinbil Gnetales.p1 Gb 10589 100 99.6 Selmoe 78688 93 83.288.1 Selapo 2001247 LGDQ Lycophytes.p2 Cycmic CMI00009517 80.498 99.5 90.7 100 Selapo 2001246 LGDQ Lycophytes.p2 Cycmic 2013207 XZUY Cycadales.p1 10010085.7 87.2100 100 83.7 83.7 Psinud 2015292 QVMR Eusporangiate Monilophytes.p1 Faltax 2061147 ROWR Conifers.p1 98.690.293.8 100 100 85 100 Osmjav 2011642 VIBO Leptosporangiate Monilophytes.p1 94.295.598.8 90.1 Osmsp. 2075851 UOMY Leptosporangiate Monilophytes gametophyte.p1 91.7 10099.3100 96.4 100 Faltax 2083513 PLYXFaltax Conifers 2058848 2 samples QHBI Coniferscombined.p1 A.p1 99.9 Dipcon 2108189 MEKP Leptosporangiate Monilophytes.p1 100 89.8 89.4 97 Hymbiv 2058398 QIAD Leptosporangiate Monilophytes.p1 Dacbal 2012910 IZGN Conifers.p1 94 98.1 10097.993.3 99.6 Plajap 2136781 UWOD Leptosporangiate Monilophytes.p1 Daccom 2056678 FMWZ Conifers.p1 89.210099.990.699.8 100 100 Thyele 2123217 EWXK Leptosporangiate Monilophytes.p1 Nagnag 2009671 UUJS Conifers.p1 Salcuc Sacu v1.1 s0066.g016078 Retmin 2072237 VGSX Conifers.p1 100 Cryacr 2007285 WQML Leptosporangiate Monilophytes.p1 Podrub 2002871 XLGK Conifers.p1 99.8 Gagari 2015479 DCDT Leptosporangiate Monilophytes.p1 Acmpan 2010005 HILW Conifers.p1 99.1 Vitapp 2103227 NDUV Leptosporangiate Monilophytes.p1 Mictet 2073870 MHGD Conifers.p1 100 10084.599.8 Leuimm 2071827 WGTU Leptosporangiate Monilophytes.p1 Lagfra 2089787 ZQWM Conifers.p1 99.8 93 99.8 Davfej 2034338 OQWW Leptosporangiate Monilophytes.p1 Lepsp. 2012533 BBDD Conifers.p1 91.1 Polamo 2069720 YLJA Leptosporangiate Monilophytes.p1 Halbid 2008681 OWFC Conifers.p1 100 80.4100 Polgly 2005383 CJNT Leptosporangiate Monilophytes.p1 Parust 2039902 JZVE Conifers.p1 100 96.3 99.1 97.4 Polhes 2026873 GYFU Leptosporangiate Monilophytes A type.p1 89.7 Polhes 2032718 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Sunama 2014328 KLGF Conifers.p1 93.7100 Pruand 2039023 EGLZ Conifers.p1 100 Asppla 2013846 KJZG Leptosporangiate Monilophytes.p1 99.8 Onosen 2002645 HTFH Leptosporangiate Monilophytes.p1 Wolnob 2058333 RSCE Conifers.p1 Hompyc 2012011 OCZL Leptosporangiate Monilophytes.p1 Psechi 2080182 YLPM Conifers.p1 91.383.8 Dipwic 2088733 UFJN Leptosporangiate Monilophytes.p1 Taxcus 2074079 ZYAX Conifers.p1 89 100 89.2 Cysfra 2025056 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Amearg 2151039 IAJW Conifers.p1 98.3 100 Cysfra 2008773 XXHP Leptosporangiate Monilophytes Stewart.p1 Tortax 2013460Pinpin EFMS PPI00018035 Conifers.p1 92.9 Cyspro 2065374 YOWV Leptosporangiate Monilophytes.p1 Pinpin PPI00073281 85.4 95.9 Scedis 2088611 EEAQ Eusporangiate Monilophytes.p1 Pinpin PPI00069125 100 96.9 Equhye 2010409 JVSZ Eusporangiate Monilophytes.p1 Pinsyl PSY00011697 98.8 96.6 97.5 98.398.3 100 99 84.8 99.7 98.2 Equhye 2006142 JVSZ Eusporangiate Monilophytes.p1 Pinsyl PSY00011696 99.2 95.4 100 99.5 Equdif 2004774 CAPN Eusporangiate Monilophytes.p1 98.197.8 100 99.8 99.5 9597.9 Equhye 2129976 JVSZ Eusporangiate Monilophytes.p1 Pinpar 2013441 IIOL Conifers.p1 94.7 100 80.4 100 Equdif 2000339 CAPN Eusporangiate Monilophytes.p1 99.6 100 98.6 100 99.2 98.6 Osmjav 2012200 VIBO Leptosporangiate Monilophytes.p1 Piceng 2051856Psemen AWQB PME00089316 Conifers.p1 100 96.8100 91.8 98.9 81.3 100 Osmsp. 2007592 UOMY Leptosporangiate Monilophytes gametophyte.p1 100 99.5 Dipcon 2013337 MEKP Leptosporangiate Monilophytes.p1 Psewil 2014572Psemen IOVS PME00089317 Conifers.p1 90.6 97.1 85.899.482.3 Picsit PSI00017359 100 94.7 95.5 Hymbiv 2058490 QIAD Leptosporangiate Monilophytes.p1 99.8 98.592.9 Thyele 2122444 EWXK Leptosporangiate Monilophytes.p1 100 98.1 99.1 100 10091 Culmac 2016108 PNZO Leptosporangiate Monilophytes.p1 Abilas 2057249Gnemon VSRH TnS000984377t02 Conifers.p1 99.3 10089.5 99.6 Salcuc Sacu v1.1 s0128.g021899

97.1 Pilglo 2007062 KIIX Leptosporangiate Monilophytes.p1 Cycmic CMI00012075 97 96.9 99.5 90.3 85 Welmir 2061125 TOXEGinbil Gnetales.p1 Gb 12199 100 98.7 97.7 Pilglo 2007061 KIIX Leptosporangiate Monilophytes.p1

82.6 96.6 100 Pittri 2013889 UJTT Leptosporangiate Monilophytes.p1 83.4 99.7 100 99.2

99.3 98.8 98.2 81.6 Ptevit 2019369 POPJ Leptosporangiate Monilophytes.p1 86.7 97.297.7 Widced 2009729 AUDE Conifers.p1 10096.8 100 Cryacr 2013529 WQML Leptosporangiate Monilophytes.p1 100 97.9 100 91.8 81.3 99.9 Disarc 2074817 GKCZ Conifers.p1 82.198.5 100100 99.8 100 Vitapp 2010590 NDUV Leptosporangiate Monilophytes.p1 97.6 95.9 85.6 100 Parcor 2011700 ZXJO Leptosporangiate Monilophytes.p1 100 100 82.4 91.1 97.1 99.9 96.7 99.9 100 95.3 Gagari 2073874 DCDT Leptosporangiate Monilophytes.p1 Calmac 2052502 RMMV Conifers March.p1 100 Neopan 2010736 JDQB Conifers.p1 96 88.3 Dendav 2008926 MTGC Leptosporangiate Monilophytes.p1

100 97.6 Auschi 2068255 YYPE Conifers.p1 99.9 93.4 89.5 100 100 Theacu 2047201 MROH Leptosporangiate Monilophytes.p1 Piluvi 2062215 ETCJ Conifers.p1 100 100 95.8 100 100 Cysfra 2070925 LHLE Leptosporangiate Monilophytes.p1 100 100 100 Plaori 2000838 BUWV Conifers.p1 94 98.5 89.2 98.7 97.6 Cysfra 2026211 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 87.7 97.6 100 99.9 Tetsp. 2069957 CGDN Conifers.p1 86.5 99.9 99.8 99.2 87.7 94.1 Dipwic 2002776 UFJN Leptosporangiate Monilophytes.p1 Chalaw 2002553 AIGO Conifers.p1 81.2 91.5 83.2 Asppla 2009897 KJZG Leptosporangiate Monilophytes.p1 100 98.5 81 96.2 88.8 96.3 100 100 100 96.7 97.3 Athfil 2065277 URCP Leptosporangiate Monilophytes.p1 84.9 99.7 98.2 95.5 99.8 99.3 93.6 100 Blespi 2005490 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 97.9 90.2 99.2 99.2 100 100 100 Cryjap 2110671 HOUF Conifers leaf.p1 89.7 100 Cryjap 2072895 DSXO Conifers.p1 99.397.4 Blespi 2005489 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 100 100 10099.3 96.3 100 84.3 Leuimm 2004431 WGTU Leptosporangiate Monilophytes.p1 Cryjap 2145362 GMHZ ConifersTaxdis 20148582 samples FHST combined.p1 Conifers.p1 100 100 97.6 98.9 84.5 99.8 99.9 100 Polacr 2073405 FQGQ Leptosporangiate Monilophytes.p1 Glypen 2046222 OXGJ Conifers.p1 95.7 96.3 93.683.5 Nepexa 2026369 NWWI Leptosporangiate Monilophytes.p1 100 99.4 Metgly 2061371 NRXL Conifers.p1 98.5 100 96.4 100 99.7 97.1 93.798.8 Nepexa 2026370 NWWI Leptosporangiate Monilophytes.p1 Athcup 2062702 XIRK Conifers.p1 98.1 97 99.9 98.2 100 94.2 Davfej 2038652 OQWW Leptosporangiate Monilophytes.p1 Taicry 2064708 QSNJ Conifers.p1 93.9 98.6 92.3 98.5 100 89.2 100 98.9 100 99.9 Phygro 2094155 ORJE Leptosporangiate Monilophytes.p1 Ausspi 2013107 BTTS Conifers.p1 96.8 100 99.7 Phlpse 2028894 ZQYU Leptosporangiate Monilophytes.p1 100 84.1 86.7 100 96.7 Psechi 2012583 YLPM Conifers.p1 100 100 100 Polgly 2079433 CJNT Leptosporangiate Monilophytes.p1 100 99.9 93.2 100 Tortax 2015453 EFMS Conifers.p1 98.8 98.7 Polhes 2016474 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 100 99.9 98.4 100 100 Amearg 2150666 IAJW Conifers.p1 100 99.4 100 Polhes 2016475 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1

99.9 100 100 87.9 Cephar 2059882 GJTI Conifers.p1 99.9 Polhes 2012011 GYFU Leptosporangiate Monilophytes A type.p1 100 100 85.8 84.4 89.3 Polhes 2012010 GYFU Leptosporangiate Monilophytes A type.p1 99.7 84.8 100 99.9 99.7 Pilglo 2007687 KIIX Leptosporangiate Monilophytes.p1 Cephar 2090060 WYAJ Conifers.p1 90.3 99.7 100 94.3 99.9 Azocar 2033128 CVEG Leptosporangiate Monilophytes.p1 Agarob 2012867 MIXZ Conifers.p1 100 87.6 92.9 89 Azofil Azfi s0002.g001448 95.7 99.4 99.4 100 Cephar 2017161 NVGZAgamac Conifers 2068927 2 samples ACWSPintae combined.p1 Conifers.p1 PTA00083392 95.9 96.3 Pilglo 2010054 KIIX Leptosporangiate Monilophytes.p1 Wolnob 2057199 RSCE Conifers.p1 86.1 Thyele 2017096 EWXK Leptosporangiate Monilophytes.p1 Sciver 2041454 YFZK Conifers.p1 97.9 Culmac 2016657 PNZO Leptosporangiate Monilophytes.p1 99.7 99.6 100 Plajap 2139207 UWOD Leptosporangiate Monilophytes.p1 Pinjef 2017657 MFTM Conifers.p1 100 87.6

92 100 Linlin 2095264 NOKI Leptosporangiate Monilophytes.p1 Pinsyl PSY00005854 100 92.3

