Sup. Fig. 1 Homogentisate phytyltransferase A | ResearchGate

A

&# "$( !"# '& %" #% $+ "$+ %"!!

Euglena gracilis ELL00000505 Ectocarpus siliculosus CBJ48519 Phaeodactylum tricornutum XP_002182033 Aureococcus anophagefferens Auran1_67156 Bigelowiella natans Bigna1_75563 Cyanidioschyzon merolae CMN202C

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Galdieria sulphuraria Gs32880 Cyanothece sp. PCC 7425 ZP_03140811 Anabaena variabilis ATCC 29413 YP_323974

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Acaryochloris marina MBIC11017 YP_001518835 Gloeobacter violaceus PCC 7421 NP_923229

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Synechococcus sp. JA-3-3Ab YP_475205 Chloroflexus aurantiacus J-10-fl YP_001637001 Chloroflexus aggregans DSM 9485 ZP_01515872 Ostreococcus lucimarinus XP_001416140

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Micromonas pusilla CCMP1545 EEH60766

Volvox carteri Volca1_45120 '' %"!! Zea mays NP_001105877 $* $% Oryza sativa Japonica Group NP_001058260 %"!! %"!! Arabidopsis thaliana NP_849984 Oryza sativa Japonica Group NP_001058202 ## "'(

Physcomitrella patens XP_001752307 #! ))

Thalassiosira pseudonana XP_002293015 Bigelowiella natans Bigna1_53372 Galdieria sulphuraria Gs34090

(# "$$

Micromonas sp. RCC299 XP_002501436 Micromonas pusilla CCMP1545 EEH56619 Ostreococcus tauri CAL53411 Ostreococcus lucimarinus XP_001418412 Chlamydomonas reinhardtii XP_001695341

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Volvox carteri Volca1_78084 Physcomitrella patens XP_001764199 Arabidopsis thaliana NP_001078138 Oryza sativa Japonica Group NP_001060083

Sup. Fig. 1 Homogentisate phytyltransferase

Eubacteria

Green plants

CR+Red

B Euglena Ectocarpus Aureococcus Phaeodactylum Bigelowiella Cyanidioschyzon Galdieria Ostreococcus Micromonas Volvox Oryza Zea Arabidopsis Physcomitrella Acaryochloris Cyanothece Anabaena Gloeobacter Synechococcus Chloroflexus

154

LAAGLALVPL LLAGAVL--LAGAALL--LFGSLWL--LIAGLLI--LLGSFSL--GSLGLIL--CSSSVIC--TTSSLVL--AGVSVWI--LIMSIAI--AAMSFGL--SIMSFWL--AAVSVGM--GLLALGL--GVVALLI--GILALAL--GVAALVI--GVASILL--LVIALT----

VYAQVAALQP ----GLAPCS ----GCDAR----GAANPV ----GFLPG----GFWLP----GLVLP----GTL------GMM------GVA------GIR------GWA------GWI------GFY------SA-------AA-------AW-------A--------AL-------GAA---

FATPALQATL LGSPGLALTV LGSEPLRRVL FSTQGLNVAL VTTAPLQFTL QSTAALRFAL KTSVPLIGTL TQSFHLLTTL SGSSALLWAL SGSCALLTTL SKSAPLLCAL VGSQPLFWAL VGSWPLFWAL VESPPLLWAL IQGYRLLWTV WEGPFLLATV LNGPYLFGMV LQNLYLFATV TGIPYLLLTV VLSTALLITV

VGSALLGTVY ILSVLIGTVY LGSALLGFAY WGSGILGTMY VASGLLGTLY VASCILGTLY FGSTLLGSMY VLSLLLGVIY VLSLILGIVY LVSLVLGVLY FISFFLGSAY FISFVLGTAY FVSFMLGTAY LVSLVLGTAY GLSMLMGTVY GSSLIIGTAY AVSLAIGTAY AASVLIGTAY LLSNGIGTAY SVIALIGSLY

194

S--LPPFRLK S--LPPFRLK S--APPLRLK S--LPPFRLK S--LPPFRFK S--LPPIRLK S--IPPIRLK STDFKLLRWK SVDYPGLRWK SVELPFMRWW SVDAPLLRWK SINLPYLRWK SINLPLLRWK SADLPFLRWK S--IPPIRLK S--LPPVRLK S--LPPIRLK S--LPPLRLK S--LPPLRLK S--LPPLRLK

