SUPPLEMENTARY INFORMATIONArticles https://doi.org/10.1038/s41559-020-1221-7

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The of Prasinoderma coloniale unveils the existence of a third within green

Linzhou Li1,2,13, Sibo Wang1,3,13, Hongli Wang1,4, Sunil Kumar Sahu 1, Birger Marin 5, Haoyuan Li1, Yan Xu1,4, Hongping Liang1,4, Zhen Li 6, Shifeng Cheng1, Tanja Reder5, Zehra Çebi5, Sebastian Wittek5, Morten Petersen3, Barbara Melkonian5,7, Hongli Du8, Huanming Yang1, Jian Wang1, Gane Ka-Shu Wong 1,9, Xun Xu 1,10, Xin Liu 1, Yves Van de Peer 6,11,12 ✉ , Michael Melkonian5,7 ✉ and Huan Liu 1,3 ✉

1State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. 2Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. 3Department of Biology, University of Copenhagen, Copenhagen, Denmark. 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China. 5Institute for Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany. 6Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium. 7Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany. 8School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China. 9Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada. 10Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China. 11College of Horticulture, Nanjing Agricultural University, Nanjing, China. 12Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa. 13These authors contributed equally: Linzhou Li, Sibo Wang. ✉e-mail: [email protected]; [email protected]; [email protected]

Nature Ecology & | www.nature.com/natecolevol

Supplementary Figure 1. The chloroplast circos map of Prasinoderma coloniale.

Supplementary Figure 2. The mitochondrial circos map of Prasinoderma coloniale.

Supplementary Figure 3. The GC depth distribution of Prasinoderma coloniale.

Supplementary Figure 4. The concatenated phylogenetic tree of 19 with 31 single-copy mitochondria gene place Prasinodermophyta (Prasinoderma coloniale) to the sister lineage of other with high bootstrap support (100.0).

Treubia lacunosa 65/- Nardia compressa 100/1 Nothoceros vincentianus 93/1 Phaeoceros sp. 74/- 87/- Takakia lepidozioides 0.05 substitutions/site 100/1 Diphyscium fulvifolium 99/1 Polytrichum juniperinum 78/1 100/1 Physcomitrella patens nuclear rRNA Huperzia selago Equisetum arvense 4646 aligned characters 96/1 90/0.99 Angiopteris lygodiifolia 78/1 Arabidopsis thaliana tree topology: ML (IQTree) 87/1 100/1 Pinus taeda Marchantia polymorpha support values: ML/MrBayes 100/1 Nitella hyalina 85/1 Chara braunii 83/1 Chaetosphaeridium globosum 100/1 Entransia_fimbriata Klebsormidium nitens Coleochaete scutata 54/- 100/1 Cosmarium ochthodes 99/1 Penium margaritaceum 78/0.98 86/1 Netrium digitus 91/1 Mesotaenium endlicherianum 76/0.99 Cylindrocystis brebissonii 99/1 Cylindrocystis cushleckae 75/1 Mesotaenium caldariorum 92/1 Mougeotia sp. viride condensata 89/1 atmophyticus 69/0.99 100/1 Eudorina sp. 100/1 Yamagishiella unicocca 99/1 Volvox carteri Chlamydomonas reinhardtii 99/1 Spermatozopsis exsultans 100/1 Chromochloris zofingiensis 100/1 Hydrodictyon reticulatum Stigeoclonium helveticum 64/- Oltmannsiellopsis sp. 69/1 100/1 Ulva mutabilis 53/- 80/0.98 Desmochloris halophila Ignatius tetrasporus 58/- 99/1 Tetraselmis cordiformis 99/1 100/1 Tetraselmis striata Scherffelia dubia 100/1 Auxenochlorella protothecoides 100/1 Chlorella varibilis 100/1 Chlorella vulgaris 98/1 100/1 Coccomyxa sp. Botryococcus braunii 58/- 69/- Stichococcus bacillaris 100/1 Koliella longiseta 90/1 Pedinomonas minor 100/1 Marsupiomonas pelliculata 98/1 Chloropicon primus Pycnococcus provasolii 100/1 Nephroselmis pyriformis 100/1 Nephroselmis olivacea 100/1 Monomastix sp. Monomastix opisthostigma 100/1 Dolichomastix tenuilepis 99/1 Crustomastix stigmatica Mamiella gilva 55/- 100/1 100/1 Bathycoccus prasinos Ostrecoccus tauri 100/1 100/1 Ostreococcus lucimarinus 89/1 Micromonas bravo 100/1 Micromonas commoda Cymbomonas tetramitiformis 59/- Pyramimonas parkeae 100/1 Pyramimonas olivacea 100/1 Pyramimonas tetrarhynchus 98/1 Prasinoderma sp. 100/1 Prasinoderma coloniale 100/1 Prasinoderma singularis Prasinococcus capsulatus Prasinodermophyta 96/1 100/1 Verdigellas peltata Palmophyllum crassum 70/0.94 Glaucocystis nostochinearum Cyanophora paradoxa 100/1 98/- Cyanoptyche gloeocystis Gloeochaete wittrockiana Glaucoplantae 96/1 Rhodogorgon sp. Sporolithon durum Porolithon onkodes 100/1 100/1 73/1 Ahnfeltia plicata Asparagopsis taxiformis Gracilariopsis chorda 96/1 83/- 81/0.99 Chondrus crispus 60/1 58/0.99 Schizymenia dubyi 100/1 Helminthocladia australis Palmaria palmata 99/1 Bangia fuscopurpurea 100/1 Porphyra umbilicalis 98/1 Porphyra purpurea 81/- Pyropia yezoensis 100/1 Rhodochaete parvula 100/1 Madagascaria erythrocladiodes_ 86/0.99 Compsopogon caeruleus 99 Erythrolobus australicus 100/1 Timspurckia oligopyrenoides Rhodoplantae Porphyridium aerugineum 100/1 Bangiopsis sp. 100/1 Rhodosorus marinus CCMP769 Rhodosorus marinus UTEX2760 Rhodella maculata sulphuraria merolae

