Supplementary Figures
Evolution of Portulacineae marked by gene tree conflict and gene family expansion associated with adaptation to harsh environments
Ning Wang, Email: [email protected] Stephen A. Smith, E-mail: [email protected]
Dendroscope view
Limeaceae_Limeum aethiopicum
Montiaceae_Phemeranthus parviflorus
Basellaceae_Anredera cordifolia
Anacampserotaceae_Anacampseros kurtzii
Portulacaceae_Portulaca amilis
Cactaceae_Leuenbergeria lychnidiflora
Cactaceae_Stenocereus yunckeri
Cactaceae_Maihuenia poeppigii
Cactaceae_Opuntia bravoana
Cactaceae_Pereskia grandifolia
Talinaceae_Talinum paniculatum A Didiereaceae_Portulacaria afra
PhyloPlot view Limeaceae_Limeum aethiopicum
Montiaceae_Phemeranthus parviflorus
Basellaceae_Anredera cordifolia
Anacampserotaceae_Anacampseros kurtzii 0.008 Portulacaceae_Portulaca amilis 0.992 0.118 Cactaceae_Leuenbergeria lychnidiflora
Cactaceae_Stenocereus yunckeri 0.24 0.146 0.76 Cactaceae_Maihuenia poeppigii 0.854
0.882 0.364 Cactaceae_Opuntia bravoana 0.636 Cactaceae_Pereskia grandifolia
B Talinaceae_Talinum paniculatum Didiereaceae_Portulacaria afra
FIG. S1. The phylogenetic network inferred using MPL method in PhyloNet. Taxa were selected from each plant family based on their gene occupancy statistics. A: network visualized in Dendroscope, and B: the same network with inheritance probabilities between hybridization lineages visualized by PhyloPlot that implemented in PhyloNetworks (Solís-Lemus et al. 2017). Anacampserotaceae Basellaceae Anacampseros A. kurtzii Talinopsis frutescens Anredera cordifolia Basella alba filamentosa Bese 400 4000 4000 3000 3000 200 2000 2000 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Portulacaceae Portulaca amilis P. cryptopetala P. grandiflora P. molokiniensis P. oleracea P. pilosa 300 500 800 800 200 200 300 150 400 400 100 100 0 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 Talinaceae P. suffrutescens P. umbraticola Talinum fruticosum T. paniculatum T. portulacifolium 8000 600 200 150 300 4000 1500 100 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Cactaceae Coryphantha Ariocarpus retusus Astrophytum asterias A.myriostigma Copiapoa desertorum maiz-tablasensis 8000 8000 8000 8000 3000 4000 4000 4000 4000 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Echinocereus pectinatus Echinopsis aurea Eriosyce Ferocactus latispinus Grusonia bradtiana wagenknechtii 2000 8000 8000 4000 6000 1000 4000 4000 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
FIG. S2. Distribution of within-taxon synonymous distances (Ks) among paralogs gene pairs based on BLASTP hits. Zoomed-in Ks plots of certain species from Didiereaceae, Montiaceae, Molluginaceae and Outgroups were shown next to corresponding species. Potential WGD has been marked by arrows. Yang* represents Yang et al. (2018). Node 13: the origin of Portulacineae, Node 27: the origin of Didiereoideae, Node 17: the origin of Calyptridium, and Node 19: the MRCA of Calandrinia and Claytonia in Montiaceae.