Supplementary Fig. 1 Homogentisate phytyltransferase (continued)

Euglena gracilis ELL00001748

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Phaeodactylum tricornutum XP_002183277 Ectocarpus siliculosus CBJ32509 Guillardia theta (nucleomorph) XP_001713221 Hemiselmis andersenii (nucleomorph) XP_001712502 Galdieria sulphuraria Gs01960

'( "((

Cyanidioschyzon merolae CMK184C Arabidopsis thaliana NP_563947 Vitis vinifera XP_002277007 Sorghum bicolor XP_002465783 #% "(&

Oryza sativa Japonica Group NP_001049109 Ostreococcus tauri CAL50118

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Ostreococcus lucimarinus XP_001415465 Volvox carteri EFJ47475 Gloeobacter violaceus PCC 7421 NP_924422

Acaryochloris marina MBIC11017 YP_001517405

Nostoc punctiforme PCC 73102 YP_001865214 Prochlorococcus marinus str. MIT 9313 NP_895197 Synechococcus sp. RS9916 ZP_01470773 '' $$ Synechococcus sp. CC9902 YP_377787 Prochlorococcus marinus CCMP1375 NP_875692

Sup. Fig. 2 Hypothetical protein


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Emiliania huxleyi Emihu1_464599 Ectocarpus siliculosus CBN76574 *$ "%$

Thalassiosira pseudonana XP_002287250 Phytophthora infestans T30-4 XP_002894798 Emiliania huxleyi Emihu1_215366

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Monosiga brevicollis MX1 XP_001750338 Galdieria sulphuraria Gs04750 (& "$&

Cyanidioschyzon merolae CMO276C Ostreococcus tauri CAL52094 Ostreococcus lucimarinus XP_001416380 Micromonas pusilla EEH58649

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Micromonas sp. RCC299 XP_002502426 Acaryochloris marina MBIC11017 YP_001514540 Arthrospira platensis str. Paraca ZP_06381313 Microcoleus chthonoplastes PCC 7420 ZP_05027383 Anabaena variabilis ATCC 29413 YP_321452 Synechococcus sp. JA-3-3Ab YP_475536 Cyanothece sp. PCC 7425 YP_002481374 Methylacidiphilum infernorum V4 YP_001940654 Chloroflexus aurantiacus J-10-fl YP_001636779 Gallionella capsiferriformans ES-2 ZP_04832094

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Gloeobacter violaceus PCC 7421 NP_924115 Allochromatium vinosum DSM 180 YP_003443295 Acidobacterium capsulatum ATCC 51196 YP_002755328 Geobacter bemidjiensis Bem YP_002138811

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Nitrosomonas europaea ATCC 19718 NP_841726 Francisella tularensis YP_513177 Thiobacillus denitrificans ATCC 25259 YP_315820

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Dechloromonas aromatica RCB YP_283819 Azoarcus sp. BH72 YP_933304 Azoarcus sp. BH72 YP_933817

Sup. Fig. 3 Glucokinase

A


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Hemiselmis andersenii (nucleomorph) XP_001712441 ,, "'* Guillardia theta (nucleomorph) XP_001713562

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Galdieria sulphuraria Gs32500 Cyanidioschyzon merolae CML155C Phaeodactylum tricornutum XP_002182335

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Thalassiosira pseudonana XP_002292583 Aureococcus anophagefferens Auran1_32730

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Ectocarpus siliculosus CBJ26347 Emiliania huxleyi CCMP1516 Emihu1_436915

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Chlorella vulgaris NP_045839 Pedinomonas minor ACQ90835 Ostreococcus tauri YP_717211 Pycnococcus provasolii YP_002600868 &' Marchantia polymorpha NP_039323 "&) Physcomitrella patens NP_904176

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Zygnema circumcarinatum YP_636469 Chaetosphaeridium globosum NP_683797 Bigelowiella natans YP_778602 $% "&'

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Synechococcus elongatus PCC 6301 YP_172283 Prochlorococcus marinus str. MIT 9313 NP_894147 Synechococcus sp. WH 8102 NP_897742 Crocosphaera watsonii WH 8501 ZP_00514880 Arthrospira sp. PCC 8005 ZP_07157112 Gloeobacter violaceus PCC 7421 NP_926712