Pinrad 2006499 DZQM Conifers.p1 98 Cryacr 2009445 WQML Leptosporangiate Monilophytes.p1 Pinpon 2071056 JBNDPinpin Conifers.p1 PPI00035899 100 99.9 Ptevit 2008609 POPJ Leptosporangiate Monilophytes.p1 99.8 99.8 Vitapp 2017080 NDUV Leptosporangiate Monilophytes.p1 Picsit PSI00007477 100 94.783.7 Pinpar 2013440 IIOL Conifers.p1 97.9 Vitlin 2000166 SKYV Leptosporangiate Monilophytes.p1 Parcor 2013845 ZXJO Leptosporangiate Monilophytes.p1 Psemen PME00004434 96.8 Gagari 2016562 DCDT Leptosporangiate Monilophytes.p1 96.3 Notmon 2007575 YCKE Leptosporangiate Monilophytes.p1 Piceng 2055035 AWQB Conifers.p1 Argniv 2017594 XDDT Leptosporangiate Monilophytes.p1 Myrruf 2001733 GSXD Leptosporangiate Monilophytes.p1 Psewil 2014573 IOVS Conifers.p1 Myrruf 2001732 GSXD Leptosporangiate Monilophytes.p1 Notlon 2066975 AREG Conifers.p1 100 100 Leuimm 2012453 WGTU Leptosporangiate Monilophytes.p1 Polacr 2074486 FQGQ Leptosporangiate Monilophytes.p1 Tsuhet 2002520Gnemon GAMH TnS000390199t05 Conifers.p1 Abilas 2057120 VSRH Conifers.p1 Davfej 2226747 OQWW Leptosporangiate Monilophytes.p1 Cycmic CMI00015031 Phygro 2002223 ORJE Leptosporangiate Monilophytes.p1 Cycmic CMI00015030 Phlpse 2006641 ZQYU Leptosporangiate Monilophytes.p1 Encbar 2007284 GNQG Cycadales.p1 Phlpse 2006640 ZQYU Leptosporangiate Monilophytes.p1 Staeri 2004559 KAWQ Cycadales.p1 Phlpse 2006639 ZQYU Leptosporangiate Monilophytes.p1 Plepol 2013391 UJWU Leptosporangiate Monilophytes dehydrating fronds.p1 Polamo 2073401 YLJA Leptosporangiate Monilophytes.p1 Polhes 2017901 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Cycmic 2009720 XZUY Cycadales.p1 Pyrcom PCP019864.1 Polgly 2008710 CJNT Leptosporangiate Monilophytes.p1 Pyrcom PCP041661.1 Polhes 2007708 IXLH Leptosporangiate Monilophytes B type.p1 Asppla 2013774 KJZG Leptosporangiate Monilophytes.p1 Hompyc 2009931 OCZL Leptosporangiate Monilophytes.p1 Pyrbre lcl NW 008989351.1 XP 018501622.1 45950 Dipwic 2001582 UFJN Leptosporangiate Monilophytes.p1 Onosen 2041863 HTFH Leptosporangiate Monilophytes.p1 Pyrbre lcl NW 008989351.1 XP 018501621.1 45949 Athfil 2012271 URCP Leptosporangiate Monilophytes.p1 Pyrbre lcl NW 008989351.1 XP 009350186.1 45948 Maldom MDP0000161050 Wooilv 2077227 YQEC Leptosporangiate Monilophytes.p1 Woosco 2007322 YJJY Leptosporangiate Monilophytes.p1 Pruper Prupe.8G269300.1 Gymdry 2015150 HEGQ Leptosporangiate Monilophytes.p1 Pyrbre lcl NW 008988372.1 XP 018507873.1Prudul Prudul26A021955P1 29925 Cysfra 2090104 XXHP Leptosporangiate Monilophytes Stewart.p1 Pyrbre lcl NW 008988372.1 XP 009378683.1 29922 Cyspro 2069441 YOWV Leptosporangiate Monilophytes.p1 Cysfra 2007841 LHLE Leptosporangiate Monilophytes.p1 Pyrbre lcl NW 008988372.1 XP 018507872.1 29923 Cysuta 2005319 HNDZ Leptosporangiate Monilophytes.p1 Pruavi Pav sc0000130.1 g390.1.mk Pyrbre lcl NW 008988372.1 XP 009378684.1 29924 Cysuta 2005317 HNDZ Leptosporangiate Monilophytes.p1 Fraves FvH4 5g39640.1 Cysuta 2005318 HNDZ Leptosporangiate Monilophytes.p1 Pintae PTA00039981 Fraana FAN iscf00149255.1.g00002.1Rubocc Bras G21811 Agamac 2007991 ACWS Conifers.p1 Fraana FAN iscf00065606.1.g00001.1 Drydru Drydr33S20582 Selmoe 404643 Prumum lcl NC 024131.1Fraana FAN XP 008235176.1iscf00034050.1.g00001.1 19262 Selmoe 419933 Roschi RchiOBHm Chr7g0241951 Ambtri evm 27.model.AmTr v1.0 scaffold00100.65 Musacu GSMUA Achr1T07490 001 Mornot L484 007459 Anacom Aco019541.1 Aposhe lcl KZ454427.1 PKA46162.1 21172 Dencat lcl NW 021319357.1 XP 028553021.1 17007 Humlup HL.SW.v1.0.G028068.1 Dencat lcl NW 021319357.1 XP 028553019.1 17005 Distri Distr133S13760 Dencat lcl NW 021319357.1 XP 028553020.1 17006 Zosmar Zosma21g01110.1 Alnglu Alngl6053S33254Jugreg g30412.t1 Parand lcl JXTB01000119.1 PON61667.1Casgla 14328 Casgl99S23720 Spipol Spipo1G0068600 Treori lcl JXTC01000272.1 PON72431.1 25233 Ambtri evm 27.model.AmTr v1.0 scaffold00100.29 Nelnuc NNU 23871-RA Helann HanXRQChr15g0478001 Utrgib Utricularia gibba unitig 21 2219352 2221968 unitig 21.g20836.t1 1 CDS 875806337 25895 Zizjuj lcl NC 029687.1 XP 015891884.1Querob 23992 Qrob P0264450.2 Zizjuj lcl NC 029687.1 XP 015891883.1 23993 Fraexc FRAEX38873 v2 000076890.2 Vigrad Vradi08g10570.1 Fraexc FRAEX38873 v2 000076890.1 Petaxi Peaxi162Scf00362g00555.1 Vigang vigan.Vang06g16340.1 Vigung Vigun07g123000.1 Petaxi Peaxi162Scf00362g00554.1 Nicben Niben101Scf06809g00033.1 Phavul Phvul.007G216500.1Cajcaj Ccajan 06699 Nicben Niben101Scf01718g01021.1 Glymax Glyma.02G014700.1 Solpen Sopen10g025360.1 Solpen Sopen10g025410.1 Glymax Glyma.10G015300.1 Cicari Ca 08048.1 Sollyc Solyc10g055620.1.1 Petaxi Peaxi162Scf00042g02413.1 Cicari Ca 10028.1 Casmol maker-scaffold05628-snap-gene-0.17-mRNA-1 Nicben Niben101Scf03459g01001.1 Nicben Niben101Scf02658g00007.1 Cepfol Cfol v3 12507 Poptri Potri.004G176400.1 Medtru MtrunA17Nissch Chr1g0195051 Nissc237S18486 LotjapLupang Lj5g3v1601890.1 Lup002653.1 Poptri Potri.009G136700.1 Tripra Tp57577 TGAC v2 mRNA20452 Riccom 29943.m000277 Trisub lcl DF973463.1 GAU31653.1 20711 Araipa Araip.9F87C Manesc Manes.11G096500.1 Manesc Manes.11G096500.2 Aradur Aradu.7VL9B Cercan Cerca147S14666 Chafas Chafa760S26725 Mimpud Mimpu3929S23605 Nissch Nissc237S01436 Casaus Castanospermum01026-PA Lupang Lup033050.1 Nissch Nissc2598S19501 Arahyp arahy.Tifrunner.gnm1.ann1.QJ9WGP.1 Cercan Cerca12S13739 Aradur Aradu.KCH1Z Mimpud Mimpu2336S20313 Datglo Datgl1099S18315 Arahyp arahy.Tifrunner.gnm1.ann1.P5I184.1 Arahyp arahy.Tifrunner.gnm1.ann1.E7P91P.1 Araipa Araip.S32V5 Lotjap Lj1g3v3330540.2 Casaus Castanospermum17649-PARiccom 30076.m004695Cepfol Cfol v3 00556 Arahyp arahy.Tifrunner.gnm1.ann1.PJ3DXF.1 Lotjap Lj1g3v3330540.1 Manesc Manes.05G001400.1 Cicari Ca 14411.1 Poptri Potri.014G123800.1 Medtru MtrunA17 Chr3g0145661 Tripra Tp57577 TGAC v2 mRNA39805 Trisub lcl DF973533.1 GAU33645.1 22703 Cajcaj Ccajan 23765 Gosrai Gorai.008G141800.1 Glymax Glyma.06G003300.1 ThecacSpiole Thecc1EG004761t1 Sp 074470 emdn.t2 Glymax Glyma.14G163500.1 Phavul Phvul.009G119000.1 Spiole Sp 074470 emdn.t1 Vigung Vigun09g276000.1 Spiole Sp 074470 emdn.t3Diacar Dca60169.1 Vigang vigan.Vang05g00320.1 Carpap evm.model.supercontig Chequi151.56 AUR62025490-RA Vigrad Vradi05g15630.1 Chequi AUR62008748-RA Datglo Datgl169S22501 Betvul Bv7 165220 nxta.t1 Begfuc Begfu255S10094 Begfuc Begfu1981S23681 Capann CA06g27370 Momcha lcl NW 019104527.1 XP 022146281.1 16856 Solpen Sopen06g035960.1 Cucmos CmoCh02G002600.1 Sollyc Solyc06g084590.2.1 Cucmax CmaCh02G002630.1 Cucpep Cp4.1LG05g13700.1 Citlan Cla020273 Lagsic Lsi10G005000.1 Cucmel MELO3C020823.2.1 Cucsat evm.model.Chr2.1363.1 Daucar DCAR 018307 Cucsat evm.model.Chr2.1363 Diacar Dca6151.1 Diacar Dca573.1 Nicben Niben101Scf03523g00008.1 Diacar Dca47121.1 Nicben Niben101Scf09444g00007.1 Betvul Bv9 213940 wcye.t1 Petaxi Peaxi162Scf00140g01352.1 Spiole Sp 148430 tqjw.t1 Setita Seita.7G268100.1 Chequi AUR62013025-RA SorbicZeamay Sobic.009G050900.1 Zm00008a030995 Bradis Bradi2g35040.1 Chequi AUR62010037-RA Fraexc FRAEX38873 v2 000266440.1 Casmol maker-scaffold11621-augustus-gene-0.4-mRNA-1 Helann HanXRQChr15g0464221 Anacom Aco007385.1 Casmol maker-scaffold11621-augustus-gene-0.4-mRNA-2 Fraexc FRAEX38873 v2 000266440.2 Jugreg g43717.t1 Phaequ PEQU 30599 Jugreg g28992.t1 Orysat LOC Os05g06360.1 Casgla Casgl308S14914 Horvul HORVU1Hr1G022790.1 Alnglu Alngl7815S05996 Phaequ PEQU 37074 Alnglu Alngl249923S21723 Zizjuj lcl NC 029687.1 XP 015893157.1 25347 Distri Distr1970S17553 Mornot L484 008373 Humlup HL.SW.v1.0.G045787.1 Spipol Spipo3G0027600 Parand lcl JXTB01000811.1 PON32495.1 36081 Treori lcl JXTC01000088.1 PON89966.1 14254 Musacu GSMUA Achr2T02140 001 Vigrad Vradi04g11350.1 Drydru Drydr380S11436 Rubocc Bras G08771 Roschi RchiOBHm Chr6g0251551 Potmic 19854 t Fraves FvH4 2g01080.1 Vigung Vigun05g004600.1Cajcaj Ccajan 19150 Fraana FAN iscf00047908.1.g00001.1 Prumum lcl NC 024131.1 XP 008236122.2 20076 Cicari Ca 05915.1 Pruavi Pav sc0000373.1 g570.1.mk Vigang vigan.Vang04g00920.1 Prudul Prudul26A016171P1 Phavul Phvul.008G004100.1 Pruper Prupe.8G166300.1 Pyrbre lcl NW 008988081.1 XP 018502852.1 8813 Glymax Glyma.18G298500.1 Pyrcom PCP000332.1 Glymax Glyma.08G363600.1 Araipa Araip.V5Y6Q Maldom MDP0000120877 Maldom MDP0000322106 Maldom MDP0000196055 Lotjap Lj1g3v3328950.1 Maldom MDP0000275429 Aposhe lcl KZ452102.1 PKA48923.1 18451 Maldom MDP0000260780 Aradur Aradu.KNH52 Ambtri evm 27.model.AmTr v1.0 scaffold00016.331 Zosmar Zosma188g00240.1 Spipol Spipo9G0065300 Aposhe lcl KZ453122.1 PKA47568.1 19729 Lupang Lup010243.1 Phaequ PEQU 07805 Lupang Lup027647.2 Dencat lcl NW 021319083.1 XP 020678018.1 11214 Dencat lcl NW 021319095.1 XP 020698060.1 11573 Dencat lcl NW 021319083.1 XP 028551133.1 11215 Medtru MtrunA17 Chr7g0214801 Lupang Lup017506.1 Musacu GSMUA Achr6T08330 001 Nissch Nissc1774S16481 Lupang Lup008858.1 Musacu GSMUA Achr5T21610 001 Musacu GSMUA Achr3T18570 001 Araipa Araip.QM1VJ Musacu GSMUA Achr10T12420 001 Ambtri evm 27.model.AmTr v1.0 scaffold00057.65 Musacu GSMUA Achr6T16220 001 Anacom Aco016161.1 Tripra Tp57577 TGAC v2 mRNA10023 Sorbic Sobic.005G142700.1 Setita Seita.8G143900.1 Trisub lcl DF973160.1 GAU16521.1 5579 Orysat LOC Os11g34110.1 Aradur Aradu.Y8ZQW Horvul HORVU3Hr1G004990.1 Horvul HORVU3Hr1G004960.1 Orysat LOC Os02g32504.1 Bradis Bradi3g44630.1 Setita Seita.1G177600.1 Sorbic Sobic.004G162200.1 Lupang Lup024756.1 Jugreg g43827.t1 Zeamay Zm00008a021901 Zeamay Zm00008a030005 Jugreg g36694.t1 Orysat LOC Os04g33200.1 Nissch Nissc426S23456 Bradis Bradi5g08907.1 Horvul HORVU2Hr1G071980.2 Horvul HORVU3Hr1G096530.1 Horvul HORVU3Hr1G096540.3 Setita Seita.7G085600.1 Sorbic Sobic.006G064800.1 Zeamay Zm00008a007505 Zeamay Zm00008a037839 Zeamay Zm00008a014655 Nelnuc NNU 22376-RA Utrgib Utricularia gibba unitig 749 597442 600064 unitig 749.g13335.t1 -1 CDS 875844339 4048 Fraexc FRAEX38873 v2 000074970.1 Fraexc FRAEX38873 v2 000175020.2 Cercan Cerca29S20651 Fraexc FRAEX38873 v2 000175020.1 Petaxi Peaxi162Scf01167g00122.1 Capann CA00g41460 Nicben Niben101Scf01727g01002.1 Solpen Sopen11g017360.1 Sollyc Solyc11g040150.1.1 Nicben Niben101Scf10785g00002.1 Nicben Niben101Scf01818g09018.1 Chafas Chafa2665S19885 Carpap evm.model.supercontig 38.18 Tarhas lcl NW 010969548.1 XP 010523186.2 37054 Tarhas lcl NW 010969548.1 XP 010523191.1 37072 EutsalThhalv10004241m Braolecap Bol043071 Brarap Brara.F03044.1 Casaus Castanospermum25918-PA Boestr Bostr.11711s0002.1 Capgra Cagra.11292s0001.1 Caprub Carub.0014s0004.1 Casgla Casgl46S02060 AT5G47900.1 Aratha Arahyp arahy.Tifrunner.gnm1.ann1.K44MMV.1 Arahyp arahy.Tifrunner.gnm1.ann1.HE2B7Z.1 Mimpud Mimpu11002S13696

Potmic 4383 t Alnglu Alngl14973S16820 Pyrcom PCP011480.1 Querob Qrob P0135150.2 Pyrcom PCP010567.1 Casaus Castanospermum28189-PA Maldom MDP0000128493 Maldom MDP0000278959

Maldom MDP0000238639 Arahyp arahy.Tifrunner.gnm1.ann1.V5MFL1.1 Rubocc Bras G21659 Fraves FvH4 4g22060.1 Pruper Prupe.1G210600.1 Rubocc Bras G08895 Arahyp arahy.Tifrunner.gnm1.ann1.L4XK4S.1

Drydru Drydr72S24153 Prudul Prudul26A028189P1 Citlan Cla017192 Mornot L484 021490

Drydru Drydr107S15109 Drydru Drydr416S04099

Distri Distr475S24844

Lagsic Lsi03G012780.1

Aralyr Aralyr AL8G19890.t2

Cepfol Cfol v3 20890

Begfuc Begfu2S29566

Roschi RchiOBHm Chr4g0428311 Datglo Datgl120S19299

Begfuc Begfu646S39465 Riccom 30128.m008595 Fraana FAN iscf00281500.1.g00001.1 Citcle Ciclev10028441m Cucmel MELO3C026757.2.1 Fraana FAN iscf00041858.1.g00001.1 Humlup HL.SW.v1.0.G033190.1 Cucsat evm.model.Chr3.4025 Begfuc Begfu2878S29172

Poptri Potri.003G159200.2 Cucpep Cp4.1LG03g09330.1 Poptri Potri.001G071500.1

Cucsat evm.model.Chr3.4025.1 Citsin orange1.1g013227m Cucmos CmoCh14G010880.1 Cucpep Cp4.1LG08g06550.1 Cucmax CmaCh14G010700.1 Thecac Thecc1EG001644t1 Cucmos CmoCh06G017350.1 Arahal Araha.28394s0007.1 Cucmax CmaCh06G017480.1 Gosrai Gorai.012G048100.1

Manesc Manes.08G098800.1

Pyrbre lcl NW 008988066.1 XP 009353479.1 6798 Prumum lcl NC 024127.1 XP 016647997.1 7124 Prumum lcl NC 024127.1 XP 008222296.1 7125 Pyrbre lcl NW 008988111.1 XP 009359837.1 12685

Casmol maker-scaffold01007-augustus-gene-0.35-mRNA-1

Treori lcl JXTC01000071.1 PON91747.1 12347

Treori lcl JXTC01000178.1 PON83451.1 20727 Zizjuj lcl NC 029690.1 XP 024922360.1 30833 Parand lcl JXTB01000655.1 PON34515.1 34379 Zizjuj lcl NC 029686.1 XP 015889939.1 22012

Momcha lcl NW 019104577.1 XP 022152408.1 22433

Tree scale: 0.1 Supplementary Figure 32: Maximum likelihood tree of TAU.