Supplementary Figure 5. The nuclear rRNA operon tree of 109 species with 4,646 aligned characters place Prasinodermophyta (Prasinoderma coloniale) to the sister lineage of other Viridiplantae with high bootstrap support (100.0/1). 100/1 Arabidopsis thaliana Pinus taeda 100/1 Nothoceros vincentianus Phaeoceros sp. Takakia lepidozioides -encoded rRNA operon 78/- Huperzia lucidula 57/- Equisetum diffusum 4172 aligned characters 100/1 Angiopteris fokiensis Polytrichum juniperinum tree topology: ML (IQTree) 100/1 64/1 Diphyscium fulvifolium 57/- Physcomitrella patens support values: ML/MrBayes Nardia compressa 100/1 57/- Treubia lacunosa Streptophyta Marchantia polymorpha 100/1 Nitella hyalina Chara braunii Mesotaenium endlicherianum 100/1 100/1 Cosmarium ochthodes Penium margaritaceum 100/1 72/1 Netrium digitus 100/1 Cylindrocystis cushleckae 81/0.99 Cylindrocystis brebissonii 100/1 60/- 100/1 Mesotaenium caldariorum Mougeotia sp. 98/1 Chaetosphaeridium globosum 100/1 Coleochaete scutata 100/1 Entransia fimbriata 0.05 substitutions/site Klebsormidium nitens 58/- 100/1 Mesostigma viride 100/1 Spirotaenia condensata Chlorokybus atmophyticus 100/1 Cymbomonas tetramitiformis 79/- 89/0.98 Pyramimonas parkeae Pyramimonas olivacea 98/1 Pyramimonas tetrarhynchus grade of 100/1 Nephroselmis pyriformis Nephroselmis olivacea Chlorophyta 100/1 Coccomyxa sp. 99/- Botryococcus braunii -/0.96 (unresolved) 100/1 Auxenochlorella protothecoides 100/1 Chlorella varibilis Chlorella vulgaris 100/1 Stichococcus bacillaris Koliella longiseta 99/1 100/1 Pedinomonas minor Marsupiomonas pelliculata 100/1 Tetraselmis cordiformis 100/1 Tetraselmis striata Scherffelia dubia 73/- Stigeoclonium helveticum 100/1 100/1 Chromochloris zofingiensis 100/1 Hydrodictyon reticulatum Spermatozopsis exsultans 100/1 Eudorina sp. 73/1 100/1 Volvox carteri 50/- Yamagishiella unicocca 94/1 Chlamydomonas reinhardtii 86/0.97 Oltmannsiellopsis sp. 100/1 Ulva mutabilis 62/1 Desmochloris halophila 91/1 Ignatius tetrasporus 96/1 Chloropicon primus Pycnococcus provasolii 100/1 Monomastix sp. Monomastix opisthostigma Crustomastix stigmatica 100/1 100/1 54/1 Dolichomastix tenuilepis 51/- 89/1 Bathycoccus prasinos 100/1 Ostrecoccus tauri 100/1 Ostreococcus lucimarinus Mamiella gilva 100/1 Micromonas bravo 98/0.97 Micromonas commoda 100/1 Prasinoderma sp. 100/1 Prasinoderma coloniale 94/1 Prasinoderma singularis 96/1 Prasinococcus capsulatus Prasinodermophyta 100/1 Verdigellas peltata Palmophyllum crassum Cyanoptyche gloeocystis 98/- Glaucocystis nostochinearum 100/1 Cyanophora paradoxa Gloeochaete wittrockiana Glaucoplantae Asparagopsis taxiformis 96/1 Chondrus crispus Ahnfeltia plicata 97/1 100/1 93/1 Gracilariopsis chorda 99/1 Schizymenia dubyi 100/1 63/0.96 Rhodogorgon sp. Sporolithon durum 68/1 100/1 Porolithon onkodes 97/1 Helminthocladia australis 100/1 Palmaria palmata Bangia fuscopurpurea 100/1 Porphyra umbilicalis 99/1 Porphyra purpurea Pyropia yezoensis 100/1 Rhodochaete pulchella 100/1 Madagascaria erythrocladiodes Compsopogon caeruleus 59/0.99 Erythrolobus australicus 86/0.99 100/1 Timspurckia oligopyrenoides Porphyridium aerugineum Rhodoplantae 58/- Rhodella maculata Bangiopsis sp. 100/1 Rhodosorus marinus CCMP769 100/1 Rhodosorus marinus UTEX2760 Cyanidioschyzon merolae