Nostoc punctiforme PCC 73102 YP_001864661

Sup. Fig. 4 Clp peptidase, proteolytic subunit

B

153 Euglena S R Guillardia(nm) S R Hemiselmis(nm) S R Cyanidioschyzon S R Galdieria S R Thalassiosira S R Phaeodactylum S R Aureococcus S R Emiliania S R Bigelowiella(pt) S R Chlorella(pt) S R Pedinomonas(pt) A R Pycnococcus(pt) A R Ostreococcus(pt) C R Chaetosphaeridium(pt) A R Zygnema(pt) A R Physcomitrella(pt) A R Marchantia(pt) A R Synechococcus S R Prochlorococcus S R Crocosphaera A R Synechococcus S R Gloeobacter S R Nostoc S R Arthrospira A R

QQ IMI IMI IMI VM I VM I IMI TM I VM I VM I V L L I MV IMI VM I VM I VM I VM I VM I VM I IMI IMI IMI IMI IMI IMI IMI

HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ HQ

P MG G A - - Q GQ P MG G A - - Q GQ P MG G A - - Q GQ P L G G A - - Q GQ P MG G A - - K GQ P MG G A - - Q GQ P MG G A - - Q GQ P MG G A - - Q GQ P MG G A - - R GQ P I MQ V - - S G Q P E G G S - - Q GQ P E G G S - - Q GQ P E G G T - - R GQ P Q G GM- - E GQ P S S S Y - Y K DQ P A S S F - Y E GQ P A S S Y - Y D GQ P A S S Y - Y D GQ P LGGT - SR RQ P L G G T - NQ R Q P LGGT GGR RQ P LGGT - GR RQ P L G G A - - Q GQ P S G G T - - R GQ P L G G T - - R GQ

ASD I KV E ASD I EV E ASD I KV E ASDLKV E ASD IQV E AQ D I K V E AED I KV E AED I KV E AED I R I E ASD I L I E AS EV L S E AS EV L S E AS E I I Y E AS EVV L E AGE L IME A G E CM I E AGEC IME AGEC IME ASD I E I E ASD I E I E AT D I E I E ASD I E I E AT D I G IQ AT D I E I E AT D I E I E

AQQ AQQ AQQ A EQ ARQ A AQ A AQ A AQ A EQ S E E SQ E S E E SV E K E E AE E AE E AE E AE E AR E AR E ANE AK E AK E AR E AK E

KSLTED I LR I R I LK I R I LR I R I LR I R I LR I K I MR I R I MR I R I I R I K I LK I K I LR LR VMR I R V LR I R I LR LR I VR LR V LK LR V LK LK V LK LR V LK LR I L R MK I LR I K I LR I R I LR I K I LYT K I LR I R I LR I R

K S L K S L K S L DA L E S L DN L DN L ENL RQ L R I L RQV RQV RQV R L I DC I DC V DY I DC I EM L DM L AQ L K L L DR L HQ L KV L

T E D Y A E MT WT T E DY A EM S GR T E DY AQMT G R T Y E Y S K MT GQ V R D Y C NM T GQ V K MY S M F T GQ V K S Y S MM T G Q V K L Y A MM T G Q V G L Y S T MT GQ T K I Y I E N I DQ G R I Y S E R T GQ G R I Y A E K T GQ G L L Y AQ R T GQ G R L Y V D L T GQ T K V Y VQR T GK T K V Y MQ R T G K T R V Y VQR I GK T K V Y VQR T GK N R S L S DM S GQ N H S MA E L T GQ NQ L L A DQ C GQ NQ I M A D R T GQ NQ I L S E R T GQ N G I Y A D K T GQ N E M L A E R S GQ

Supplementary Fig. 4 Clp peptidase, proteolytic subunit (continued)

197 T L SY PY PY PY T T TQ TQ TQ T I T L P L S I P L P I PM P L P L S F S F S L P L P L T I T L

Euglena gracilis AAX13964

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Guillardia theta AAX13960 Thalassiosira pseudonana XP_002289281

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Phaeodactylum tricornutum XP_002186456 +$ &"!!