Cysfra 2009343 XWDM Leptosporangiate Monilophytes 2 samples combined.p1

Polhes 2012928 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Polhes 2012929 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1

Cysfra 2011130 XXHP Leptosporangiate Monilophytes Stewart.p1

Plepol 2011651 UJWU Leptosporangiate Monilophytes dehydrating fronds.p1

Cyspro 2067356 YOWV Leptosporangiate Monilophytes.p1

Cysfra 2006175 LHLE Leptosporangiate Monilophytes.p1 Gymdry 2000576 HEGQ Leptosporangiate Monilophytes.p1 Cysree 2001675 RICCCysfra Leptosporangiate 2006176 LHLE Leptosporangiate Monilophytes.p1 Monilophytes.p1 Gymdry 2000575 HEGQ Leptosporangiate Monilophytes.p1 Gymdry 2000577 HEGQ Leptosporangiate Monilophytes.p1Cysuta 2004390 HNDZ Leptosporangiate Monilophytes.p1 Theacu 2047667 MROH Leptosporangiate Monilophytes.p1

Woosco 2076406 YJJY Leptosporangiate Monilophytes.p1 Polhes 2001795 GYFU Leptosporangiate Monilophytes A type.p1 Onosen 2040502 HTFH Leptosporangiate Monilophytes.p1 Dipwic 2086492 UFJN Leptosporangiate Monilophytes.p1 Athfil 2003179 URCP Leptosporangiate Monilophytes.p1 Leuimm 2072123Hompyc WGTU 2057322 Leptosporangiate OCZL Leptosporangiate Monilophytes.p1Aspnid 2011765Monilophytes.p1 PSKY Leptosporangiate Monilophytes.p1 Asppla 2010264 KJZG Leptosporangiate Monilophytes.p1

Polacr 2071839 FQGQ LeptosporangiateBlespi 2096941 Monilophytes.p1 VITX Leptosporangiate Monilophytes.p1

Didtru 2034527 RFRB Leptosporangiate Monilophytes.p1

Polamo 2005242 YLJA Leptosporangiate Monilophytes.p1 Phygro 2010218 ORJEPolgly Leptosporangiate 2077961 CJNT LeptosporangiateMonilophytes.p1 Monilophytes.p1 Davfej 2009402 OQWW Leptosporangiate Monilophytes.p1 Nepexa 2017481 NWWI Leptosporangiate Monilophytes.p1

Encbar 2085743 GNQG Cycadales.p1

Pseama 2079046AQFM Conifers.p1 Notmon 2063058 YCKEParcor Leptosporangiate 2010094 ZXJO Leptosporangiate Monilophytes.p1 Monilophytes.p1 Larspe 2051268 WVWN Conifers.p1 Cycmic 2004357 XZUY Cycadales.p1 Dioedu 2118780 WLIC Cycadales.p1 Gagari 2073034 DCDT Leptosporangiate Monilophytes.p1 Staeri 2054532 KAWQ Cycadales.p1 Piceng 2054483AWQB Conifers.p1 Ginbil 2006152 SGTW Ginkgoales.p1 Gnemon 2056337 GTHK Gnetales.p1

Isoesp. 2072393 PYHZ Lycophytes.p1 Catagr 2121763 NPRL Conifers.p1 Tsuhet 2054178 GAMH Conifers.p1 Keteve 2003230 JUWL Conifers.p1 Cedlib 2067476 GGEA Conifers.p1

Argniv 2004400 XDDT Leptosporangiate Monilophytes.p1 Abilas 2008597 VSRH Conifers.p1 Psewil 2007487 IOVS Conifers.p1 Myrruf 2061054 GSXD Leptosporangiate Monilophytes.p1 Isoteg 2096291 PKOX Lycophytes.p1

Adiale 2003414 WCLG Leptosporangiate Monilophytes.p1 Ephsin 2003130 VDAOWelmir Gnetales.p1 2009612 TOXE Gnetales.p1 Pinpar Conifers.p1 2014160 IIOL Adiale 2003416 WCLG Leptosporangiate Monilophytes.p1 Trelac 2089739 FITN Liverworts.p1 Adirad 2059839 BMJR Leptosporangiate Monilophytes.p1 Vitapp 2002927 NDUV Leptosporangiate Monilophytes.p1 Cryacr 2066960 WQML Leptosporangiate Monilophytes.p1

Pteens 2003776Vitlin FLTD 2012759 Leptosporangiate SKYV Leptosporangiate Monilophytes.p1 Monilophytes.p1 Pteens 2003777 FLTD Leptosporangiate Monilophytes.p1

Gnemon TnS000401465t16 Ptevit 2004956 POPJ Leptosporangiate Monilophytes.p1

Psemen PME00093907 Linmic 2054833 YIXP Leptosporangiate Monilophytes.p1 Pittri 2025679 UJTT Leptosporangiate Monilophytes.p1 Azocar 2025153 CVEG Leptosporangiate Monilophytes.p1 Linlin 2094599 NOKI Leptosporangiate Monilophytes.p1

Cycmic CMI00026367

Culmac 2006771 PNZO Leptosporangiate Monilophytes.p1 Picsit PSI00006128 Culmac 2006773 PNZO Leptosporangiate Monilophytes.p1

Plajap 2137574 UWODPilglo Leptosporangiate 2087277 KIIX Leptosporangiate Monilophytes.p1 Monilophytes.p1 Osmsp. 2007593 UOMY Leptosporangiate Monilophytes gametophyte.p1 Thyele 2018762 EWXK Leptosporangiate Monilophytes.p1 AnetomCyaspi 2024422 2069807 CQPW GANB Leptosporangiate Leptosporangiate Monilophytes.p1 Monilophytes.p1 Ginbil Gb 02714

Lygjap 2014865 PBUU Leptosporangiate Monilophytes.p1

Ophvul 2102494 QHVS Eusporangiate Monilophytes leaf.p1 Botvir 2004139 BEGM Eusporangiate Monilophytes.p1 Botvir 2004141 BEGM Eusporangiate Monilophytes.p1 Scedis 2006883 EEAQ Eusporangiate Monilophytes.p1 Ophpet 2021466 WTJG Eusporangiate Monilophytes.p1 OsmjavAngeve 2076177Tmepar 2001292 VIBO 2102811 LeptosporangiateNHCM ALVQ Eusporangiate Eusporangiate Monilophytes.p1 Monilophytes.p1 Monilophytes.p1