Supplementary Figure 6. The plastid-encoded rRNA operon tree of 109 species with 4,172 aligned characters place Prasinodermophyta (Prasinoderma coloniale) to the sister lineage of other Viridiplantae with high bootstrap support (94.0/1).

Supplementary Figure 7. The coalescent phylogenetic tree of 23 species with 45 single-copy genes using ASTRAL place Prasinodermophyta (Prasinoderma coloniale) to the sister lineage of other Chlorophyta with high support (85.5).

Supplementary Figure 8. The coalescent phylogenetic tree of 28 species with 213 single-copy genes using ASTRAL place Prasinoderma coloniale to the sister lineage of other Chlorophyta with relatively lower support (79.0). In order to increase the number of single-copy genes to construct the phylogenetic tree, we allowed gene absence up to 8 species in one gene family. As for the species, 5 transcriptome data were added including Prasinococcus capsulatus, Cymbomonas sp., Pyramimonas parkeae, Monomastix opisthostigma, Dolichomastix tenuilepis but removed the Ostreococccus sp. RCC809.

Supplementary Figure 9. The concatenated phylogenetic tree of 23 species with 45 single-copy genes using RAxML place Prasinoderma coloniale to the sister lineage of Mamiellales (). PROTCATGTR AA substitution model and 500 bootstraps were used in phylogenetic analysis. The Prasinodermophyta, represented only by Prasinoderma coloniale, was resolved as sister to the Mamiellales (Mamiellophyceae) with high support (81). This artificial placement (i.e. Prasinoderma coloniale diverging within the Chlorophyta) gained high support by bootstrapping (100).