Cactaceae (continue)
Gymnocalycium Leuenbergeria bleo Leuenbergeria L. lychnidiflora Lophophora williamsii mihanovichii guamacho 8000 150 3000 3000 3000 4000 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Maihuenia poeppigii Maihueniopsis Matucana aurantiaca Opuntia arenaria Opuntia bravoana conoidea 12000 4000 8000 6000 3000 6000 2000 4000 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Opuntia cochenillifera Pachycereus gatesii Peniocereus Pereskia aculeata P. grandifolia cuixmalensis 4000 300 8000 6000 1500 2000 150 4000 3000 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Pterocactus tuberosus Rhipsalis baccifera Salmiopuntia salmiana Stenocereus yunckeri Stetsonia coryne 8000 8000 2000 6000 4000 4000 4000 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Tacinga lilae Tephrocactus articulatus T. bonnieae Tunilla corrugata 8000 8000 8000 WGD in Node 13 6000 4000 4000 4000 Base Potential WGD 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
FIG. S2. Continued
Didiereaceae
Alluaudia dumosa Alluaudia humbertii Alluaudia procera Didi Didi Didi Didi Didi Didi 3000 2000 12000 1500 15000 15000 1500 6000 1000 0 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 0.4 0.8 0.01 1.0 2.0 3.0 0.01 0.4 0.8 0.01 1.0 2.0 3.0 0.01 0.4 0.8
Alluaudiopsis marnieriana Decarya madagascariensis Didierea madagascariensis
Didi Didi Didi Didi Didi Didi 1200 12000 1000 8000 1000 600 6000 6000 600 4000 0 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 0.4 0.8 0.01 1.0 2.0 3.0 0.01 0.4 0.8 0.01 1.0 2.0 3.0 0.01 0.4 0.8
Didierea trollii Portulacaria afra Portulacaria pygmaea
Didi
Didi 800 10000
1000 Didi WGD in Node 27 2000 400 4000 WGD in Node 13 0 0 0 0
0.01 1.0 2.0 3.0 0.01 0.4 0.8 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Montiaceae
Calandrinia grandiflora Calyptridium pygmaeum Calyptridium umbellatum
Cagr Cagr Caly Caly Caly 1200 Caly 800 1200 8000 4000 600 6000 400 600 4000 0 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 0.4 0.8 0.01 1.0 2.0 3.0 0.01 0.4 0.8 0.01 1.0 2.0 3.0 0.01 0.4 0.8
Lewisia nevadensis Claytonia nevadensis Claytonia virginica Mont Mont Lewi Lewi Mont 3500 Mont Mont Mont 3000 2000 1500 15000 6000 1000 0 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 0.4 0.8 0.01 1.0 2.0 3.0 0.5 1.5 2.5 0.01 1.0 2.0 3.0 0.5 1.5 2.5
FIG. S2. Continued
Montiaceae (continue) Montia chamissoi Cistanthe grandiflora Phemeranthus parviflorus Mont WGD in Node 13 1200 6000 Caly WGD in Node 17 4000
Mont 3000 Mont WGD in Node 19 600 2000 3000 1500 Cagr Potential WGD 0 0 0 0 Lewi Potential WGD 0.01 1.0 2.0 3.0 0.5 1.5 2.5 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Molluginaceae
Mollugo cerviana Mollugo nudicaulis Pharnaceum exiguum Suessenguthiella caespitosa 1200 2000 3000 200 600 100 1000 1500 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Mollugo pentaphylla Mollugo verticillata Glinus dahomensis
Moll 500 200 1200 Moll 300 600
6000 Moll Potential WGD 100 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.5 1.5 2.5 0.01 1.0 2.0 3.0
Outgroups
Sesuvium Delosperma echinatum Anisomeria littoralis Guapira obtusata Beta vulgaris portulacastrum 600 200
PHYT2 PHYT2 400 3000 300 100 1500 200 0 0 0 0 0
0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0 0.01 1.0 2.0 3.0
Limeum aethiopicum Stegnosperma halimifolium
Lime Lime Steg 2000 2000 12000 Lime Potential WGD 15000 Steg
1000 Potential WGD
6000 Steg 1000 0 0 0 0 PHYT2 WGD as in Yang*
0.01 1.0 2.0 3.0 0.01 0.4 0.8 0.01 1.0 2.0 3.0 0.5 1.5 2.5
FIG. S2. Continued
FIG. S3. The probability density Ks plots inferred form the within species paralogs and reciprocal orthologs (within the vertical panel). Considering the high number of gene duplication events mapping on the phylogenetic tree (fig. 1), the WGD probably occurred before the speciation of Montia chamissoi and Claytonia, and at approximately the same time as the divergence of Lewisia, but possibly after the divergence of Calandrina grandiflora. Ks values > 0.8 and < 0.01 are not shown. The Ks peaks are identified by eye and marked with the red line with an estimated value.
A Portulacaceae B Portulacaceae Anacampserotaceae Anacampserotaceae Talinaceae Talinaceae Didiereaceae Didiereaceae
1 Montiaceae 1 Montiaceae
3 3 Cactaceae Cactaceae
2 4 2 4 Molluginaceae Molluginaceae
60 50 40 30 20 60 50 40 30 20
bioclim1 bioclim12 cold hot wet dry
FIG. S4. Reconstruction of mean annual temperature (left) and mean annual precipitation (right) on the ‘big time’ tree of Portulacineae built with NCBI data. Node labels indicate clades with WGD/extensive gene duplication (1: Didiereoideae, 2: Portulacineae, 3: Cactaceae, 4: Montiaceae except for Phemeranthus).