Hymbiv 2005697 QIAD Leptosporangiate Monilophytes.p1

Pinpin Pinpin PPI00009115 Pinsyl PSY00006980 Pinpin PPI00004968 Dipcon 2013311 MEKP Leptosporangiate Monilophytes.p1 Pinjef 2010834 MFTM Conifers.p1 Pinpon 2070811 JBND Conifers.p1 Pinrad 2009459 DZQM Conifers.p1 Pintae PTA00003245 Pintae PTA00081385 Sciver 2043523 Conifers.p1 YFZK Ararul 2064505 XTZO Conifers.p1 Wolnob 2057025 RSCE Conifers.p1 Agarob 2076239 MIXZ Conifers.p1 Agamac 2009431 ACWS Conifers.p1 Halbid 2053172 OWFC Conifers.p1 Lepsp. 2075943 BBDD Conifers.p1 Pruand 2037590 EGLZ Conifers.p1 Sunama 2093142 KLGF Conifers.p1 Mancol 2060476 CDFR Conifers.p1 Lagfra 2088084 ZQWM Conifers.p1 Hupsel 2036043 YHZW Lycophytes 2 samples combined.p1 Parust 2037772 JZVE Conifers.p1 Salcuc Sacu v1.1 s0049.g013662 Mictet 2071847 MHGD Conifers.p1 Saxcon 2073157 QCGM Conifers.p1 Nagnag 2113831 UUJS Conifers.p1 Retmin 2070052 VGSX Conifers.p1 Hupsel 2036044 YHZW Lycophytes 2 samples combined.p1 Acmpan 2112367 HILW Conifers.p1 Equhye 2130009 JVSZ Eusporangiate Monilophytes.p1 Podrub 2056403 XLGK Conifers.p1 Podcor 2050718 SCEB Conifers.p1 Daccom 2056438 FMWZ Conifers.p1 Dacbal 2071216 IZGN Conifers.p1 Faltax 2007829 QHBI Conifers A.p1 Equdif 2040362 CAPN Eusporangiate Monilophytes.p1 Faltax 2001002 PLYX Conifers 2 samples combined.p1 Faltax 2003392 ROWR Conifers.p1 Taxbac 2011039 WWSS Conifers.p1 Taxcus 2011698 ZYAX Conifers.p1 Psechi 2082772 YLPM Conifers.p1 Ausspi 2079283 BTTS Conifers.p1 Azofil Azfi s0045.g029943 Amearg 2149824 IAJW Conifers.p1 Tornuc 2135636 HQOM Conifers.p1 Cephar 2011681 WYAJ Conifers.p1 Cephar 2110176 NVGZ Conifers 2 samples combined.p1 Cephar 2007742 GJTI Conifers.p1 Cunlan 2052105 OUOI Conifers.p1 Cunlan 2012144 ZQVF Conifers 2 samples combined.p1 Cunlan 2016718 ESYX Conifers branch apex with needles.p1 Taicry 2064001 QSNJ Conifers.p1 Athcup 2061659 XIRK Conifers.p1 Seqgig 2060936 QFAE Conifers Glaucum.p1 Metgly 2002116 NRXL Conifers.p1 Metgly 2002117 NRXL Conifers.p1 Taxdis 2009787 FHST Conifers.p1 Glypen 2044730 OXGJ Conifers.p1 Cryjap 2009705 HOUF Conifers leaf.p1 Cryjap 2144341 GMHZ Conifers 2 samples combined.p1 Cryjap 2074218 DSXO Conifers.p1 Piluvi 2060844 ETCJ Conifers.p1 Pappap 2083743 OVIJ Conifers.p1 Auschi 2006630 YYPE Conifers.p1 Auschi 2006629 YYPE Conifers.p1 Disarc 2073875 GKCZ Conifers.p1 Widced 2011862 AUDE Conifers.p1 Calgra 2142976 IFLI Conifers March.p1 Calmac 2053680 RMMV Conifers March.p1 Neopan 2011320 JDQB Conifers.p1 Fokhod 2059319 UEVI Conifers.p1 Hupsel 2105147 GTUO Lycophytes.p1 Chalaw 2067912 AIGO Conifers.p1 Hupluc 2097054 GKAG Lycophytes.p1 Thupli 2039902 VFYZ Conifers.p1 Thudol 2049664 NKIN Conifers.p1 Caldec 2012102 FRPM Conifers.p1 Phydru 2002148 ZZEI Lycophytes.p1 Micdec 2054523 XQSG Conifers.p1 Hupmyr 2060126 CBAE Lycophytes.p1 Plaori 2051297 BUWV Conifers.p1 Phydru 2002149 ZZEI Lycophytes.p1 Tetsp. 2004509 CGDN Conifers.p1 Hupsqu 2016537 GAON Lycophytes.p1 Junsco 2004233 XMGP Conifers.p1 Cupdup 2072580 QNGJ Conifers.p1 Lycdeu 2008600 PQTO Lycophytes.p1 Ambtri evm 27.model.AmTr v1.0 scaffold00056.111 Utrgib Utricularia gibba unitig 32 837659 838245 unitig 32.g10988.t1 1 CDS 875816855 390 Denobs 2002731 XNXF Lycophytes.p1 Zosmar Zosma317g00260.1 Zosmar Zosma6g02240.1 Dipdig 2068177 WAFT Lycophytes.p1 Aposhe lcl KZ451903.1 PKA64484.1 2650 Lycann 2016622 ENQF Lycophytes.p1 Phaequ PEQU 25989 Dencat lcl NW 021318534.1 XP 028551701.1 1286 Lycapp 2006516 ULKT Lycophytes.p1 Spipol Spipo8G0040500 Lycapp 2006515 ULKT Lycophytes.p1 Musacu GSMUA Achr11T12340 001 Anacom Aco009966.1 Psecar 2007185 UPMJ Lycophytes.p1 Anacom Aco009965.1 Psecar 2016857 UPMJ Lycophytes.p1 Sorbic Sobic.007G040301.1 Phacar 2001183 WCZB Hornworts gametophyte.p1 Horvul HORVU3Hr1G019720.2 Selapo 2043310 LGDQ Lycophytes.p1 Bradis Bradi2g05640.2 Phacar 2001182 WCZB Hornworts gametophyte.p1Sellep 2007390 ABIJ Lycophytes.p1 Orysat LOC Os01g09430.1 Setita Seita.5G134500.1 Sorbic Sobic.003G035900.1 Phacar 2021795 RXRQ Hornworts sporophyte.p1 Zeamay Zm00008a010840 Selsta 2052791 ZZOL Lycophytes.p1 Zeamay Zm00008a010841 SelacaSelwil 2041547 2010973 ZYCD KJYC Lycophytes.p1 Lycophytes.p1 Nelnuc NNU 16890-RA Fraexc FRAEX38873 v2 000268830.1 Selwal 2014155 JKAA Lycophytes.p1 Fraexc FRAEX38873 v2 000159780.2 Fraexc FRAEX38873 v2 000159780.1 Selkra 2039721 ZFGK Lycophytes.p1 Utrgib Utricularia gibba unitig 32 837300 837599 unitig 32.g10987.t1 1 CDS 875816853 29469 Petaxi Peaxi162Scf00038g01029.1 Phacar 2021796 RXRQ Hornworts sporophyte.p2 Nicben Niben101Scf01374g13001.1 Nicben Niben101Scf10650g01007.1 Capann CA03g35870 Sollyc Solyc03g121040.2.1 NotaenParhal 2036042 2053803 DXOU FAJB Hornworts.p1 Hornworts.p1 Solpen Sopen03g039870.1 Daucar DCAR 026353 Notvin 2017826 TCBC Hornworts.p3 Diacar Dca35006.1 Megfla 2050912 UCRN Hornworts.p1 Betvul Bv9 224730 wkzj.t1 Spiole Sp 103740 qrrz.t1 Selmoe 90998 Chequi AUR62022211-RA Chequi AUR62031925-RA Helann HanXRQChr09g0275651 Calcor 2002518 TAVP Mosses.p1 Helann HanXRQChr09g0275641 Calcor 2002519 TAVP Mosses.p1 Helann HanXRQChr09g0276271 Thudel 2006398 EEMJ Mosses.p1 Helann HanXRQChr09g0275611 Pseele 2006917 QKQO Mosses.p1 Helann HanXRQChr08g0227201 Pseele 2006918 QKQO Mosses.p1 Helann HanXRQChr15g0472091 Anoatt 2060144 QMWB Mosses.p1 Helann HanXRQChr05g0162581 Necdou 2012209 TMAJ Mosses.p1 Helann HanXRQChr10g0280841 Helann HanXRQChr10g0280871 Necdou 2012210 TMAJ Mosses.p1 Helann HanXRQChr10g0280781 Helann HanXRQChr09g0275631 LeubraCliden 2098895 2086072 ZACW MIRS Mosses.p1 Mosses.p1 Helann HanXRQChr05g0139181 Helann HanXRQChr09g0275621 Fonant 2000402 DHWX Mosses.p1 Poptri Potri.001G190100.1 Leujul 2009142 IGUH Mosses.p1 Riccom 30146.m003504 Stesub 2067918 LNSF Mosses.p1 Manesc Manes.11G033300.1 Anocla 2011110 VBMM Mosses.p1 Cepfol Cfol v3 04783 Cepfol Cfol v3 04784 Rhyser 2047355 JADL Mosses.p1 Aulhet 2003552 WNGH Mosses.p1 Cepfol Cfol v3 32141 Cepfol Cfol v3 09849 Ortlye 2001416 CMEQ Mosses.p1 Gosrai Gorai.010G231000.1 Plains 2079643 BGXB Mosses.p1 Thecac Thecc1EG028897t1 Bryarg 2010820 JMXW Mosses.p1 Gosrai Gorai.010G230900.1 Roscap 2003601 XWHK Mosses.p1 Carpap evm.model.supercontig 25.16 Citcle Ciclev10025881m Phifon 2006900 ORKS Mosses.p1 Citsin orange1.1g019661m Hedcil 2050245 YWNF Mosses.p1 Citsin orange1.1g020626m Citcle Ciclev10026083m Physsp. 2080271 YEPO Mosses.p1 Mimpud Mimpu12737S14883 Mimpud Mimpu2250S20071 Synpri 2006626 GRKU Mosses.p1 Mimpud Mimpu12737S05923 Synpri 2006627Phypat GRKU Pp3c15 Mosses.p1 16500V3.1 Chafas Chafa96054S30719 Cerpur 2007120 FFPD Mosses.p1 Cercan Cerca47S25218 Dicsco 2100293 NGTD Mosses.p1 Casaus Castanospermum07967-PA Leualb 2129850 VMXJ Mosses.p1 Lupang Lup004418.1 Lotjap Lj3g3v0290090.1 Leugla 2010327 RGKI Mosses.p1 Racelo 2077050 ABCD Mosses.p1 Cicari Ca 00224.1 Polcom 2004434 SZYG MossesRacvar 2118148gametophyte.p1 RDOO Mosses.p1 Medtru MtrunA17 Chr2g0330991 Scoaqu 2009911 BPSG Mosses.p1 Trisub lcl DF973130.1 GAU13151.1 2209 Tripra Tp57577 TGAC v2 mRNA6765 Timaus 2066760 ZQRI Mosses.p1 Glymax Glyma.15G019700.1 Encstr 2060369 KEFD Mosses.p1 Cajcaj Ccajan 00433 Phavul Phvul.005G166000.2 Dipfol 2071715 AWOI Mosses.p1 Vigung Vigun05g280600.1 Vigang vigan.Vang0030ss00080.1 BuxaphAtrang 2008270 2012442 HRWG ZTHV Mosses.p1 Mosses.p1 Vigrad Vradi05g20720.1 Aradur Aradu.0HC1A AndrupTetpel 2095039 2130871 WOGB HVBQ Mosses.p1 Mosses.p1 Arahyp arahy.Tifrunner.gnm1.ann1.V9WMHM.1 Arahyp arahy.Tifrunner.gnm1.ann1.E2FDBV.1 Aradur Aradu.G9994 Arahyp arahy.Tifrunner.gnm1.ann1.TE5PEC.1 SphlesSphrec 2017172 2094150 GOWD UHLI Mosses.p1 Mosses.p1 Araipa Araip.I7NVN Sphfal Sphfalx0226s0017.1 Arahyp arahy.Tifrunner.gnm1.ann1.5H969I.1 Sphpal 2004007 RCBT Mosses.p1 Arahyp arahy.Tifrunner.gnm1.ann1.H3WDBY.1 Aradur Aradu.5T6PH Sphpal 2004006 RCBT Mosses.p1 Nissch Nissc1008S04773 BaztriTaklep 2009397 2077937Sphfal WZYK SKQD Sphfalx0226s0018.1 Liverworts.p1 Mosses.p1 Araipa Araip.LLK88 Arahyp arahy.Tifrunner.gnm1.ann1.D20K5B.1 Baztri 2009401 WZYK Liverworts.p1 Aradur Aradu.X4LTN Baztri 2009398 WZYK Liverworts.p1 Arahyp arahy.Tifrunner.gnm1.ann1.ENMN1I.2 MixspeCalfis 2014035 2180747 NWQC RTMU Liverworts.p1 Liverworts.p1 Tarhas lcl NW 010965216.1 XP 010535192.1 11307 Eutsal Thhalv10021117m Barbar 2130926 OFTV Liverworts.p1 Braolecap Bol038363 Odopro 2014687 YBQN Liverworts.p1 Brarap Brara.E02070.1 Fruspp 2019061 CHJJ Liverworts.p1 Boestr Bostr.19424s0514.1 Frusp. 2014728 TGKW Liverworts.p1 Aratha AT3G21360.1 Schisp. 2017065 LGOW Liverworts.p1 Aralyr AL3G35430.t1 Pornav 2008606 KRUQ Liverworts.p1 Caprub Carub.0003s2141.1 Capgra Cagra.1954s0019.1 Pornav 2008608 KRUQ Liverworts.p1 Datglo Datgl1189S19217 Porpin 2149358 UUHD Liverworts.p1 Begfuc Begfu6327S39251 Radlin 2012305 BNCU Liverworts.p1 Momcha lcl NW 019104489.1 XP 022144439.1 2084 Cucmos CmoCh08G007010.1 Marpal 2084435 LFVP LiverwortsPtipul 2 samples 2135652 combined.p1 HPXA Liverworts.p1 Cucpep Cp4.1LG17g05230.1 Pelepi 2004943 PIUF Liverworts.p1 Cucmax CmaCh08G007380.1 Pelnee 2110834 JHFI Liverworts.p1 Marpal 2053697 HMHLMetcra Liverworts 2098801 non NRWZ mycorrizal.p1 Liverworts.p1 Cucpep Cp4.1LG12g08550.1 Citlan Cla000905 Pallye 2106887 YFGP Liverworts.p1 Lagsic Lsi02G029840.1 Marpal 2066476 IHWO Liverworts mycorrizal.p1 100 Cucmel MELO3C024436.2.1 Marpal scaff17454 FGenesh6.1 Cucsat evm.model.Chr7.2290 Casgla Casgl119S03387 100 Alnglu Alngl27387S22492 Alnglu Alngl10419S13279 Marpol 2005027 JPYU Liverworts.p1 100 Jugreg g10858.t1 Marema 2072244 TFYI Liverworts.p1 Jugreg g1393.t1 Marpol Mapoly0024s0085.1 Casmol maker-scaffold24060-snap-gene-0.4-mRNA-1 Ricnat 2007435 WJLO Liverworts.p1 Casmol augustus masked-scaffold18984-abinit-gene-0.0-mRNA-1 Concon 2044961 ILBQ Liverworts.p1 Casmol augustus masked-scaffold19424-abinit-gene-0.2-mRNA-1 Sphtex 2004819 HERT Liverworts.p1 Casmol maker-scaffold03004-augustus-gene-0.18-mRNA-1 Luncru 2013422 TXVB Liverworts.p1 98.4 Casmol maker-scaffold09962-augustus-gene-0.15-mRNA-1 91 Casmol maker-scaffold03004-augustus-gene-0.16-mRNA-1 BlaspNW c320034 g2 i1 m.49127 Mornot L484 026281 Humlup HL.SW.v1.0.G046375.1

100 Parand lcl JXTB01000196.1 PON54358.1 19589

83.8 93.5 Treori lcl JXTC01000104.1 PON88547.1 15614 88.3 98.7 99.9 88.5 99.2 85.3 Distri Distr2026S17860 84.3 Zizjuj lcl NW 015453528.1 XP 015902421.1 35238 91.4 95.6 94.3 Zizjuj lcl NW 015453527.1 XP 015902392.1 35209 83.8 99.9 95 Rubocc Bras G20149 92.9 81.4 98.6 94.5 Roschi RchiOBHm Chr2g0140571 97.6 Potmic 27504 t 99.9 95.5 96.9 Fraana FAN iscf00255510.1.g00001.1 Fraana FAN icon20533774.1.g00001.1 93.3 99.6 83.8 Fraves FvH4 6g32420.1 99.4 82.2 97.8 Fraana FAN icon20067503.1.g00001.1 93.9 83.2 Drydru Drydr344S20824 93.7 96.9 99.9 100 98.2 96.8 100 Maldom MDP0000950997 Pyrcom PCP023960.1 98.7 Maldom MDP0000119991 89.7 100 Pyrbre lcl NW 008988063.1 XP 009352919.1 6290 Pyrcom PCP006376.1 95 97.599.5 100 88.9 100 Pruavi Pav sc0000759.1 g070.1.mk 99.9 Prumum lcl NC 024129.1 XP 008228422.1 12866 80.1 98.7 Pruper Prupe.3G058800.1 87.3 96.1 90.9 100 100 Prudul Prudul26A000607P1 9889.2 Maldom MDP0000886356 93.4 Maldom MDP0000406399 Maldom MDP0000311349 Pyrbre lcl NW 008988067.1 XP 009353541.1 6838 98 98.8 100 100 99.9 92.2 Pyrcom PCP003906.1 99.3 85 100 97.3 Pyrbre lcl NW 008988691.1 XP 009342539.1 38998 93.7 Pelepi 2090895 PIUF Liverworts.p1 100 100 99.1 95.8 86.3 93.7 Pelnee 2110427 JHFI Liverworts.p1 97.9 97.3 99.6 91.4 Pelnee 2112517 JHFI Liverworts.p1 99.8 84.1 96.6 87.2 88.1 99.3 92.8 98 99.8 Pelepi 2004791 PIUF Liverworts.p1 93 92.8 100 81 100 97.8 Pelepi 2004792 PIUF Liverworts.p1 84.5 97.4 100 Pallye 2106427 YFGP Liverworts.p1 91.1 99.580.2 100 100 BlaspNW c325491 g2 i1 m.64105 99.1 81 99.5 97.3 89.3 99.6 99.9 99.7 99.6 100 86.8 100100 BlaspNW c325491 g1 i2 m.64107 92.1 97.1 Sphtex 2008776 HERT Liverworts.p1 99.2 88.7 100 Faltax 2004203 QHBI Conifers A.p1 100 Luncru 2073431 TXVB Liverworts.p1 80.2 97.8 81.9 91.3 99.9 90.8 89.5 99.3 Faltax 2004205 QHBI Conifers A.p1 87.4 99.9 99.9 96.3 Concon 2044229 ILBQ Liverworts.p1 90.7 100 100 99.6 Faltax 2004204 QHBI Conifers A.p1 95.2 96.1 Ricnat 2035540 WJLO Liverworts.p1 100 85.6 95.2 100

100 Faltax 2002262 ROWR Conifers.p1 99.6 Ricnat 2035654 WJLO Liverworts.p1 99.4 100 93.4 97.9 Faltax 2002263 ROWR Conifers.p1 99.6 99.8 Marema 2073943 TFYI Liverworts.p1 Faltax 2001219 PLYX Conifers 2 samples combined.p1 95 99.5 85.9 Marpol 2002233 JPYU Liverworts.p1 Dacbal 2002418 IZGN Conifers.p1 94.5 99.598.7 Dacbal 2000800 IZGN Conifers.p1 97.2 99.6 100 92.6 97.9 92.1 Marpol 2002235 JPYU Liverworts.p1 83 97.9 Marpol Mapoly0064s0118.1 10095.4 90 88.4 100 92.5 99 100 100 Marpol Mapoly0070s0057.1