Supplementary Figure 10. Taxon distribution of the best BLAST hits of the P. coloniale genes in the NCBI non-redundant protein database.

calvin cycle

Fructose-6-p Maltose Glucose

2 1 1 1 2 1 1 1 3 2 3 2 2 1 1 1 PGI 2 3 6 2 2 2 2 2 BAM 4 3 3 2 DPE1 1 2 1 1 BAM 1 1 1 1 Glucose-6-p 3 3 1 1 1 1 1 1 2 2 1 2 1 1 1 1 0 0 0 0 3 2 3 3 PGM 3 2 3 2 2 1 2 0 LSF2 4 3 3 3 1 1 1 1 0 3 0 0 Glucose-1-p ISA3 Linear glucans

2 1 1 1 2 2 4 1 AGPase 1 1 1 1 4 3 2 4 1 1 1 1 1 2 1 0 1 2 1 6 ISA3 1 2 1 1 1 2 1 1 2 2 1 1 SEX4 0 0 2 5 1 0 1 0 ADP-Glucose 1 1 1 1 1 1 1 0 2 3 1 1 LDA 0 1 1 1 1 1 2 16 1 7 4 2 2 2 2 1 GBSS 5 4 10 2 1 1 1 0 0 1 0 4 7 3 3 2 AMY 0 1 0 0 0 3 0 0 Branched glucans 0 0 1 1 1 1 1 1 DBE 2 2 2 1 0 0 0 0 PWD 1 3 1 1 3 1 2 2 1 1 4 5 4 3 3 2 BE 0 1 1 3 3 2 4 4 SS GWD 1 2 1 12 4 8 6 4 Starch 2 4 3 3 P. coloniale M. pusilla B. prasinos O. tauri M. viride C. atmophyticus K. nitens Chara braunii 6 7 6 3 2 3 2 1 C. variabilis U. mutabilis C. reinhardtii V. carteri 5 4 8 7 2 3 4 2 C. merolae P. purpureum C.crispus C. paradoxa 1 1 1 1 1 3 1 7

Light Dark Supplementary Figure 11. Reconstruction the Pathways of starch synthesis and degradation in 16algae . Fructose-6-p, fructose 6-phosphate; Glucose-6-p, glucose 6-phosphate; Glucose-1-p, glucose 1-phosphate; ADP-Glucose, ; PGI, phospho- glucose iosomerase; PGM, hosphoglucomutase; AGPase, ADP-glucose pyrophophory- lase; GBSS, granule-bound starch synthase; DBE, debranching enzyme; BE, branching enzyme; SS, Starch synthase; GWD, α-glucan,water dikinase; PWD, phosphoglu- can,water dikinase; AMY, α-amylase; SEX4, Phosphoglucan phosphatase DSP4; ISA3, Isoamylase 3; LSF2, Phosphoglucan phosphatase LSF2; BAM, β-amylase; DPE1, Glucanotransferase (dpe1); LDA, Protein LIMIT DEXTRINASE; the gene copy number of each species is shown in the Supplementary Table 16.

Supplementary Figure 12. Structural Features of KYU and HAAO Protein Domains Constructed by Swiss-Model Homology-Based Approach. a) KYU based on the crystal structure of P. coloniale. b) HAAO domain based on the crystal structure of P. coloniale. c) KYU domain based on the crystal structure of human. d). HAAO domain based on the crystal structure of human. e) KYU domain alignment of a and c. f) HAAO domain alignment of b and d.

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Supplementary Figure 15. The phylogenetic tree of NNP (nicotinate nucleoside pyro- phosphatase) based on IQ-TREE method, using the best model predicted by IQ-TREE with 5000 replicates. The important bootstraps are highlighted by the red color. JA T62665

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0 lular 0000308 S 0.1-Can g-pr 2866.1-

-

llular proteob 6 -cellul purpur i-g- 582.1-S EDQ8673 um-ce 1-g- 7 0 nculture deum iopsis cho andida TDX16 EGD7537 3 obia bacter 8 rine Gro bia bacter 2712- .1-San Chondr 7 pure ia sulph 8 ryarch bacteria lata-cel 8 GNS bacter T23O DICDI-ce idium olae strai sis-g- ii B1 7 s bacterium

sum-ce 0 cterium UM4b- 4 s-GNS bacter yticus-g- PRCOL acleodi Halian didatus Hei

S um discoi 6 tus Poseido -cyanob m lacteum oran

140.1Gracila- r 7 . d archae

ium pur 1 1 daraci rphyr 1 Galdier aeota arcuph II euryarcha

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p ium

E ranea menen ium 13 2 20 -GNS bacter Q55DB4.1- s gium cel

n r ia eria fascic subglobu o gium och

h mosteliu h - acteria verru -ver 005712786.1- lla aestuar monas m y .1-Dictyosteli C 3.1-Po us amylol naceae ba schyzon mer g ia on MedD XP ia theta CCMP ieghe 28900.1- r mdall rucom o niales ar 3.1-Dictyostel Cavend rina xia comicr PXF4 m aeon- 646217 s mediter lulosum Altero niradi EME llard y ia raceum CM 55 10- XP cytostelium 849303 x 77.1-T archae yanidio icrobia shewane a eote-ar Sali Idioma obia EGC3179 s CM-OCT archae KAA cterium chaeon omona a