FIG. S5. Diversification rate shifts on a species level phylogeny (A) and a reduced phylogeny of major lineages (B).
FIG. S6. The frequency distribution of the number of duplication genes at the focal nodes (under SH-like support > 80) generated from 1000 replicates of randomly selecting 29 homologs. The node number can be referred to in fig. 1. Nodes 13, 17 and 19 were identified with WGD events. The solid black line indicates the number of duplication genes from the 29 stress responding genes that targeted on in the main text.
FIG. S6. Continued. Calculation of gene duplication without support constraint.
FIG. S7. Gene duplication and lineage positive selection patterns on a collapsed species tree from the 29 targeted genes (tables 2 and S7). Green labeled branches indicated the focal clades with more gene duplication and positive selected lineages. The number of sampling taxa in each major clade are indicated after clade name. The numbers above a certain internal edge represent the total number of duplication events (if any) for that edge from the 29 genes (generated directly from Phyparts analyses), with number before slash being generated under no support constraint, while number after slash being generated under SH-like support > 80. The bolded numbers within each clade are calculated based on table 2: the first number before parentheses represents the number of genes exhibiting positive selection within this clade. The two numbers within the parentheses are the number of genes showing duplication (i.e., duplicated homologs) within the whole clade (number before slash calculated based on “no support constraint” column in table S7 and number after slash calculated based on “SH80” column in table 2).
● ● ●●●● 80 ●●●●●● ●●●●●●●●● ●●●●●●●●●● ●●●●●●●●●●●● ●●●●●●●●●●● ●●●●●●●●●●●● ●●●●●●●●●●●● ●●●●●●●●●● ●●●●●●●●●●●● ●●●●●●●●●●●● 70 ●●●●●●●●●●● ●●●●●●●●●●● ●●●●●●●●●●● ●●●●●●●●●●● ●●●●●●●●●●● ●●●●●●●●●●● ●●●●●●●●●● ●●●●●●●●● ●●●●●●●● ●●●●●●●●● 60 ●●●●●●●● ●●●●●●●● ●●●●●●●● ●●●●●●●● ●●●●●●● ●●●●●●● ●●●●●● ●●●●●● ●●●●● ●●●●●● 50 ●●●●●● ●●●●● ●●●●●
Number of Taxa in Each Ortholog Number of Taxa ●●●●● ●●●● ●●●● ●●●● ●●● ●●●● ●●●● 40 ●●● ●●● ●●● ●●● ●●● ●●
0 2000 4000 6000 8000 10000
Sorted1:10000 ortholog groups
FIG. S8. Ortholog groups ranked from high to low by number of taxa represented. Only ortholog groups with at least 30 taxa were shown. Full taxon occupancy includes 82 taxa.
FIG. S9. Species tree from RAxML analysis of the 841-gene supermatrix, with number labeled for each node.
Lophophora williamsii_22745 Coryphantha maiz-tablasensis_36240 Matucana aurantiaca_3664 Ariocarpus retusus_79487 Echinopsis aurea_4086 Ferocactus latispinus_30481 Stetsonia coryne_41308 Astrophytum asterias_6907 Gymnocalycium mihanovichii_12116 Astrophytum myriostigma_39808 Eriosyce wagenknechtii_44153 Rhipsalis baccifera_22257 Rhipsalis baccifera_93340 Stetsonia coryne_17794 Stenocereus yunckeri_88980 Gymnocalycium mihanovichii_48572 Pachycereus gatesii_25377 Echinopsis aurea_82334 Echinocereus pectinatus_18836 Matucana aurantiaca_32691 Eriosyce wagenknechtii_64204 Peniocereus cuixmalensis_47052 Copiapoa desertorum_51378 Copiapoa desertorum_3394 Stenocereus yunckeri_29647 Lophophora williamsii_5900 matK Pachycereus gatesii_54227 Ariocarpus retusus_30877 Echinocereus pectinatus_16797 rbcL Ferocactus latispinus_3160 Peniocereus cuixmalensis_40748 Astrophytum myriostigma_80292 Salmiopuntia salmiana_50632 Astrophytum asterias_28361 Opuntia bravoana_47223 Opuntia bravoana_33082 