Faltax 2000368 ROWR Conifers.p1 98.4 98 100 99.484.1 99.2 100 99.9 Marpal 2066862 IHWO Liverworts mycorrizal.p1 Faltax 2000366 ROWR Conifers.p1 100 99.4 100 89.9 99.7 81.6 Marpal scaff1994 FGenesh1.1 Acmpan 2112765 HILW Conifers.p1 84.4 83.4 97.8 89.5 88.9 99.2 84.7 Marpal 2085178 LFVP Liverworts 2 samples combined.p1 Podcor 2001520 SCEB Conifers.p1 Marpal 2010005 HMHL Liverworts non mycorrizal.p1 Podcor 2001519 SCEB Conifers.p1 92.1 100 97.3 81.6 98.1 Fruspp 2134074 CHJJ Liverworts.p1 Faltax 2001218 PLYXPodcor Conifers 2001521 2 samples SCEB combined.p1 Conifers.p1 100 Calfis 2014657 RTMU Liverworts.p1 99.2 99.5 92.8 Podcor 2001522 SCEB Conifers.p1 100 100 95.8 100 Equhye 2012690 JVSZ Eusporangiate Monilophytes.p1 Faltax 2001216 PLYX Conifers 2 samples combined.p1 95.4 Equdif 2039438 CAPN Eusporangiate Monilophytes.p1 97 100 Faltax 2002261 ROWR Conifers.p1 100 Equhye 2012691 JVSZ Eusporangiate Monilophytes.p1 93.5 Equdif 2004198 CAPN Eusporangiate Monilophytes.p1 100 98.6 100 Parust 2000771 JZVE Conifers.p1 96.4 89.184.9 99.1 Dipdig 2009892 WAFT Lycophytes.p1 Phyhyp 2002661 JRNA Conifers.p1 100 85.1 99 90.8 Isoteg 2097615 PKOX Lycophytes.p1 81 100 97.1 99.8 Isoesp. 2011860 PYHZ Lycophytes.p1 Lepsp. 2001369 BBDD Conifers.p1 99.1 99.6 95.6 100 100 99.6 Trelac 2088368 FITN Liverworts.p1 Pruand 2000132 EGLZ Conifers.p1 99.983.4 82.7 99.9 90.6 Isoteg 2006629 PKOX Lycophytes.p1 Pruand 2000131 EGLZ Conifers.p1 86.4 99.9 87.9 81.9 100 96.2 87.1 100 98.5 Isoesp. 2004629 PYHZ Lycophytes.p1 Sunama 2002766 KLGF Conifers.p1 83 98.1 94.3 Trelac 2006500 FITN Liverworts.p1 99.9 83.7 99.9 96.9 Pruand 2000134 EGLZ Conifers.p1 93.1 80.2 94.5 100 Isoesp. 2004628 PYHZ Lycophytes.p1 Pruand 2000130 EGLZ Conifers.p1 100 92.3 98 99.1 97.1 Selkra 2039512 ZFGK Lycophytes.p1 99.7 90.6 Sunama 2002767 KLGF Conifers.p1 100 100 Selsel 2042731 KUXM Lycophytes.p1 93.3 100 86.5 96.7 Lagfra 2004716 ZQWM Conifers.p1 99.9 96.1 86.9 99.4 Selsel 2042964 KUXM Lycophytes.p1 Lagfra 2004715 ZQWM Conifers.p1 92.6 96.7 Selwil 2012006 KJYC Lycophytes.p1 100 100 99.9 Sellep 2006961 ABIJ Lycophytes.p1 Lagfra 2004140 ZQWM Conifers.p1 97.9 98.6 80.7 Saxcon 2007391 QCGM Conifers.p1 100 99.7 97.1 88.1 94.6 100 93.289.4 99.5 Selapo 2041212 LGDQ Lycophytes.p1 Halbid 2002056 OWFC Conifers.p1 100 92 80.8 82.2 Selsta 2003893 ZZOL Lycophytes.p1 Selmoe 66708 Halbid 2002057 OWFC Conifers.p1 99.2 89.4 100 99.2 99 100 99 90.7 91.9 Selwil 2006538 KJYC Lycophytes.p1 100 88.8 Mancol 2000655 CDFR Conifers.p1 98.9 97.7 Selwil 2006539 KJYC Lycophytes.p1 Mancol 2000657 CDFR Conifers.p1 97.4 Selsel 2010035 KUXM Lycophytes.p1 Mancol 2000654 CDFR Conifers.p1 100 100 98.1 95.2 98.399.6 99.5 98.9 93.5 100 Selsel 2010761 KUXM Lycophytes.p1 Parust 2004050 JZVE Conifers.p1 91.2 99 Selkra 2005578 ZFGK Lycophytes.p1 Parust 2004051 JZVE Conifers.p1 99.9 97.2 100 98.6 Selwal 2177412 JKAA Lycophytes.p1 Faltax 2003531 PLYXFaltax Conifers 2009436 2 samples QHBI Coniferscombined.p1 A.p1 99.4 Selsta 2052318 ZZOL Lycophytes.p1 97.8 99.695.3 95.9 97.7 Selmoe 425605 Faltax 2002196 ROWR Conifers.p1 100 100100 90.6 Selsel 2042872 KUXM Lycophytes.p1 Dacbal 2071952 IZGN Conifers.p1 100 99.6 Selapo 2042862 LGDQ Lycophytes.p1 Daccom 2002002 FMWZ Conifers.p1 100 99.7 99.4 100 99.9 100 Sellep 2010242 ABIJ Lycophytes.p3 Daccom 2002003 FMWZ Conifers.p1 97.6 97 98.2 Selsta 2006694 ZZOL Lycophytes.p1 98.4 94.2 Podcor 2052031 SCEB Conifers.p1 98.3 100 Selmoe 71180 100 Selapo 2000743 LGDQ Lycophytes.p2 Nagnag 2112559 UUJS Conifers.p1 99.398.5 99.7 Selmoe 439273 Podrub 2002175 XLGK Conifers.p1 100 Selmoe 449061 Acmpan 2010804 HILW Conifers.p1 98.5 100100 Selsta 2002628 ZZOL Lycophytes.p2 100 88.1 100 Saxcon 2001813 QCGM Conifers.p1 99.1 82.3 96.8 100 Selsta 2002627 ZZOL Lycophytes.p2 Mancol 2010053 CDFR Conifers.p1 97.6 99.9 99.7 Selkra 2005055 ZFGK Lycophytes.p1 Lagfra 2087066 ZQWM Conifers.p1 99.9 Selapo 2011064 LGDQ Lycophytes.p2 90.1 98.2 98.7 99.3 Athcup 2061080 XIRK Conifers.p1 94.8 86.399.3 Selsel 2000225 KUXM Lycophytes.p3 Pruand 2001189 EGLZ Conifers.p1 94.695.3 94.5 Selsel 2000224 KUXM Lycophytes.p3 Parust 2000174 JZVE Conifers.p1 99.9 Selaca 2009776 ZYCD Lycophytes.p2 Pruand 2001187 EGLZ Conifers.p1 96.7 93.2 97.4 Selkra 2040506 ZFGK Lycophytes.p1 94.5 Pruand 2001188 EGLZ Conifers.p1 96.2 97.8 100 100 92.6 87.8 Selwal 2009223 JKAA Lycophytes.p1 Parust 2000692 JZVE Conifers.p1 89.5 Selmoe 442390 96.2 96.8 96.7 Selsta 2000203 ZZOL Lycophytes.p1 Parust 2000693 JZVE Conifers.p1 84.6 87 100 Selmoe 414524 Lagfra 2008237 ZQWM Conifers.p1 Cryacr 2062505 WQML Leptosporangiate Monilophytes.p1 Agarob 2011757 MIXZ Conifers.p1 100 92.6 96.7 100 93.7 84 Polacr 2073004 FQGQ Leptosporangiate Monilophytes.p1 Agamac 2066814 ACWS Conifers.p1 100 100 99.9 98.7 85.3 100 Dipwic 2006600 UFJN Leptosporangiate Monilophytes.p1 Wolnob 2054379 RSCE Conifers.p1 99.4 100 Dipwic 2006599 UFJN Leptosporangiate Monilophytes.p1 Ararul 2002809 XTZO Conifers.p1 94.6 100 97.284.4 Deplob 2005757 FCHS Leptosporangiate Monilophytes crenata.p1 Micdec 2055128 XQSG Conifers.p1 92.584.7 Dipwic 2010174 UFJN Leptosporangiate Monilophytes.p1 Plaori 2010325 BUWV Conifers.p1 100 97 93.5 91.1 100 Deplob 2005423 FCHS Leptosporangiate Monilophytes crenata.p1 Caldec 2059001 FRPM Conifers.p1 94.4 99.9 85.9 100 96.493.8 Blespi 2047972 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Tetsp. 2069407 CGDN Conifers.p1 95.1 99.1 Athfil 2011691 URCP Leptosporangiate Monilophytes.p1 Cupdup 2071744 QNGJ Conifers.p1 98.4 92.298.7 Selwal 2004139 JKAA Lycophytes.p1 Thupli 2039529 VFYZ Conifers.p1 86.8 Selsta 2006140 ZZOL Lycophytes.p1 Thudol 2004633 NKIN Conifers.p1 93.2 Selmoe 74242 88.3 99.8 Sellep 2003063 ABIJ Lycophytes.p1 Fokhod 2012445 UEVI Conifers.p1 93.5 99.9 99.8 85.299.2 87.7 95 Selapo 2042096 LGDQ Lycophytes.p1 Chalaw 2010460 AIGO Conifers.p1 98.1 84.5 86.4 88.2 100 Isoteg 2097070 PKOX Lycophytes.p1 Widced 2056363 AUDE Conifers.p1 95.7 83.2 93.7 100 86.2 Isoesp. 2072246 PYHZ Lycophytes.p1 Cryjap 2012446 GMHZ Conifers 2 samples combined.p1 98.4 81.2 Trelac 2089762 FITN Liverworts.p1 Cryjap 2012447 GMHZ Conifers 2 samples combined.p1 97.4 86.2 95.6 Davfej 2226043 OQWW Leptosporangiate Monilophytes.p1 Cryjap 2008285 DSXO Conifers.p1 100 90.3 93.2 98.8 Selkra 2039576 ZFGK Lycophytes.p1 Taxdis 2014004 FHST Conifers.p1 Selaca 2001105 ZYCD Lycophytes.p1 Glypen 2011733 OXGJ Conifers.p1 97.491.2 86 Selapo 2004461 LGDQ Lycophytes.p1 Seqgig 2061004 QFAE Conifers Glaucum.p1 99.7 100 Selsta 2007900 ZZOL Lycophytes.p1 Metgly 2061183 NRXL Conifers.p1 97.7 100 100 Selwil 2047827 KJYC Lycophytes.p1 Taicry 2001007 QSNJ Conifers.p2 100 96.7 Selapo 2002385 LGDQ Lycophytes.p2 Taicry 2001005 QSNJ Conifers.p1 87.299.9 92.1 Selkra 2038737 ZFGK Lycophytes.p1 Taicry 2001006 QSNJ Conifers.p2 98.6 Selkra 2004836 ZFGK Lycophytes.p1 Selkra 2004837 ZFGK Lycophytes.p1 100 100 80.4 98.4 Selkra 2004834 ZFGK Lycophytes.p1 Cunlan 2099684 ZQVFCunlan Conifers 2051272 2 samples OUOI combined.p1 Conifers.p1 86.7 99.9 99.6 98.7 99.5 100 Selkra 2004835 ZFGK Lycophytes.p1 99.6 87.5 TAU 98.1 98.3 Selaca 2009281 ZYCD Lycophytes.p1 Cunlan 2086638 ESYX ConifersPsechi branch 2010169 apex YLPM with Conifers.p1needles.p1 99.5 Selwal 2009922 JKAA Lycophytes.p1 Ausspi 2011120 BTTS Conifers.p1 99.8 98 Selwal 2004590 JKAA Lycophytes.p1 Taxbac 2011406 WWSS Conifers.p1 100 Selaca 2005877 ZYCD Lycophytes.p2 Tornuc 2135970 HQOM Conifers.p1 Isoteg 2095949 PKOX Lycophytes.p1 Tortax 2080076 EFMS Conifers.p1 100 Selkra 2007041 ZFGK Lycophytes.p1 Amearg 2016714 IAJW Conifers.p1 9684.5 95.8 Selsel 2011071 KUXM Lycophytes.p1 Cephar 2059238 GJTI Conifers.p1 96.683 99.6 93.7 Sellep 2038070 ABIJ Lycophytes.p1 99.6 96.2 Selapo 2043930 LGDQ Lycophytes.p1 Cephar 2110043 NVGZCephar Conifers 2015659 