6581.1- l -d-

i

513.1-A n KYQ889 .1-Ali EGG21340.1- 19.1-C -d- ota archae

a proteob chaea 412.1-Gui Alter - verr

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b

a XP obia

c

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i

a

ea Proteobacteria

Tree scale: 10

Supplementary Figure 16. The phylogenetic tree of TDO/IDO (Tryptophan-/ Indoleamine 2,3-dioxygenase) based on IQ-TREE method, using the best model predicted by IQ-TREE with 5000 replicates. The important bootstraps are highlighted by the red color. Viridiplantae

ts

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s XP t ants

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C 5 runus yed nd plants XP KAB121230 w 0 XP E u plants PTQ4120 9 icrob 0 KHG2290 k 015892 PON8812 9 8 024400 a Strep

4 XP 5 6.1-Pa

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rella a

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l cteria - bacteria -land 5.1-Zea -land a l 940.1-E

2 e-lan a REG1064 reum n ella sor -land

3 n us sp.-d-p -CFB oup bacter pha- land pl -ver Streptop d 4.1-T a-lan 1 d roteoba roteoba tens-lan crobiu

62.1-Le 3 1264.1- p proteo 877280 moda Gre plants Cyanobacteria p plants roteoba 0 -land d plants l Streptop plants a cteria l rebou okinian lla-Gr a 0 29313.1- GAP105 n rhabd d plants CFB gr iolicum n 8.1-Pe A 018729 ants t KAE philus osh WR81412.1- s cidimi nse-a- t PWZ2857 cta-d-p s-a-p vilinea A TKY7 TDW80138 plants s GAP153 d plants hyta R XP PRCOL K xia sp.-Gree een algae PSS itskevichiause sp.-a-p 62.1-B loline a-Greeen algae proteoba ia saccharol hyta Picro m fumar cteria yntropho patname REG3101 49.1-Lo a submar Methyla tella ere AGI39255.1- .1-Lar ellili 0000027 atus-a- tumefacien acteria ia n algae la sp. CF465- iphilu cyanoba nea caldi Gillisia methylosin TDY45 kinella ngilin n algae 1504.1- cyanobacter 7.1-Ar ytica-GNS 74.1-S Stigma The ina- nobactera 3-RA 07725.1- um visakhus gema m -cyanob 0315A- r 222.1-A sp. BK230ea- arvor acterium NUN1- moclostr changi fistulae-GNGNS Sbacteri ethylacid SMD3 3526.1-817.1-M .1-Niastel orph rdhii cteria 0550.1- grob obacteri licyclob um geph VVM 7122-cya ABQ171 idium GBF1 yzae-GNS bacteria OPY008 hodovul stercorar CFB gr forme CC cyanoba 1009.1- RKS5 540.1-M epidam um sp. UHCC m-cyan 98.1-De acillus sacch TDX60SEU0 T ica PCC yra-d bacteriaa 250.1-A isporu 9414- ia ium subTepidi oup bacte bacteriar TCQ40123 584.1-R nktothrix aga halococco -pro TFE76 osperm bacillu teobacteri 1367.1- na cylindr AFD00 sp. stercorar ari- TCV49 .1-Pla ostoc flagelli um ovagenal CCY oteobacter ides mccar firmicu TDX32 Dolich 845.1-M s sp.-firmi ia TCT1 nabae micutes TCO95707 a rysospoiar spumi sp.-a-pr AFZ33 ethanoce tyi BA ium- tes 1114.1-N ides-fir cutes cutes GCL34165 dular firmi 794.1-S .1-Chthon V1- firmicu 876.1-A zobium ia lla conr AUB4QEI40267.139.1-C- h esentero tanier GNS bactertesi eorhi KTB4 iobacter AFZ57 10.1-No s aureuscutes- oteobacter 8801.1- ia cyanosph adii HZ2 100 g-pr flavus-ver CEJ468 223.1-N