Odontella sinensis CAA69902

Heterosigma akashiwo ABQ42600 '% "))

Vaucheria litorea AAK21910 Prymnesium parvum AAX13966 Pavlova lutheri AAX13959 Oryza sativa Japonica Group NP_001047825 Arabidopsis thaliana NP_174486 Physcomitrella patens subsp. patens XP_001771011

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Ostreococcus lucimarinus CCE9901 XP_001417260 Micromonas sp. RCC299 XP_002508184 Chlamydomonas reinhardtii XP_001694038 Volvox carteri Volca1_104265

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Galdieria sulphuraria CAC80070

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Chondrus crispus AAX13965 Cyanidioschyzon merolae CMF117C

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Thermosynechococcus elongatus BP-1 NP_682704 Acaryochloris marina MBIC11017 YP_001519202 Trichodesmium erythraeum IMS101 YP_723190 Anabaena variabilis ATCC 29413 YP_321300 Synechococcus sp. PCC 7002 YP_001735897 Synechococcus elongatus PCC 6301 YP_171277

Sup. Fig. 5 Phosphoribulokinase

## ,,

Euglena gracilis ELL00002525 Perkinsus marinus XP_002767872 Perkinsus marinus XP_002773802 Bigelowiella natans Bigna1_55893 (% "%& Bigelowiella natans Bigna1_155784 Thalassiosira pseudonana XP_002292246 &' "%' Micromonas sp. RCC299 XP_002500082 Ostreococcus tauri CAL54718 Bigelowiella natans Bigna1_141201 +( Emiliania huxleyi Emihu1_436447 "%% +( Emiliania huxleyi Emihu1_416249 "&# Physcomitrella patens XP_001761713 Populus trichocarpa XP_002308712 Arabidopsis thaliana NP_196643 %) Arabidopsis thaliana NP_197886 $" (% Populus trichocarpa XP_002309684 "%( Arabidopsis thaliana NP_178089 &( $" Oryza sativa Japonica Group NP_001057012 %' Oryza sativa Japonica Group NP_001053217 $" Physcomitrella patens XP_001777977 (( Arabidopsis thaliana NP_200297 "%) Oryza sativa Japonica Group NP_001042562 (% Phytophthora infestans T30-4 EEY58118 $"!! &+ Phytophthora infestans T30-4 EEY53200 (( $" Phytophthora infestans T30-4 EEY60273 "%( Tetrahymena thermophila XP_001019413 Paramecium tetraurelia d4-2 XP_001444200 Chlamydomonas reinhardtii XP_001691336 Chlamydomonas reinhardtii XP_001699010 #$ "%! Zea mays NP_001151432 Oryza sativa Japonica Group NP_001059000 Populus trichocarpa XP_002314687 &% $" %' Arabidopsis thaliana NP_565734 $" Physcomitrella patens XP_001781346 Physcomitrella patens XP_001778772 %! &* Ostreococcus lucimarinus XP_001418597 $" $" Ostreococcus tauri CAL54316 Micromonas sp. RCC299 XP_002501584 &$ Phaeodactylum tricornutum XP_002182346 $" Thalassiosira pseudonana XP_002286929 () "%# Ectocarpus siliculosus CBN78031 Cyanidioschyzon merolae CMN318C #$ Synechococcus elongatus PCC 7942 YP_399216 "%& #' Crocosphaera watsonii WH 8501 ZP_00518975 "() Anabaena variabilis ATCC 29413 YP_321756 Acaryochloris marina MBIC11017 YP_001517415 !"#

(% "%+

Sup. Fig. 6 Folate-biopterin transporter

;4U3-8,!U6,0737B!;FF!!!!&@?%

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;5737,87,!+4
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Euglena gracilis ABF68597

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Emiliania huxleyi Emihu1_229121

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Emiliania huxleyi Emihu1_417528 Guillardia theta ABF68595 Phaeodactylum tricornutum XP_002176527

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%$Lingulodinium polyedrum ABF68596 Aureococcus anophagefferens Auran1_28857 Ectocarpus siliculosus CBN74703 Bigelowiella natans AAP79192 $% "&%

Oryza sativa Japonica Group NP_001049664 Arabidopsis thaliana NP_190973 Physcomitrella patens XP_001772678 Chlamydomonas reinhardtii XP_001690872 Volvox carteri Volca1_103791 Ostreococcus lucimarinus XP_001416538 Micromonas sp. RCC299 XP_002505568 Galdieria sulphuraria Gs54210

%# '"!!