2 samples WYAJ combined.p1 Conifers.p1 93.9 100 100 Ginbil Gb 33797 Sciver 2010955 YFZK Conifers.p1 88.1 95.1 Musacu GSMUA Achr9T21800 001 88.2 Anacom Aco005422.1 Thudol 2004539 NKIN Conifers.p1 93 98.5 100 84.2 98.2 Sorbic Sobic.002G173700.1 Thupli 2039623 VFYZ Conifers.p1 97 81.7 Bradis Bradi4g28240.2 Fokhod 2006771 UEVI Conifers.p1 93.4 92 88.210080.2 92.6 91.3 Horvul HORVU0Hr1G012680.2 Taxdis 2012306 FHST Conifers.p1 100 Horvul HORVU5Hr1G056300.4 Glypen 2046159 OXGJ Conifers.p1 100 Orysat LOC Os08g29510.1 Athcup 2061576 XIRK Conifers.p1 Bradis Bradi3g34920.1 92.5 94.3 Horvul HORVU2Hr1G088620.1 Seqgig 2002159Metgly QFAE 2062194 Conifers NRXL Glaucum.p1 Conifers.p1 98.4 99.8 Setita Seita.6G127300.1 Taicry 2009395 QSNJ Conifers.p1 Sorbic Sobic.007G117200.1 100 95.1 88.5 Zeamay Zm00008a016100 Cunlan 2011564 OUOI Conifers.p1 100 Fraexc FRAEX38873 v2 000238950.1 Cunlan 2018658 ZQVFCephar Conifers 2003385 2 samples WYAJ combined.p1 Conifers.p1 99.9 99.3 Fraexc FRAEX38873 v2 000134580.1 80.8 98.9 93.2 Fraexc FRAEX38873 v2 000343650.1 Cephar 2003387 WYAJ Conifers.p1 Fraexc FRAEX38873 v2 000342400.1 99.9 97.4 97.5 Fraexc FRAEX38873 v2 000065190.1 Cephar 2003386 WYAJ Conifers.p1 100 93.2 100 82 93.6 100 Fraexc FRAEX38873 v2 000039230.1 Cephar 2012696 NVGZ CepharConifers 2011118 2 samples GJTI combined.p1 Conifers.p1 98.6 86.9 Daucar DCAR 023692 Tornuc 2007493 HQOM Conifers.p1 96.6 88.9 Helann HanXRQChr15g0476021 Taxbac 2006057 WWSS Conifers.p1 100 99.5 Petaxi Peaxi162Scf00367g00738.1 Ausspi 2076287 BTTS Conifers.p1 99.1 97.5 100 Nicben Niben101Scf01338g05001.1 96.1 Nicben Niben101Scf00570g02009.1 Calgra 2003796 IFLI Conifers March.p1 86.7 Neopan 2068138 JDQB Conifers.p1 Nicben Niben101Scf00570g02008.1 93.7 86.4 Capann CA11g01770 Calmac 2002813 RMMV Conifers March.p1 86.3 100 Sollyc Solyc05g009960.2.1 Calmac 2002814 RMMV Conifers March.p1 94.5 100 Solpen Sopen05g005770.1 Calmac 2002812Piluvi 2002542RMMV Conifers ETCJ Conifers.p1 March.p1 99.9 99.8 99.2 100 98.4 96.4 Solpen Sopen05g005770.2 Piluvi 2002540 ETCJ Conifers.p1 94.5 99.8 Carpap evm.model.supercontig 1.233 99 94.1 82.5 100 99.9 94.7 88.6 Begfuc Begfu369S32385 Widced 2001552 AUDE Conifers.p1 95.1 99.2100 Begfuc Begfu850S42416 Thudol 2049765 NKIN Conifers.p1 100 86.6 99 Momcha lcl NW 019104713.1 XP 022157607.1 27088 Thupli 2007107 VFYZ Conifers.p1 99.8 92.6 99.7 85.8 97.4 Cucmax CmaCh15G014190.1 Tetsp. 2010010 CGDN Conifers.p1 100100 91.1 Cucpep Cp4.1LG13g00220.1 Plaori 2002048 BUWV Conifers.p1 99.9 80.7 Cucmos CmoCh15G014960.1 Chalaw 2067315 AIGO Conifers.p1 100 100 99.1 100 99.1 Citlan Cla002319 97.288.1 93.4 100 96.5 Lagsic Lsi09G006100.1 Cryjap 2005230 HOUF Conifers leaf.p1 80.399.9 100 Cucmel MELO3C005355.2.1 100 90 95.1 84.7 100100 Cucsat evm.model.Chr5.1978 Cryjap 2002839 DSXO Conifers.p1 88.1 Chafas Chafa35894S21553 Mimpud Mimpu2373S08724 Cryjap 2004415 GMHZ ConifersCryjap 2002838 2 samples DSXO combined.p1 Conifers.p1 98.5 87.3 96.4 Cryjap 2004416 GMHZ Conifers 2 samples combined.p1 92.8 Mimpud Mimpu12238S14574 100 99.5100 97.2 95.3 Chafas Chafa2787S20094 Taxdis 2012228 FHST Conifers.p1 98.9 Cercan Cerca45S24890 Glypen 2011732 OXGJ Conifers.p1 99.9 100 Casaus Castanospermum02174-PA Cryjap 2004417 GMHZ ConifersAthcup 20038442 samples XIRK combined.p1 Conifers.p1 99.890.3 98.3 99.6 Nissch Nissc525437S03662 100 100 100 99.7 Athcup 2003845 XIRK Conifers.p1 91.5 99.4 99.6 98 Arahyp arahy.Tifrunner.gnm1.ann1.R322MX.1 Metgly 2000767 NRXL Conifers.p1 100 100 Aradur Aradu.XBE20 Metgly 2000766 NRXL Conifers.p1 100 97.9 Araipa Araip.IG5LD Taxdis 2006819 FHST Conifers.p1 92.1 99.1 97.9 Arahyp arahy.Tifrunner.gnm1.ann1.N1LRBA.1 Taxdis 2006820 FHST Conifers.p1 95.5 100 100 Lotjap Lj2g3v1172600.1 90.5 Cicari Ca 26553.1 Junsco 2009016 XMGP Conifers.p1 100 Medtru MtrunA17 Chr0c05g0492121 Cupdup 2071226 QNGJ Conifers.p1 98.1 100 85.7 Tripra Tp57577 TGAC v2 mRNA2753 Tetsp. 2009392 CGDN Conifers.p1 Trisub lcl DF973231.1 GAU21475.1 10533 Chalaw 2063705 AIGO Conifers.p1 Cajcaj Ccajan 30509 Thudol 2010189 NKIN Conifers.p1 88.2 Glymax Glyma.02G101400.1 90.9 96.1 95.2 98.6 Glymax Glyma.01G089800.1 96.289.995.9 100 99.7100 99.2 Phavul Phvul.003G025800.1 Cunlan 2006216 OUOI Conifers.p1 86.5 88.8 Vigung Vigun02g027100.1 Taicry 2001942 QSNJ Conifers.p1 98.6 97.7 97.3 Vigrad Vradi11g12070.1 Taicry 2001943 QSNJ Conifers.p1 81 100 100 93 Vigang vigan.Vang0004ss01130.1 Cunlan 2000905 ESYX Conifers branch apex with needles.p1 Neopan 2011100 JDQB Conifers.p1 95.3 98.5 Datglo Datgl825S35408 Cunlan 2000904 ESYX Conifers branch apex with needles.p1 94 95.6 99.7 Casmol augustus masked-scaffold13146-abinit-gene-0.2-mRNA-1 99 100 Querob Qrob P0039810.2 Auschi 2005852 YYPE Conifers.p1 88.8 88.3 97.6 92.5 Calmac 2053898 RMMV Conifers March.p1 92.5100 99.9 Casmol snap masked-scaffold24080-abinit-gene-0.2-mRNA-1 Widced 2055102 AUDE Conifers.p1 100 100 Jugreg g42913.t1 Pappap 2007829 OVIJ Conifers.p1 98.9 97.6 90.3 Jugreg g28912.t1 Cupdup 2004037 QNGJ Conifers.p1 99.5 Alnglu Alngl9449S37817 Plaori 2002046 BUWV Conifers.p1 97.2 95.2 86.5 Alnglu Alngl9449S37818 Micdec 2000826 XQSG Conifers.p1 98.9 96.2 97.6 99.3 85.4 Alnglu Alngl427281S04251 Junsco 2003014 XMGP Conifers.p1 93.7 100 88.4 99.6 99.9 99.9 92.8 Casgla Casgl64S20566 Fokhod 2008695 UEVI Conifers.p1 100 Casgla Casgl64S05772 Cephar 2003960 GJTI Conifers.p1 100 Casgla Casgl64S20300 Cephar 2003961 GJTI Conifers.p1 Casgla Casgl64S20301 100 100 99.9 Citcle Ciclev10033372m Amearg 2000953 IAJW Conifers.p1 94.7 99.6 94.8 100 Citsin orange1.1g036171m Amearg 2000949 IAJW Conifers.p1 98 99.5 99.8 Gosrai Gorai.008G187300.1 Amearg 2000950 IAJW Conifers.p1 83.7 100 Thecac Thecc1EG011883t1 Amearg 2000952 IAJW Conifers.p1 99.2 99.2 99.3 98.9 100 Manesc Manes.06G073700.1 Poptri Potri.010G131300.1 Taxbac 2043738 WWSS Conifers.p1 96.9 80.6 100 Taxcus 2073913 ZYAX Conifers.p1 83.7 94.9 98.9 Poptri Potri.010G131200.1 Psechi 2008135 YLPM Conifers.p1 100 100 92.1 Riccom 29738.m001031 Tornuc 2134309 HQOM Conifers.p1 96.2 100 Manesc Manes.14G096400.1 Tortax 2014234 EFMS Conifers.p1 100 100 87.8 Manesc Manes.06G073800.1 Sciver 2042528 YFZK Conifers.p1 96.5 85.1 99.9 Zizjuj lcl NC 029688.1 XP 015895747.1 28136 92 Mornot L484 022941 Ararul 2001365 XTZO Conifers.p1 99.2 Ararul 2001366 XTZO Conifers.p1 Treori lcl JXTC01000498.1 PON49638.1 31692 100 Parand lcl JXTB01000271.1 PON48730.1 23435 Ararul 2001367 XTZO Conifers.p1 100 Humlup HL.SW.v1.0.G005126.1 100 Wolnob 2055223 RSCE Conifers.p1 Humlup HL.SW.v1.0.G005127.1 Sciver 2010044 YFZK Conifers.p1 100 89.7 86.1 94.6 99.3 Poptri Potri.008G115000.1 Agarob 2013534 MIXZPinsyl Conifers.p1 PSY00024338 88.4 Drydru Drydr94S24659 Pinjef 2004822 MFTMPinpin Conifers.p1 PPI00004016 Rubocc Bras G02617 Pinjef 2004819 MFTM Conifers.p1 99.2 98.8 98.9 Roschi RchiOBHm Chr4g0436031 Pintae PTA00022764 99.8 100 Potmic 6608 t Pinrad 2051025 DZQMPinpin Conifers.p1 PPI00057060 92.3 99.4 99.1 90.8 100 Fraana FAN iscf00071079.1.g00002.1 100 99.4 Fraves FvH4 4g28230.1 100 96 100 100 99.9 Fraana FAN iscf00291349.1.g00001.1 88.2 Pintae PTA00031826 100 91.6 98.8 Fraana FAN iscf00257102.1.g00001.1 92.9 Pruavi Pav co4018071.1 g010.1.mk Pinpar 2003320 IIOLPicsit Conifers.p1 PSI00010369 86.5 83.7 96.2 100 100 Prumum lcl NW 007362496.1 XP 008243156.1 26754 Pinpar 2003319 IIOL Conifers.p1 84.2 94.9 93.3 81.4 Picabi MA 10425962g0020 94.2 90.2 100 Pruper Prupe.1G303900.1 96.6 99.8 96.8 86.3 93.9 Prudul Prudul26A026283P1 87.3 95.2 86.1 84.3 Pyrbre lcl NW 008988477.1 XP 009336638.1 33667 Picabi MA 498632g0010 99.7 99.9 91.1 100 97 Pyrcom PCP007668.1 95.6 99.9 80.3 95.7 98.7 93.7 100 99.4 80.2 99.1 Pinpin PPI00016888 92.4 87.5 Maldom MDP0000428604 Piceng 2050440 AWQB Conifers.p1 99.7 100 90.8 100 Maldom MDP0000122618 99.8 97.2 86