7

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4

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9

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icrobi . Paen

4 8 rovide Geobacter igigne cyanoba 4 . TDV92 ns-GNS ba a 1 QBS061007.11 - oteobacter sulfurre cteria 79 38.1-P a-pr 45.8 TDP1 bacteria ducens- cteria 99.8 TCT368 rthaii- GCL65016 a d-pr 98.9 bium ba flavus-actino .1-Aqu oteobacter obacteri ALL62 abacteri 91.4 phingo yces albido 73-actin 925.1-P 12.8 arab um pictum ia 82.1-S Ac-25 urkholderia -b-p treptom acteria cariben roteoba 89.6 TDN847 a sp. VKM sis-b- 168.1-S ibbell -actinob VDY1 proteoba cteria 60.3 .1-Kr la oryzae 8510.1- 97.9 PWW71 cteria Thiomonas sp. CB2- cteria ctinophytoco s-a-proteoba 92.7 TDW75968 b-proteobacter 100 056.1-A trophicu ia 77.4 TDV55 raeibacter diazo RMG6507 82.9 76.6 0.1-Chl 81.7 oroflexi 79.9 97.893.4 acteria bacterium 65.5 762.1-Oha proteob -GNS ba 57.6 96.3 TDP87 m sp.-a- 45.6 cteria 95.5 96.2 66.8 hizobiu 96 97.8 728.1-R 89.3 78.834.1 TDP21 73 26.465.1 99.8 75.7 100 96.8 proteobacteria 96 285.1-Variovorax sp.-b- 99.5 100 TCM34 99.2 81.8 99.5 98.1 95.799.5 100 99.8 27.8 9147.471.46798.2 SFE46845.1-Acidovorax wautersii-b-proteobacteria KleflGAQ84280.1 92.9 57.367.4 89.7 TDN435 80.6 34.1-Azoarcus indigens- 99.8 TCT021 b-proteobacteria 87.7 30.1-P SFV1 aralcaligenes ureilyticu 89.2 3352.1- s-b-p 99.9 Massili roteobacteria 65.6 83.3 94.3 TDS44 a namucu 74.6 98 286.1-N onensis- 44.4 86.747.9 85.6 b-pr 12.3 95.4 ovosphin oteobacter 14.3 56 35.2 75.5 gobium ia 90.7 55 98.6 96.8 97.3 97.3 sp. GV01 98.7 1-a-proteo 94.7 bacteria 5.34 92.1 100 95 100 100 9

7

.

3 100 ALI3464 99.4 99.1 GBL4141 2.1-Can didatus Nitr

6 92.8 . 2.1-Nitr 85.1 RAS3

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e p bacteria 3 879.1-T cteria Strep odococcus op nse-actin ium- t robiu ycolicib d tobacteria cteria .1-Meso

. - c a flocculi- sa DSM 41 gi-CF s-d-p 1 357.1-C -CFB s TDW45491 a ensis- linea sub nensis- Eukaryota rans- - -CFB u a TIC90070 PFG1497 b m sacchar FB gro n r o annhe icoletell B grou c a

e

h 746.1-M 62.1-Rh t 71091.1- c estudiniba group ba sp. PhB15 ix hazakensi i

a o kyonggie philum roteoba FB gro x r cricetiba CFB gr

e sp. CNZ285- ricetiba up bacteria io indicu e bacterium p GNS bacteri obia bacter o marin 26-CF PKV - p bacteria imia ha

m n

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n v ucomicr um thalpo i sulfovibr 2 emolytica athayibacter llum al t rmosp o

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c

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5

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Tree scale: 10

Supplementary Figure 17. The phylogenetic tree of AFM (Arylformamidase) based on IQ-TREE method, using the best model predicted by IQ-TREE with 5000 replicates. The important bootstraps are highlighted by the red color. AEM

71 XP

ADV4 129.1-M 018275

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r ckettsiales endo 814.1-M s DSM 132 s campestri l e setta-choan onas mar e

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vorans- - symbion PZR31 e s inosum- hizoctonia ypsizygus ma als ilitaris- 1 37-CF n arus-