Porphyra yezoensis ABF68598 Cyanidioschyzon merolae CMO245C Arabidopsis thaliana NP_201243 Oryza sativa Japonica Group NP_001058297 Physcomitrella patens XP_001768187 Bigelowiella natans Bigna1_73754 Ectocarpus siliculosus CBN76290

Sup. Fig. 8 FBPase, plastidic

Euglena gracilis ABF68600

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Aureococcus anophagefferens Auran1_23344 () '"

Emiliania huxleyi Emihu1_434018 Phaeodactylum tricornutum XP_002184240 Thalassiosira pseudonana XP_002288820

(( "%% +! "%*

Aureococcus anophagefferens Auran1_31061 Bigelowiella natans Bigna1_85805 Phytophthora infestans T30-4 EEY61702

+' "%%

Monosiga brevicollis MX1 XP_001746201 $$ "%*

$$ ")!

Aedes aegypti XP_001658173 Nematostella vectensis XP_001626835 Branchiostoma floridae XP_002246331

+# "%)

Ciona intestinalis XP_002124545 Galdieria sulphuraria Gs02220

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)* "%* )% '" (( '"

Chondrus crispus ABF68601 Porphyra yezoensis BAG09539 Galdieria sulphuraria Gs13870 Cyanidioschyzon merolae CMP129C Dictyostelium discoideum AX4 XP_646323

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Lodderomyces elongisporus XP_001526399 Ustilago maydis 521 XP_758850 && '"

Arabidopsis thaliana NP_175032 Oryza sativa Japonica Group NP_001044906

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$$ "%& $$ "%&

Physcomitrella patens subsp. patens XP_001751507 Micromonas sp. RCC299 XP_002506051 Peranema trichophorum 00138 Guillardia theta ABF68599 Tetrahymena thermophila XP_001007592

Sup. Fig. 9 FBPase, cytosolic

Euglena gracilis BAG32441

86 1.

0.2

Peranema trichophorum BAG32442 Phytophthora infestans AAL76320 Phytophthora sojae Physo1_1_108585

60 .93

Laminaria digitata CAB61332

79 1.

Phaeodactylum tricornutum XP_002179525 Thalassiosira pseudonana XP_002289820 Bigelowiella natans Bigna1_56762 51 .73

Spinacia oleracea AAK51690 Oryza sativa Japonica Group NP_001056586

-.97

72 .99

Arabidopsis thaliana NP_186885

Zea mays NP_001104910 Selaginella moellendorffii EFJ26095 64 .99 88 1.

97 1.

97 1.

Physcomitrella patens XP_001770880 Arabidopsis thaliana NP_198982 Spinacia oleracea AAK49897 Zea mays ACG41643 Oryza sativa Japonica Group NP_001067912 Ostreococcus tauri CAL54686 Ostreococcus lucimarinus CCE9901 XP_001418779

68 --

Micromonas sp. RCC299 XP_002502811

79 1.

Volvox carteri Volca1_109207 Chlamydomonas reinhardtii XP_001696880 Cyanophora paradoxa BAG32444

93 1. 63 .91

Gloeochaete wittrockiana BAG32445 Cyanoptyche gloeocystis BAG32446 Acrasis rosea AAL76319 Naegleria gruberi strain NEG-M XP_002681464

58 .87

Galdieria sulphuraria Gs02840

91 1.

Cyanidioschyzon merolae CML059C 93 97 1. 1.

Synechocystis sp. PCC 6803 NP_442035 Nostoc punctiforme PCC 73102 YP_001869525 Synechococcus elongatus PCC 7942 YP_399058 Gloeobacter violaceus PCC 7421 NP_924063

Sup. Fig. 10, 6-phosphogluconate dehydrogenase

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)) "''

Peranema trichophorum 04251 Euglena gracilis ELL00004273 Emiliania huxleyi Emihu1_115320

(* +"

Ectocarpus siliculosus CBJ29086 Aureococcus anophagefferens Auran1_60513

(& +"

'* +"

Phaeodactylum tricornutum XP_002185087 Thalassiosira pseudonana XP_002290313 Ectocarpus siliculosus CBN75651 Phaeodactylum tricornutum XP_002185892 Thalassiosira pseudonana XP_002293715 Methylobacterium sp. 4-46 YP_001768319