100 100 89.3 Pinsyl PSY00022848 83 87 86.3 95.3 100 83.3 99.4 81 99.4 100 91.3 Maldom MDP0000188886 Pinpon 2013265 JBNDPinsyl Conifers.p1 PSY00026290 100 91.7 Maldom MDP0000603111 Pinpin PPI00006015 86.4 87.3 95.5 98.9 Pinjef 2004820 MFTM Conifers.p1 93.4 99.9 Maldom MDP0000314475 96.4 100 99.7 88 Pintae PTA00021647 100 100 98.7 Equdif 2003140 CAPN Eusporangiate Monilophytes.p1 99.9 100 100 99.8 84.5 100 99.9

99 100 Equhye 2000020 JVSZ Eusporangiate Monilophytes.p1 99.4 Scedis 2085994 EEAQ Eusporangiate Monilophytes.p1 100 98.8100 100 Botvir 2102338 BEGM Eusporangiate Monilophytes.p1 Psemen PME00027230 99.3 Hymbiv 2007412 QIAD Leptosporangiate Monilophytes.p1 Psemen PME00027231 97.9 Osmjav 2009281 VIBO Leptosporangiate Monilophytes.p1 96.3 100 97.8 96.3 81.3 Catagr 2008294 NPRLPsemen Conifers.p1 PME00027228 99.5 99.8 81.8 Osmsp. 2007548 UOMY Leptosporangiate Monilophytes gametophyte.p1 87.9 Catagr 2008295 NPRL Conifers.p1 93.5 99.1 100 99.3 94.2 Osmsp. 2007547 UOMY Leptosporangiate Monilophytes gametophyte.p1 97.5 Scedis 2086766 EEAQ Eusporangiate Monilophytes.p1 98.6 89 99.9 100 98.2 99.9 Botvir 2023864 BEGM Eusporangiate Monilophytes.p1 87.8 Scedis 2010056 EEAQ Eusporangiate Monilophytes.p1 91.8 99.9 87.3 Ophpet 2003558 WTJG Eusporangiate Monilophytes.p1 97.9 95.7 Larspe 2052145 WVWN Conifers.p1 88.5 Ophpet 2016080 WTJG Eusporangiate Monilophytes.p1 Keteve 2002899 JUWL Conifers.p1 Ophvul 2011811 QHVS Eusporangiate Monilophytes leaf.p1 Keteve 2002900 JUWL Conifers.p1 97.5 82.5 90.7 Psinud 2011754 QVMR Eusporangiate Monilophytes.p1 83.1 Keteve 2002898 JUWLPicabi Conifers.p1 MA 938243g0010 84.5 Tmepar 2004790 ALVQ Eusporangiate Monilophytes.p1 Abilas 2005808 VSRHPsemen Conifers.p1 PME00077733 83.2 Psinud 2010102 QVMR Eusporangiate Monilophytes.p1 Notlon 2006789 AREGPsemen Conifers.p1 PME00000341 Tmepar 2024835 ALVQ Eusporangiate Monilophytes.p1 Notlon 2006790 AREGPsemen Conifers.p1 PME00077735 99 100 Tmepar 2001809 ALVQ Eusporangiate Monilophytes.p1 Psemen PME00025245 Psinud 2016972 QVMR Eusporangiate Monilophytes.p1 100 Plajap 2137659 UWOD Leptosporangiate Monilophytes.p1 Marsp. 2008773 UXCS Eusporangiate Monilophytes.p1 Marsp. 2008772 UXCS Eusporangiate Monilophytes.p1 Psemen PME00005762 96.9 Angeve 2008036 NHCM Eusporangiate Monilophytes.p1 Psemen PME00025418 94.2 Angeve 2014145 NHCM Eusporangiate Monilophytes.p1 Psewil 2000069 IOVS Conifers.p1 Marsp. 2008106 UXCS Eusporangiate Monilophytes.p1 Pinpin PPI00051341 100 Angeve 2011948 NHCM Eusporangiate Monilophytes.p1 Cedlib 2000944 GGEA Conifers.p1Pinpin PPI00067707 88 Osmjav 2010327 VIBO Leptosporangiate Monilophytes.p1 Pinsyl PSY00013871 97.5 Osmsp. 2012073 UOMY Leptosporangiate Monilophytes gametophyte.p1 Pintae PTA00060864 Osmjav 2003261 VIBO Leptosporangiate Monilophytes.p1 Osmsp. 2003501 UOMY Leptosporangiate Monilophytes gametophyte.p1 LarspeCatagr 2051717 2011197 WVWN NPRL Conifers.p1 Conifers.p1 Osmjav 2003262 VIBO Leptosporangiate Monilophytes.p1 Osmsp. 2000567 UOMY Leptosporangiate Monilophytes gametophyte.p1 Anetom 2014805 CQPW Leptosporangiate Monilophytes.p1 Psemen PME00046377 Anetom 2014806 CQPW Leptosporangiate Monilophytes.p1 PsemenCycmic PME00046376 CMI00024965 Hymbiv 2057998 QIAD Leptosporangiate Monilophytes.p1 91.3 100 Dipcon 2000234 MEKP Leptosporangiate Monilophytes.p1 Catagr 2008654 NPRL Conifers.p1Cycmic CMI00002509 Lygjap 2012574 PBUU Leptosporangiate Monilophytes.p1 Notlon 2001163 AREG Conifers.p1 Plajap 2014896 UWOD Leptosporangiate Monilophytes.p1 87.4 100 Thyele 2015753 EWXK Leptosporangiate Monilophytes.p1 Cycmic CMI00009879 Thyele 2015752 EWXK Leptosporangiate Monilophytes.p1 Thyele 2015751 EWXK Leptosporangiate Monilophytes.p1 Linlin 2093986 NOKI Leptosporangiate Monilophytes.p1 Linmic 2053633 YIXP Leptosporangiate Monilophytes.p1 Cycmic 2001635 XZUY Cycadales.p1 Cryacr 2066089 WQML Leptosporangiate Monilophytes.p1 Cycmic CMI00025149 Cryacr 2004355 WQML Leptosporangiate Monilophytes.p1 Pteens 2069613 FLTD Leptosporangiate Monilophytes.p1 Cycmic 2001636 XZUY Cycadales.p1 Cycmic CMI00011415 Pittri 2090179 UJTT Leptosporangiate Monilophytes.p1 Ptevit 2017035 POPJ Leptosporangiate Monilophytes.p1 Staeri 2005442 KAWQ Cycadales.p1 Adirad 2058869 BMJR Leptosporangiate Monilophytes.p1 Staeri 2005444 KAWQ Cycadales.p1 Ginbil Gb 16263 Adiale 2009051 WCLG Leptosporangiate Monilophytes.p1 Adiale 2010809 WCLG Leptosporangiate Monilophytes.p1 Encbar 2004806 GNQG Cycadales.p1 Ginbil Gb 16262 Adirad 2060765 BMJR Leptosporangiate Monilophytes.p1 Dioedu 2004756 WLIC Cycadales.p1 Ginbil Gb 16264 Vitapp 2103400 NDUV Leptosporangiate Monilophytes.p1 Ginbil Gb 16266 Vitlin 2004260 SKYV Leptosporangiate Monilophytes.p1 Cycmic 2011069 XZUY Cycadales.p1 Ginbil Gb 16265 Argniv 2006653 XDDT Leptosporangiate Monilophytes.p1 Ginbil Gb 09862 Argniv 2006652 XDDT Leptosporangiate Monilophytes.p1 Notmon 2011322 YCKE Leptosporangiate Monilophytes.p1 Cycmic 2001634 XZUY Cycadales.p1 Ginbil Gb 36355 Parcor 2007029 ZXJO Leptosporangiate Monilophytes.p1 Staeri 2001687 KAWQ Cycadales.p1 Ginbil Gb 06041 Parcor 2006156 ZXJO Leptosporangiate Monilophytes.p1 Ginbil Gb 08596 Myrruf 2004490 GSXD Leptosporangiate Monilophytes.p1 EncbarDioedu 2004694 2014558 GNQG WLIC Cycadales.p1 Cycadales.p1 Ginbil Gb 16281 Myrruf 2004493 GSXD Leptosporangiate Monilophytes.p1 Ginbil Gb 16278 Parcor 2000152 ZXJO Leptosporangiate Monilophytes.p1 Ginbil Gb 35146 Gagari 2010646 DCDT Leptosporangiate Monilophytes.p1 Ginbil 2036697 SGTW Ginkgoales.p1 Ginbil Gb 16279 Gagari 2010645 DCDT Leptosporangiate Monilophytes.p1 Dendav 2001298 MTGC Leptosporangiate Monilophytes.p1 Aspnid 2003085 PSKY Leptosporangiate Monilophytes.p1 Aspnid 2009833 PSKY Leptosporangiate Monilophytes.p1 Asppla 2012575 KJZG Leptosporangiate Monilophytes.p1 Gymdry 2010518 HEGQ Leptosporangiate Monilophytes.p1 Cysfra 2012858 LHLE Leptosporangiate Monilophytes.p1 Cysree 2063967 RICC Leptosporangiate Monilophytes.p1 Cyspro 2067100 YOWV Leptosporangiate Monilophytes.p1 Cysfra 2020121 XWDM Leptosporangiate Monilophytes 2 samples combined.p1 Cysfra 2087778 XXHP Leptosporangiate Monilophytes Stewart.p1 Wooilv 2074855 YQEC Leptosporangiate Monilophytes.p1 Woosco 2004770 YJJY Leptosporangiate Monilophytes.p1 Theacu 2048025 MROH Leptosporangiate Monilophytes.p1 Hompyc 2008481 OCZL Leptosporangiate Monilophytes.p1 Onosen 2040802 HTFH Leptosporangiate Monilophytes.p1 Faltax 2055602 QHBI Conifers A.p1 Blespi 2002977 VITX Leptosporangiate Monilophytes.p1 Dipwic 2085940 UFJN Leptosporangiate Monilophytes.p1 Faltax 2005326 ROWR Conifers.p1 Blespi 2012496 RWYZ Leptosporangiate Monilophytes 2 samples combined.p1 Didtru 2034281 RFRB Leptosporangiate Monilophytes.p1 Faltax 2005327 ROWR Conifers.p1 Leuimm 2008346 WGTU Leptosporangiate Monilophytes.p1 Leuimm 2002059 WGTU Leptosporangiate Monilophytes.p1 Dacbal 2070198 IZGN Conifers.p1 Nepexa 2004084 NWWI Leptosporangiate Monilophytes.p1 Bolrep 2016918 JBLI Leptosporangiate Monilophytes.p1 Polgly 2001557 CJNT Leptosporangiate Monilophytes.p1 DaccomPodcor 2055965 2051878 FMWZ SCEB Conifers.p1 Conifers.p1 Polhes 2021791 IXLH Leptosporangiate Monilophytes B type.p1 Polhes 2006619 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Nagnag 2113821 UUJS Conifers.p1 Polamo 2000107 YLJA Leptosporangiate Monilophytes.p1 Acmpan 2111557 HILW Conifers.p1 Polamo 2000109 YLJA Leptosporangiate Monilophytes.p1 Davfej 2018601 OQWW Leptosporangiate Monilophytes.p1 Mancol 2002344 CDFR Conifers.p1 Davfej 2018602 OQWW Leptosporangiate Monilophytes.p1 MancolParust 2002343 2038050 CDFR JZVE Conifers.p1 Conifers.p1 Bolrep 2008450 JBLI Leptosporangiate Monilophytes.p1 Phygro 2012641 ORJE Leptosporangiate Monilophytes.p1 Phygro 2012642 ORJE Leptosporangiate Monilophytes.p1 Faltax 2008182 PLYX Conifers 2 samples combined.p1 Phlpse 2006683 ZQYU Leptosporangiate Monilophytes.p1 SaxconHalbid 2006090 2012301 QCGM OWFC Conifers.p1 Conifers.p1 Phlpse 2006684 ZQYU Leptosporangiate Monilophytes.p1 Polamo 2000108 YLJA Leptosporangiate Monilophytes.p1 Lepsp. 2075129 BBDD Conifers.p1 Polhes 2016834 GYFU Leptosporangiate Monilophytes A type.p1 Pintae PTA00065918 Polgly 2014092 CJNT Leptosporangiate Monilophytes.p1 Polhes 2006319 ZRAV Leptosporangiate Monilophytes 2 samples combined.p1 Faltax 2008183 PLYX Conifers 2 samples combined.p1 Sunama 2012557 KLGF Conifers.p1 Pintae PTA00053205 Ephsin 2002369 VDAO Gnetales.p1 Pintae PTA00053970 Ephsin 2004805 VDAO Gnetales.p1 Auschi 2064095 YYPE Conifers.p1 Pintae PTA00063024 Ginbil Gb 34217 Larspe 2052331 WVWN Conifers.p1 Metgly 2005791 NRXL Conifers.p1 Pintae PTA00077374 Psewil 2009318 IOVS Conifers.p1 Metgly 2005790 NRXL Conifers.p1 Pintae PTA00006520 Psemen PME00016881 Cryjap 2108314 HOUF Conifers leaf.p1 Picsit PSI00010220 Keteve 2007286 JUWL Conifers.p1 Ausspi 2077098 BTTS Conifers.p1 Psemen PME00019003 Tortax 2010819 EFMS Conifers.p1 Psewil 2011310 IOVS Conifers.p1 Psemen PME00101267 Catagr 2014310 NPRL Conifers.p1 Picsit PSI00006479 TornucTortax 2006992 2004846 HQOM EFMS Conifers.p1 Conifers.p1 Pinsyl PSY00026181 Tortax 2004845 EFMS Conifers.p1 Pinjef 2078474 MFTM Conifers.p1 Picabi MA 10431045g0030 Pintae PTA00083086 Psemen PME00005698 Cedlib 2004486 GGEA Conifers.p1 Pseama 2010323 AQFM Conifers.p1 Ginbil Gb 16261 Tsuhet 2053432 GAMH Conifers.p1 Notlon 2004823 AREG Conifers.p1 Piceng 2009048 AWQB Conifers.p1 Picabi MA 10428501g0020 Catagr 2012110 NPRL Conifers.p1 Cycmic CMI00006760 Pintae PTA00014717 Pintae PTA00001463 Pintae PTA00019993 Pintae PTA00017671 Pinsyl PSY00023887 Pinpin PPI00071012 Pintae PTA00056177 Pintae PTA00012120 Cryjap 2143533 GMHZ Conifers 2 samples combined.p1 Pintae PTA00066480 Pintae PTA00042822 Catagr 2122944 NPRL Conifers.p1 Pintae PTA00039248 Pintae PTA00040027 Pintae PTA00019492 Psewil 2014500 IOVS Conifers.p1 Pintae PTA00012563 Cedlib 2004048 GGEA Conifers.p1 Abilas 2004669 VSRH Conifers.p1 Abilas 2004668 VSRH Conifers.p1 Psewil 2004257 IOVS Conifers.p1 Psemen PME00007681 Picsit PSI00009251 Gnemon TnS000524655t01 Picabi MA 220550g0010 Notlon 2006936 AREG Conifers.p1 Picsit PSI00004254 Larspe 2051533 WVWN Conifers.p1 Picsit PSI00008051 Gnemon TnS000767275t03 Pinrad 2012388 DZQM Conifers.p1 Pinjef 2077090 MFTM Conifers.p1 Pintae PTA00079138 Gnemon TnS000640079t01 Pinpin PPI00017737 Pinsyl PSY00025445 Pinpin PPI00017738 Abilas 2010287 VSRH Conifers.p1 Notlon 2067255AREG Conifers.p1 Tsuhet 2008635 GAMH Conifers.p1 Psewil 2011173 IOVS Conifers.p1 Dioedu 2010977 WLIC Cycadales.p3 Psemen PME00017205 Picabi MA 10427711g0010 Picabi MA 10097034g0010 Picsit PSI00012300 Picabi MA 867753g0010 Pinjef 2014502 MFTM Conifers.p1 Pinjef 2014503 MFTM Conifers.p1 Pinpin PPI00018104 Pintae PTA00047465 Pinpar 2074953 IIOL Conifers.p1 Pinpin PPI00031432 Pintae PTA00006944 Pinpon 2067740 JBND Conifers.p1 Pinjef MFTM 2011912 Conifers.p1 Halbid 2051271 OWFC Conifers.p1 Mancol 2059050 CDFR Conifers.p1 Encbar 2083984 GNQG Cycadales.p1

Encbar Dioedu2014013 2010094 GNQG WLICCycadales.p1 Cycadales.p1

Ephsin 2000377 VDAO Gnetales.p1

Cryjap 2009357 DSXO Conifers.p1 Cryjap 2009356 DSXO Conifers.p1

Glypen 2010667Taxdis 2063132 OXGJ Conifers.p1 FHST Conifers.p1

Cryjap 2009746 HOUF Conifers leaf.p1Cupdup 2011094 QNGJ Conifers.p1 Cryjap 2009747 HOUF Conifers Cupdupleaf.p1 Caldec2011093 2059457Plaori QNGJ 2051198 FRPMConifers.p1 Conifers.p1 BUWV Conifers.p1 Thudol 2049906 NKIN Conifers.p1 Thupli 2039512 VFYZ Conifers.p1

Fokhod 2059066 UEVI Conifers.p1 Chalaw 2007583 AIGOTaicry Conifers.p1 2064537 QSNJ Conifers.p1

Cunlan 2002285 OUOI Conifers.p1 Athcup 2061903 XIRK Conifers.p1

Neopan 2067744 JDQBDisarc Conifers.p1 2073117 GKCZ Conifers.p1

Pappap 2012798 OVIJ Conifers.p1 Widced 2058765 AUDE Conifers.p1

Micdec 2002258 XQSG Conifers.p1 Micdec 2002260 XQSG Conifers.p1 Micdec 2002259 XQSG Conifers.p1 Cryjap 2007434 GMHZ Conifers 2 samples combined.p1 Cephar 2000938 WYAJ Conifers.p1 Cephar 2011335 GJTI Conifers.p1 Cryjap 2007433 GMHZ Conifers 2 samples combined.p1 Seqgig 2006909 QFAE Conifers Glaucum.p1 Cephar 2000939 WYAJ Conifers.p1 Cephar 2011336 GJTI Conifers.p1

Cephar 2000937 WYAJ Conifers.p1Taxcus 2002124 ZYAX Conifers.p1

Calmac 2053056 RMMV Conifers March.p1 Psechi 2008181 AusspiYLPM Conifers.p12011412 BTTS Conifers.p1 Tortax 2005222 EFMS Conifers.p1