Nopalea cochenillifera_9662 Nopalea cochenillifera_21607 Tacinga lilae_67651 Opuntia arenaria_102255 Opuntia arenaria_85310 Salmiopuntia salmiana_50199 Tunilla corrugata_67571 Maihueniopsis conoidea_67748 Tacinga lilae_61279 Grusonia bradtiana_35917 Tunilla corrugata_1451 Pterocactus tuberosus_67567 Tephrocactus articulatus_72357 Tephrocactus articulatus_5155 Tephrocactus bonnieae_95117 Tephrocactus bonnieae_45586 Maihueniopsis conoidea_8496 Maihuenia poeppigii_51701 Pterocactus tuberosus_79129 Leuenbergeria bleo_62934 Grusonia bradtiana_72334 Pereskia grandifolia_50407 Maihuenia poeppigii_4487 Pereskia aculeata_2691 Leuenbergeria lychnidiflora_14882 Leuenbergeria lychnidiflora_43482 Portulaca amilis_62549 Leuenbergeria guamacho_17666 Anacampseros filamentosa_22909 Portulaca suffrutescens_46357 Anacampseros kurtzii_44656 Portulaca oleracea_37532 Talinopsis frutescens_34657 Pereskia aculeata_c2947_g1_i1_1_708_plus Portulaca amilis_62323 Leuenbergeria guamacho_10411 Portulaca suffrutescens_48063 Pereskia grandifolia_27316 Portulaca pilosa_10927 Anacampseros filamentosa_22887 Portulaca oleracea_38182 Anacampseros kurtzii_39706 Portulaca molokiniensis_108214 Talinopsis frutescens_10822 Portulaca umbraticola_67558 Talinum portulacifolium_5048 Portulaca cryptopetala_135776 Talinum paniculatum_37732 Talinum fruticosum_46417 Alluaudia humbertii_83188 Talinum portulacifolium_17742 Talinum paniculatum_38935 Didierea trollii_17895 Claytonia nevadensis_51107 Didierea madagascariensis_46283 Claytonia virginica_60693 Decarya madagascariensis_3730 Montia chamissoi_53554 Alluaudiopsis marnieriana_10927 Calandrinia grandiflora_49646 Anredera cordifolia_23373 Lewisia nevadensis_90586 Basella alba_26605 Cistanthe grandiflora_17654 Ceraria pygmaea_12413 Calyptridium pygmaeum_78212 Portulacaria afra_30658 Calyptridium umbellatum_12490 Claytonia nevadensis_58385 Phemeranthus parviflorus_26250 Claytonia virginica_38264 Didierea trollii_28471 Montia chamissoi_37406 Didierea madagascariensis_1735 Decarya madagascariensis_78750 Lewisia nevadensis_26354 Alluaudia dumosa_78655 Calandrinia grandiflora_32493 Alluaudia humbertii_31940 Calyptridium pygmaeum_44340 Alluaudia procera_103776 Calyptridium umbellatum_84000 Alluaudiopsis marnieriana_22231 Phemeranthus parviflorus_55659 Ceraria pygmaea_12555 Suessenguthiella caespitosa_58663 Portulacaria afra_12148 Pharnaceum exiguum_35160 Basella alba_20153 Mollugo cerviana_5372 Anredera cordifolia_33892 Mollugo verticillata_41954 Anisomeria littoralis_13639 Mollugo nudicaulis_172665 Guapira obtusata_55187 Delosperma echinatum_67173 Mollugo pentaphylla_47993 Sesuvium portulacastrum_101731 Anisomeria littoralis_17842 Limeum aethiopicum_16336 Guapira obtusata_49075 Pharnaceum exiguum_17081 Delosperma echinatum_64915 Suessenguthiella caespitosa_47909 Stegnosperma halimifolium_78258 Mollugo cerviana_10046 Limeum aethiopicum_75182 Mollugo nudicaulis_21874 Glinus dahomensis_25363 Mollugo verticillata_168159 Mollugo pentaphylla_48676 Stegnosperma halimifolium_54025 0.03 Beta vulgaris_Bv_027550_qgiu_t1 0.02 FIG. S10. ML trees built in RAxML with GTRGAMMA model based on matK (left) and rbcL (right) genes that extracted from the transcriptome data.
Refereces:
Solís-Lemus C, Bastide P, Ané C. 2017. PhyloNetworks: a package for phylogenetic networks. Mol Bio Evol. 34(12): 3292–3298. Yang Y, Moore MJ, Brockington SF, Mikenas J, Olivieri J, Walker JF, Smith SA. 2018. Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events. New Phytol. 217(2):855–870