#& ))

Congregibacter litoralis KT71 ZP_01101586 marine gamma proteobacterium ZP_05094663

#$ "

%$delta proteobacterium NaphS2 ZP_07202616 Mariprofundus ferrooxydans PV-1 ZP_01452623 Polaribacter sp. MED152 ZP_01052499

%& "'(

Leeuwenhoekiella blandensis MED217 ZP_01061465 Croceibacter atlanticus HTCC2559 YP_003716609 Candidatus Solibacter usitatus Ellin6076 YP_822721

Sup. Fig. 11 Nucleotide transporter


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Thalassiosira pseudonana XP_002288452 Phaeodactylum tricornutum XP_002183238 Emiliania huxleyi Emihu1_428168

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Ectocarpus siliculosus CBJ33047 Bigelowiella natans Bigna1_57692 Oryza sativa Japonica Group BAD28023 Arabidopsis thaliana NP_196482 Physcomitrella patens XP_001752830

)! #"

Micromonas sp. RCC299 XP_002507846 Ostreococcus lucimarinus XP_001418297 Volvox carteri Volca1_105177 Galdieria sulphuraria Gs59530

)! #"!!

Cyanidioschyzon merolae CMD021C %& #"

Acaryochloris marina MBIC11017 YP_001519536 Nodularia spumigena CCY 9414 ZP_01630875 Synechococcus elongatus PCC 6301 YP_171750

'( #"!!

Gloeobacter violaceus PCC 7421 NP_925709 Synechococcus sp. JA-3-3Ab YP_474061 Synechococcus sp. WH 5701 ZP_01085950 Prochlorococcus marinus str. MIT 9312 YP_396913

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Synechococcus sp. WH 8102 NP_897775

Sup. Fig. 12 GTP-binding protein LepA

'( "%)

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$$ $$ "(! "() +! (( "%* &" '+ "%% +& '* &" &" $$ "+! $$ "%+

*( "(+

*# "%+ $$ "() $$ "(! '( $$ $$ "%& *# &"

Karenia brevis EX967366_959202 Cylindrotheca closterium BAH30217 Aureococcus anophagefferens Auran1_55209 Ditylum brightwellii BAH30218 Thalassiosira pseudonana XP_002288883 Emiliania huxleyi Emihu1_198673

MATX clade

*+ "%%


Ditylum brightwellii BAH30214 Phaeodactylum tricornutum XP_002176347 Cylindrotheca closterium BAH30213 Aureococcus anophagefferens Auran1_34401 Ectocarpus siliculosus CBJ30117 Thalassiosira pseudonana XP_002288884

Phytophthora sojae Physo1_1_108486 Phytophthora infestans AAN31489 Perkinsus marinus ATCC 50983 XP_002765341 Tetrahymena thermophila XP_001023309 Bigelowiella natans Bigna1_87384 %) &" Zea mays NP_001130734 Oryza sativa Japonica Group NP_001042794 Arabidopsis thaliana NP_192094 Physcomitrella patens XP_001778741 Micromonas sp. RCC299 XP_002506656 Ostreococcus lucimarinus XP_001421225 Volvox carteri Volca1_110084 Chlamydomonas reinhardtii XP_001696661 Aureococcus anophagefferens Auran1_23508 Cyanidioschyzon merolae CMN227C Porphyra yezoensis ACJ38094 Galdieria sulphuraria Gs03900 Nematostella vectensis XP_001629888 Canis lupus familiaris XP_532980 Malassezia globosa XP_001730059 Coprinopsis cinerea XP_001833159 Naegleria gruberi strain NEG-M XP_002679392 Polysphondylium pallidum PN500 EFA84075 Dictyostelium discoideum AX4 XP_635383