Taxbac 2002771 WWSS Conifers.p1 Tortax 2014816 EFMS Conifers.p1 Tornuc 2134473 HQOM Conifers.p1 Amearg 2149033 IAJW Conifers.p1 Sciver 2011918 YFZK Conifers.p1 Ausspi 2005085 BTTS Conifers.p1 Taxcus 2008999 ZYAX Conifers.p1 Tornuc 2010829 HQOM Conifers.p1

Podrub 2007799 XLGK Conifers.p1 Podrub 2007800 XLGK Conifers.p1 Podcor 2051823 SCEB Conifers.p1

Parust 2003902 JZVE Conifers.p1 Nagnag 2113749 UUJS Conifers.p1Retmin 2069192 VGSX Conifers.p1 Parust 2003904 JZVE Conifers.p1

Faltax 2007058 ROWR Conifers.p1 Faltax 2007057 ROWR Conifers.p1 Mictet 2001063 MHGD Conifers.p1

Acmpan 2111400 HILW Conifers.p1

Lepsp. 2001677 BBDD Conifers.p1 Faltax 2009914 QHBI Conifers A.p1 Pruand 2008537 EGLZ Conifers.p1 Phyhyp 2008732 JRNA Conifers.p1

Lagfra 2004658 ZQWM Conifers.p1 Lagfra 2004659 ZQWM Conifers.p1 Daccom 2055132 FMWZ Conifers.p1

Cunlan 2008341 ESYX Conifers branch apex with needles.p1

Cephar 2001285 NVGZ Conifers 2 samples combined.p1 Cephar 2001283 NVGZ Conifers 2 samples combined.p1

Cephar 2001284 NVGZ Conifers 2 samples combined.p1

Cephar 2001282 NVGZ Conifers 2 samples combined.p1

Faltax 2010672 PLYX Conifers 2 samples combined.p1

Faltax 2010671 PLYX Conifers 2 samples combined.p1

Tree scale: 0.1 Supplementary Figure 33: Alignment of Nelumbo nucifera CCaMK from 3 assemblies with reference sequences showing an indel in the kinase domain and an amino acid switch on the essential for phosphorylation Serine 343 Kinase domain CaM binding domain EF-hand domains

Intron

Medtru_CCamK CDS GGGGTTATTCTATATATCTTACTTTCAG------// -GGTATCCACCTTTCATTGCCCAAAATAATCGCCAAAAACAA CAAATGATTCGTGCAGCTGCAATTGCTAGT Medtru_CCAMK protein SVWSST I Orysat_CCamK CDS GGGGTAATTCTGTACATTCTTTTATCTG------// -GATGCCCACCATTTCATGCTGCAACCAATCGAGAAAAGCAGCA AAGGATGCGGGCAGCTGCGATAGCCAGC Orysat_CCAMK protein SVLSCKV Nelnuc_CCamK CDS GGA------// ------GCGTGCAGCTG CAATTGACAGC Nelnuc_CCAMK protein SMCGSAL Nelnuc_CCamK genomic v1.1 GGAGT------// ------GAAATAATCGGCATAAGCAACAAA TGATGCGTGCAGCTGCAATTGACAGC Nelnuc_CCamKgenomic v1.1 SMCGSAL Nelnuc_CCamK genomic ASM303368v1 GGAGT------// ------GAAATAATCGGCATAAGCAACAAA TGATGCGTGCAGCTGCAATTGACAGC Nelnuc_CCamKgenomic ASM303368v1 SMCGSAL Nelnuc_CCamK genomic ASM303369v1 GGAGT------// ------GAAATAATCGGCATAAGCAACAAA TGATGCGTGCAGCTGCAATTGACAGC Nelnuc_CCamKgenomic ASM303369v1 SMCGSAL Orysat_CCamK genomic GGGGTAATTCTGTACATTCTTTTATCTGGGTATGTTGGCC // TTTCT------CAGATGCCCACCATTTCATGCTGCA ACCAATCGAGAAAAGCAGCAAAGGATGCGGGCAGCTGCGATAGCCAGC Orysat_CCamK genomic SVLSCKV Medtru_CCamK genomic GGGGTTATTCTATATATCTTACTTTCAGGGTATGTTTTTA // TTTCTTTCTTGCAGGTATCCACCTTTCATTGCCCAAAATA ATCGCCAAAAACAACAAATGATTCGTGCAGCTGCAATTGCTAG T Medtru_CCamKgenomic SVWSST I S343 Consensus // GG+GT+ATTCT+TA+AT++T++T+TC+GGGTATGTT++++ T TTCTTTCTTGCAG+T++CCACC+TT+++TGC++GAAATAATCGGCAA AAGCAACAAATGATGCGTGCAGCTGCAATTG+CAGC Supplementary Figure 34: Sites under positive selection in CYCLOPS in non-mycorrhizal mosses

NLS coiled coil

249 338 454

249 338 454

Medtru_MtrunA17_Chr5g0409341 TLQRKKLEC--SGEPSQSES--ILKRCENLE// // Marpal_2000586_LFVP SLERKKLSS---NAHSPSES--AVKRCEALE// // Hosts Taklep_2007702_SKQD SLERKKMAP--QLTQATSDS--SVKRCEALE// // Leualb_2015077_VMXJ SLNRAKQRL--PPVTQISDS--ALKRLDALE// // Leugla_2065124_RGKI SLNRAKQRL--PPVTQISDS--ALKRLDALE// // Hedcil_2011049_YWNF SLNRAKQRL--SPFTQISDS--ALKRLDALE// // Necdou_2184024_TMAJ SLNRAKQRL--SPVTQISDS--AMKRLDALE// // Calcor_2002155_TAVP SLNRAKQRL--SPITQISDS--AMKRLDALE// // Calcor_2002153_TAVP SLNRAKQRL--SPITQISDS--AMKRLDALE// // Cliden_2008278_MIRS SLNRAKLRL--SPVTQISDS--AMKRLDALE// // Rhyser_2011179_JADL SLNRAKQRL--STVTQISDS--AMKRLEGLE// // Leubra_2100051_ZACW SLNRAKQRL--SPVTQISDS--AMKRLDALE// // Leujul_2167700_IGUH SLNRAKQRL--SPVTQISDS--AMKRLDALE// // Loebre_2002298_WSPM SLNRAKQRL--SPVTQISDS--AMKRLDALE// // Mosses Anocla_2010668_VBMM SLNRAKQRL--SPVTQISDS--AMKRLEALE// // Non-hosts Aulhet_2090541_WNGH SLNRAKQRL--SPVTQISDS--AMKRLDALE// // Cerpur_2009225_FFPD SLNRAKQRL--PLVTQISDS--AMKRLEALE// // Scoaqu_2005245_BPSG SLNRAKHRL--PPVAQISDA--AMKRLDALE// // Dicsco_2102368_NGTD SLTRAKQRL--VQVTQISDS--AMKRLEALE// // Pseele_2007014_QKQO SLNRAKQRL--SPVTQISDS--AMKRLEALE// // Stesub_2009136_LNSF SLNRAKQRV--SPVTQISDS--AMKRLDALE// // Buxaph_2070490_HRWG T L H KK Q R----SPVVQVFEA--IMKKNEALE// // Roscap_2010673_XWHK SLNRARQRQ--NTVTQISDS--ALKRLDALE// // Anoatt_2061729_QMWB SLNRAKQRL--SPVTQISDS--AMKRLDALE// // Andrup_2014899_WOGB SLDKAKQRL--SPVLQSADP--ALKRLDALE// // Dipfol_2073705_AWOI SLNKAKQRL--SPVTQISDS--ALKRLDVLE// // Phifon_2011404_ORKS SLNRAKQRQ---SVQILSDS--ALKRLDALE// // Supplementary Figure 35: Sites under positive selection in CCaMK in non-mycorrhizal mosses Kinase domain CaM binding domain EF-hand domains

161 200-203 264 312-318 355 382 463 219 278

161 200-203 219 264 278 312-318 355 382 463

Medtru_MtrunA17_Chr8g0355131 SGLEAVHRA--SSVEEFTDPVVG--VSPEALSQ// // G--IMNGNFSFY--GISQPAKNL--GE// // // KAKDVQMDPEIVS--KKLKSLVGS--CADRDNATL// // --EEVASMLRA// Marpal_2014928_LFVP SGLASLHQA--SHIDGVTSPVVG--VAPEALL// // RK--ILSGDFNFG--KVTSSAKQL--G// // // DAAKREPVGQDVIK--KKLKTLVGN--STNGASV// // TV--EELASMLRA// Hosts Taklep_2008135_SKQD AGLCSLHAA--SHIDGVTSPVVG--VAPEALMR// // E--ILDGDFSME--GVTGSAKQL--GDV// // // AKPHPVDPDVFR--KNLRNLIPS--SANGVSA// // SL--DELASMLRA// Leualb_2008773_VMXJ SGLATLHQA--SYIHNVTNSVVG--MAPEQLNL// // S--ILTGSYSME--GISLEAKEL-// // // -GVTATRELIHEDVIM--KYLKELLGN--S// // ANGKTVTL--DELARVLGA// Leugla_2003923_RGKI SGLATLHQA--SYIHNVTNSVVG--MAPEQLNL// // S--ILTGSYSME--GISLEAKEL-// // // -GVTATRELIHEDVIM--KYLKELLGN--S// // ANGKTVTL--DELARVLGA// Dipfol_2002244_AWOI AGLSKLHQV--SYIRNMTHSVVG--VAPEQLNQT// // --ILTGSFDMD--GVSPEAKQL--GETA// // // SRELIHEDIFT--KYLKELLGN--SSNGQT// // ATL--DELVRVLGV// Scoaqu_2014956_BPSG SGLSMLHQA--SYIHNVTNSVVG--MAPEQLNLS// // --ILTGAYSMD--GISSEAKEL--GDT// // // ATRELIHEDVFM--KYLKELLGD--SSNGRTA// // TL--DELGRVLGA// Aulhet_2014847_WNGH TGLCSLHQA--SYIHDVTIAVGG--MAPEQLRL// // S--IVTGSYNME--GISLEAKEL--// // // GAVASRELIHEDVFM--KYLKELLGD--SSNG// // RTATL--DELVSVLGA// Racvar_2018405_RDOO SGLTMLHQA--SYIYNVTNSVVG--MAPEQLNL// // S--ILAGSYSME--GISSEAKEL--// // // GDTATRELIHEDVFM--KYLKELLGD--SST// // GQTATL--DELARVLGV// Physsp._2003262_YEPO SGLAALHQA--SYIHHNTNSIVG--MAPEQLSL// // S--ILTGSYSME--GISHEAKQL--G// // // DTANRDLLHKDVFM--RYLKELLGD--SSNGQTA// // TL--GELARVLGA// Mosses Stesub_2009164_LNSF TGLHALHRA--SYLHNETNNVVG--MAPEQLRL// // S--IMTGSYSMD--SISSEAKEL--GA// // // VARRELIHNDVFM--KYLKELLGD--SSNGRTA// // TL--EELASVLGA// Encstr_2007124_KEFD AGLAMLHQA--SYIHNVTNSVAG--MAPEQLNLS// // --ILTGAYSME--GISSEAKEL--GD// // // TATRELIHEDVFI--KYLKELIGD--SS// // NGRTATL--DELVSVLGA// Non-hosts Ortlye_2013487_CMEQ AGLCSLHQA--SYIQNVTNAVVG--MAPEQLRL// // S--ILTGSYTMD--GISMNAKEL--GA// // // VASREVIHEDVIM--KYLKEILGD--SANGK// // TATL--DELVSVLGA// Necdou_2023616_TMAJ AGLLALHRA--SSLPEVTRPVVG--VAPEQL// // SFA--ILTGAYSMD--GISLEAKAL-// // // -GDTASKELIHEDVFT--KYLKELVGD--SS// // NGQTATL--DELARVLGA// Rhyser_2048106_JADL AGLLALHRA--SSLPEVTRPVVG--VAPEQL// // SFT--ILTGAYSMD--GISLEAKTL-// // // -GDTASKEFIHEDVFT--KYLKELVGD--SS// // NGQTATL--DELARVLGA// Anocla_2052700_VBMM AGLLALHRA--SSLPEVTRPVVG--VAPEQL// // SFA--ILTGAYSMD--GISLEAKAL-// // // -GDTASNEFIHEDVFM--KYLKELVGD--SSNGQ// // TATL--DELARVLGA// Racvar_2007958_RDOO AGLAALHHA--SFIHNVTNPVEG--VAPEQLN// // FS--ILKGAYSMD--GISLEAKEL-// // // -GDTASREFIHDDIFM--KYLKELIGD--SS// // NGHTATL--DELARVLGA// Physsp._2000990_YEPO AGLAALHQC--SHIHNVTNAVVG--MAPEQLNMS-// // // -ILMGAYSME--CISLEAKEL--GESATRE// // LIHEDVFI--KYLKELIGD--TSNGRTAT// // L--DELALVLGA// Phifon_2011379_ORKS AGLAALHRA--SFLVNVTHPVVG--VTPEQLS// // FS--ILTGAYSMD--GISSQAKDL--G// // // DTASRELIHEDVFM--KYLKELVGD--SSNGQT// // ATL--DELARVLGA// Supplementary Figure 36: Comparative alignment of 1kb from CYCLOPS among the three subspecies genomes and 35 accessions of Marchantia polymorpha.

0 1000 2000 3000 4000 5000

Marpal CYCLOPS Marpol pol Marpol mon Marpol rud

Marpol pol Marpol mon Marpol rud Ber-C Ber-D Bid-A Bie-A Bot-X Bul-B Cas-A Cas-C Cas-D Cas-E Caz-A Dur-A Esc-A Gen-A Gen-B Hec-A Hec-C Lac-A Luc-B Mns-A Mou-A Mur-A Nor-A Nor-B Nor-C Nor-D Pra-A Pra-B Pra-C Tou-A Tou-B Tou-C Tou-D Tou-E Voe-A Supplementary Figure 37: Presence/absence pattern of 11 genes in Ericaceae compared to species with different symbiotic abilities

SymRK CCaMK CYCLOPS RAD1 STR STR2 CASTOR EXO70 FatM SYN VAPYRIN Arabidopsis thaliana No symbiosis

Medicago truncatula AMS / RNS

Phalaenopsis equestris

Dendrobium catenatum OM

Apostasia shenzhenica

Lupinus angustifolius RNS

Cavendishia cuatrecasassii

Monotropa uniflora

Rhododendron fortunei Ericoid

Rhododendron scopulorum

Sarcodes sanguinea

Ortholog Absent (from genome) Not Detected (from transcriptome)