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4 901.1-A c t of 16823- enense- 7027.1-

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proteob 99.3 4.1-Can minis- a 93.8 ABW006 1227.1- uganela sp. HH101- a didatus Hei d-pr acteria 100 T3-D oteobacter 100 BBN8 ganell obacteri mdall 85.1 E7VP 97.2 archae 87.690.1 100 9 ia . 81.1-Du 16.1 7.54

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cteria 7 ADP7 ospora A0A2G1C5A2- . ctinobacter 98.7 7786.8 3 88.3 4505.1- ocarp Rhodo 9 45 ra sp. L5-a GER5980 bacteraceae ADB3 9.1-Acr acteria 3.1-Ulvi 82.7 onospo bacter ma 90.6 icrom -actinob rinus- 100 100 86.5 GER9823 a noduli CFB group bacter 9 9.22 867.1-M 9 nospor a ia 95 38.4 . obacteri 100 8 ADU08 cromo 87.627.7 xaci-actin 99.9 0.1-Mi ora tara 95.6 94.8 95.8 A0A3E0PFD8-A 74.2 55.1 RAO1896 Micromonosp cidobacteria 99.6 79.7 100 23.4 99.9 TWG16214.1- 98.846.375.9 93.939.3 99.9 100 92.7 37 88.1 100 94 100 13.995.5 98.9 99.9 71.2 97.5 bacteria 100 m-d-proteo 95.2 ngium cellulosu 47.1 4089.1-Sora 9 56.4 AUX2

5

. acteria 9 VUF10601.1-Methylobacterium dankookense-a-proteob 92.4 71.378.6

9 TWB12400.1-Nitr . ospirillum amazonense-a-proteob 8 acteria 9 KPI095 47.1-Actinobacteria bacteri um OK006-actinobacteria 74.8

86.7 84

94.5 99 99.9

85.995.9 A 96.2 YM52426.1-C 86.488.6 83 orallococcus sp.-d- VTR08 proteobacteria 72.3 544.1-C 95.8 99.9 lostridioides dif

41.2 COS1984 ficile- 95.1 firmicu 41.5 4.1-Str tes 98.4 91.8 100 eptococcus pne 99.9 96 VVE 82.3 56.3 100 92.3 STQ974081818.1- 88.1 95 umoni 98.4 100 Pand 98.9 99.5 14.9 8.1-Janthi ae-fir 93.2 oraea 99.4 27.672.2 micutes 98.284.1 79.3 6 89.7 nobacter sputorum lebsormidium nitens 91.6 4 KleflGAQ88986.1-K . 100 2 Cocsu628 midium nitens 100 ium livi -b-proteoba 589.1-Klebsor 100 75.1 KleflGAQ86 midium nitens 60.3 55-Co dum- cteria

lebsor 8 KleflGAQ79 . b-pr 065.1-K 94.3 99.8 um nitens 53.4 97.6 7 96.4 ccomyxa sube oteobacter 88.2 KleflGAQ89 midi 9 lebsor 69.1 96.8 Pp3c8 39 um nitens 10053.1 515.1-K 100 100 37.9 579.1-K ia midi 100 99.9 lebsor 78.6 KleflGAQ81 hyta 97.3 99.5 llipsoi 97.3 60V3.1.p-lebsor 238.1-K Streptop 73.6 dea KleflGAQ86 scicola- eptophyta 100 midi a-Str 100 99.1 Por loea mu um nitens 99.3 phyrid um nitens pirog a muscicol midi um nitens 100 21107-S ogloe midi s 99.7 ium pur 0071S Spir lebsolebsor r ChocrPor6 u SM00 12104- 828.1-K m755- pure 0032S 010.1-K des 574-C um SM00 us atmophyticu llata 100 PRCOPorL u Porphyra umbilicalis KleflGAQ89 9 hondr fii 8 m4969 95.5

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Supplementary Figure 18. The phylogenetic tree of KMO (Kynurenine 3-monooxy- genase) based on IQ-TREE method, using the best model predicted by IQ-TREE with 5000 replicates. The important bootstraps are highlighted by the red color. a