Sup. Fig. 13 Methionine adenosyltransferase

A

!"#

Euglena gracilis AAQ19605 Thalassiosira pseudonana XP_002297444 Thraustochytrium aureum AAN75709 Pavlova lutheri AAQ98793 93 1.00 Rebecca salina AAY15136 Aureococcus anophagefferens Auran1_11873 63 Caligus rogercresseyi ACO10922 .98 Oblongichytrium sp. SEK 347 BAG71007 Phaeodactylum tricornutum XP_002182858 79 Phaeodactylum tricornutum ABP65280 .95 Volvox carteri Volca1_121243 Chlamydomonas reinhardtii XP_001690117 61 -Ostreococcus lucimarinus CCE9901 XP_001422856 Micromonas pusilla CCMP1545 EEH54893 54 Ostreococcus lucimarinus CCE9901 XP_001415743 .99 -Micromonas sp. RCC299 XP_002507621 .85 Phaeodactylum tricornutum XP_002183026 Paramecium tetraurelia strain d4-2 XP_001450363 Tetrahymena thermophila XP_001017267 Naegleria gruberi strain NEG-M XP_002680269 Pythium irregulare AAL13311 Phytophthora infestans T30-4 EEY61364 -Porphyra yezoensis ACB11556 .87 Dictyostelium discoideum AX4 XP_640331 Polysphondylium pallidum PN500 EFA77163 Mortierella alpina AAR28035 Trichoplax adhaerens XP_002117357 58 Nematostella vectensis XP_001621650 1.00 81 Mantoniella squamata CAQ30478 1. Micromonas sp. RCC299 XP_002507174 58 .96 Ostreococcus lucimarinus CCE9901 XP_001420855 Parietochloris incisa ADB81956 Marchantia polymorpha AAT85663 92 61 1.00 .99 Picea sitchensis ABR18163 Physcomitrella patens subsp. patens XP_001766264 77 Acaryochloris marina MBIC11017 YP_001515426 .99 Nodularia spumigena CCY9414 ZP_01632618 Synechocystis sp. PCC 6803 NP_441824 Lyngbya sp. PCC 8106 ZP_01619238 58 70 -Cyanothece sp. CCY0110 ZP_01727982 .99 Gemmata obscuriglobus UQM 2246 ZP_02732323 Flavobacteria bacterium MS024-2A ZP_03701937 76 Pedobacter heparinus DSM 2366 YP_003090863 .99 Chitinophaga pinensis DSM 2588 YP_003125301

Sup. Fig. 14 Fatty acid desaturase

Greens

CR

Excavata CR

B Euglena Thalassiosira Thraustochytrium Naegleria Trypanosoma Trypanosoma Leishmania Pavlova Aureococcus Phaeodactylum Paramecium Tetrahymena Chlamydomonas Volvox Ostreococcus Ostreococcus Dictyostelium Porphyra Synechocystis Acaryochloris

239

EYQHVIGHHQ ELQHMLGHHP EMQHVLGHHP KMIHSVGHHV IIHHDFIHHI IIHHDFIHHV IVNHDYVHHV LQEHVVMHHL LQEHVVLHHM QEQH-WTHHA RRSHNFGHHS RRSHNYGHHG RYHHQVSHHI RYHHQVSHHV RYHHQVSHHI RYHHMVSHHS CHQHVIGHHL RNQHVIGHHV RYRHNYLHHT KFRHNQLHHI

YTNLVS---YTNVLDGVEE YTNLIEMENG NTN------YTN------YTN------YTN------HTN------HTG------YTN------CVN------CVN------HCN------HCN------HCN------YCN------YTN------YTN------YTN------YTN-------

---------D ERKERGEDVA LAKVKGADVD ----------------------------------------------------------------------------------------------------------------------------------------------------------

TLFSLPENDP LEEKDQESDP PKKVDQESDP ----IEERDP ----DPHRDL ----EPHHDL ----EPGRDA ----DVDADP ----DVEYDP ----HAEMDP ----HLELDR ----HYELDR ----DDALDE ----DDAFDE ----DNAMDQ ----DADLDQ ----VRNADP ----VMGADP ----ILGHDV ----IEGYDN

Supplementary Fig. 14 Fatty acid desaturase (continued)

DVFSSY-PLM DVFSSF-PLM DVFSTY-PML DIHTGE-PHF DLE--I-PLL DL--DI-PLL DLE--I-PLL DQK-AH-GVL DAQ-LA-PVM DSFGAE-PML AFDTTF-PYI AFDTTF-PLL DVFSAF-PML DVFSAF-PFL DVYTAM-PLL DVYTAL-PLL DLGQGE-IDF DLPVALSGDP EIH-GD-GAV EIE-GD-GVV