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8 AGU681 nas muscar stids 17.8 loides- 84.8

li-kin 9 100 acteria . 0026286rchang etoplastids 4 19.1-A um- WP proteob ngom kinetopla 99.8 151.1-A yxococcus maccoccusr coral onas desou 100 rallo AGU6822 stids A91 48.1-M tiaca-d- ia 99.9 KF 8.1-Str zai-kine 100100 99.6 18.1-Co a auran ESL0 igomo toplastids 96.2 AEI627 tigmatell d-proteobacter 8559.1- nas galati- 97.3 20.687.7 0143937 99.4 nutum- Trypan kinetopl 85.5 WP 68.1-S osoma r 97.5 ium mi angeli astids 98.4 SC58-ki 91.5 0026155 Hyalang XP 00931 61.2 WP bacteria 1906.1- netoplastid 89.7 3890.1- proteo 99.6 100 ia Trypan s 38.375.5 inis-d- osoma gr 96.8 100 KFE6 ayi-kinetoplastid onas sedim CFB group bacter

s 100 99.4 2588- 64 99.6 nsis DSM 90.2 736.1-Bradym 85.8 TDP75 aga pine PRCOL 100 98.7 56.3 hitinoph 0000308 93.1 645.1-C 4-RA 100 93.7 acteria -left part 35.4 ACU58 -cyanob 85.956.9 48.5 97.813.3 93.4 dea VB512170 100 92.285.6 llia byssoi 88.1 6

99.2 . PRCOL 99.1 62.8 6.1-Hassa ia

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62.1 97.6 ia ABW202 99.9 100 EUJ263 64.1-A

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Tree scale: 10

Supplementary Figure 19. The phylogenetic tree of KYU (kynureninase) based on IQ-TREE method, using the best model predicted by IQ-TREE with 5000 replicates. The important bootstraps are highlighted by the red color. al

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2 950.1-A faveolata-ston ls . XP TPX4 yzae 70- 4 cropo als 9 1076.1- 8.1-Y ta-fungi ra mil 98.5 002843 aria or XP lepor y corals XP scovopsis web 020891 a-stony cora 99.5 92 TPX6 817487 yricul ia pustula DJ-fungi XP 004993 982.1-E 31.9 KAE 46.1-E xaiptasia ls 70.5 bilicar E-fungi 644.1-Salpin pallida 501.1-P ngipes B goeca ro 98.5 bicolor setta-choan -anim 78.5 1.1-Um lara lo 46.2 KOS186 al 85.3 34.3 oflagella 7679.5 003718 tes-Opisthokon 91.2 76 XP 1.1-Chayaloscypha e-fungi ta 92.4 KAA641563 roma 84.785 95.9 99.7 938149908.1-H 93.4 ium theob 78.399.6 KAE gi 98.4 024728 79.2 XP atobasid PRCOL 93.1 ides-fun 00003084-RA 89.3 86.6 -right part 85.9 4.1-Cer la torulo 64.6 88.1 559319 odotoru um f. sp.-fungi 38.5 KAB 13.1-Rh m oxyspor PRCOL 00003084-RA 90.7 99.9 usariu GEM087 488.1-F 100 031053 gensis-fungi 55.7 XP 95.4 99.7 91.7 oniella shandon 97.7 3.1-Kw fungi 98.7 51.6 552813 la imperatae- 92.1 KAA 99 021867721.1-Kockovael 73.494.6 XP 56.2 94.5 58.993.7 KAE8540889.1-Cryptococcus cf. gattii-fungi 91.8 95.3 97.9 73.994.7 90.1 89.6 17.991.5 AUB23137.1-Cryptococcu 93.8 87.6 s neoform 87.787.8 ans var. grubii-fungi 94.8 63.5 88.7 97.2 90

5

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Tree scale: 10

Supplementary Figure 20. The phylogenetic tree of HAAO (3-hydroxyanthranilate 3,4-dioxygenase) based on IQ-TREE method, using the best model predicted by IQ-TREE with 5000 replicates. The important bootstraps are highlighted by the red color. ASS

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Tree scale: 10

Supplementary Figure 21. The phylogenetic tree of ACMSD (amino-β-carboxymuco- nate-semialdehyde-decarboxylase) based on IQ-TREE method, using the best model predicted by IQ-TREE with 5000 replicates. The important bootstraps are highlighted by the red color.