288

R R R R R R R R R L R R R R R R R R R R

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Euglena gracilis ELL00002167 Euglena longa AAV65492 Euglena longa AAV65491 Cyanidioschyzon merolae CMQ172C Gracilaria gracilis xxP48492 Galdieria sulphuraria Gs29840 Bigelowiella natans Bigna1_87329 Zea mays NP_001131642 Oryza sativa Japonica Group NP_001063777 Arabidopsis thaliana NP_179713 &+ ("!! Populus trichocarpa XP_002312980 Physcomitrella patens XP_001751243 Ostreococcus lucimarinus XP_001422591 Arabidopsis thaliana NP_191104 Populus trichocarpa XP_002314179 Oryza sativa Japonica Group NP_001042016 Ciona intestinalis XP_002130790 Nematostella vectensis XP_001633516 Branchiostoma floridae XP_002232270 Drosophila grimshawi XP_001990150 Ustilago maydis 521 XP_759446 Moniliophthora perniciosa XP_002388914 Cryptococcus neoformans XP_775227 Monosiga brevicollis MX1 XP_001744473 Achlya bisexualis AAF44720 Phytophthora infestans ABU99207 Phytophthora sojae ABU99222 Ectocarpus siliculosus CBJ30340 Thalassiosira pseudonana XP_002290574 Odontella sinensis AAF34328 Paramecium tetraurelia XP_001425288 Tetrahymena thermophila XP_001008794 Perkinsus marinus ATCC 50983 XP_002768175 Guillardia theta CAH25342 Thalassiosira pseudonana XP_002295570 Phaeodactylum tricornutum XP_002181761 Aureococcus anophagefferens Auran1_72255 Ectocarpus siliculosus CBJ32973 Phytophthora infestans T30-4 EEY59956 Naegleria gruberi strain NEG-M XP_002683097 Acrasis rosea ABK81122

Sup. Fig. 15 Triose-phosphate isomerase

B

CR

Exca. unikonts Greens

CR+Red

150

Euglena gracilis Euglena longa 1 Euglena longa 2 Bigelowiella Galdieria Cyanidioschyzon Gracilaria Arabidopsis Physcomitrella Ostreococcus Cryptococcus Monosiga Nematostella Drosophila Naegleria Acrasis Tetrahymena Paramecium Perkinsus Guillardia Aureococcus Phytoph. inf. 1 Phaeodactylum Thalassiosira 1 Ectocarpus 1 Odontella Thalassiosira 2 Ectocarpus 2 Achlya Phytoph. inf. 2 Phytoph. soj.

WVILGHSERR WVILGHSERR WVILGHSERR WVILGHSERR WVILGHSERR HVILGHSERR WVILGHSERR WVILGHSERR WVIQGHSERR WVILGHSERR WVILGHSERR WVILGHSERR WVIIGHSERR WVILGHSERR STLLGHSERR YAIVGHSERR WAILGHSERR WVILGHSERR WTILGHSERR WVILGHSERR WVIVGHSERR WTITGHSERR WVIIGHSERR WVILGHSERR WVITGHSERR WVVIGHSERR WAIVGHSERR WCIIGHSERR YTIIGHSERR YTLVGHSERR YTLVGHSERR

-SLPEIKETD -SLPEIMETD -HLPELKESD -HLPEIKETD -HLPELQETD -HLPEIRESD -HIAQLKESD -HV--IGEKD -HV--IGESN -NL--FNESN -SL--FGDTD -SI--FGESN -NI--FGEKD -AI--FNESD -HV--FGESN -SL--YHETD -QY--YGETN -QY--NGETN -HL--FNETN -EY--FKEDN -TN--QKESS -AY--YNETD EGFEMPGETP EGFGMAGEDS VGFGCAGESS -GK---GEAD -GK---GEAD -QK---GETN -QK---GETN -EK---GETN -EK---GETN

172

ETVATK ATVATK ETVAIK EVIAKK ETIAQK DVIGRK HTIAMK EFIGKK ETIGKK EFVGKK KLVADK ELIGEK ELIGEK ELIAEK TVIAKK EVAAHK EVVANK EIVGKK EDLAAK EMLRQK ALVATK EIVAKK DLCAKK ELVAKK DLIAEK EEVARK EEIAKK EECAVK EEVASK EVVAKK EVVAKK

Supplementary Fig. 15 Triose-phosphate isomerase (continued)