10um MGD X1 10um TGD X3 X2 10um Pl PPC Nm 500 nm a b 80 MGD Green algal 80 TGD Green algal Natural logarithm 70 of FPKM 70 7 6 60 5 60 4 3 2 1 50 0 50 -1 %GC for 1st codon position 40 40 30 30 0 20 40 60 80 100 0 20 40 60 80 100 %GC for 3rd codon position %GC for 3rd codon position 80 c d MGD Alveolate 80 TGD Alveolate 70 70 60 60 50 50 %GC for 1st codon position 40 40 30 30 0 20 40 60 80 100 0 20 40 60 80 100 %GC for 3rd codon position %GC for 3rd codon position TGD Low %GC High %GC 1 2 3 4 5 6 LHC HemA eIF4A PetE PetF PetC (bp) 1,000 800 600 400 200 MGD Low %GC High %GC 1 2 3 4 5 6 RNA RP-S1 PFK PetE PsaD PetC helicase (bp) 1,000 800 600 400 200 a MGD b TGD %GC for 1st codon position %GC for 3rd codon position %GC for 3rd codon position Green algal house-keeping transcript % c MGD G d TGD 室蘭株C 鶴岡株 f o r 1 pos iti ons o f codon s %GC for 1st codon position %GC for 3rd codon position %GC%GC for 3 forrd pos3rd codonitions position of codons Green algal photosynthesis related transcript Large subunit ribosomal protein L21 (plastid) >MGD_42250_c0_seq1 SignalP-4.1 prediction (euk networks): MGD_42250_c0_seq1 C-score 1.0 S-score Y-score MMRSIAALISFAYIASCAEQGDAQGSMNKLADKLADRVLN 0.8 VDPCTTDLENAVVAKGPGHLSSPTIQNRAPIMQPRGALSV 0.6 QSLARPVYCRSATEAAPWDAIIEVGGSQKIVETGRYYDTN Score 0.4 RLKGDLAPGTKVAFPRVLAVKKGAGEYTIGQPWVQGAKVE 0.2 AEVLENFKGKKVIVYKMRAKKHYRKKNGHRQLLTRFLVTN 0.0 VVKP M M R S I A A L I S F A Y I A S C A E Q G D A Q G S M N K L A D K L A D R V L N V D P C T T D L E N A V V A K G P G H L S S P T I Q N R A P 0 10 20 30 40 50 60 70 Position Tocopherol O-methyltransferase >MGD_65218_c0_seq1 SignalP-4.1 prediction (euk networks): MGD_65218_c0_seq1 C-score 1.0 S-score Y-score MSSLLLMIIFVFTISWQAYTVNPQSLQGYHVGDTIDSLDT 0.8 LADRLANRLFDRVFKTKAMSPCALFSPSIKRWPHLLKKKI 0.6 PESGGNKWIVRSSRTREELNSGIAEFYDESSALWEGMWGE Score 0.4 HMHHGYYPGGKFRSDHQQAQIDMVDRVLDWAGVADVKNFL 0.2 DVGCGIGGSSRHIARRYGFPRHKISEKIARRYGLPLGVTG 0.0 QGITLSPNQAARANQLSSEQGLGEKLLFRVADALNMPFTD M S S L L L M I I F V F T I S W Q A Y T V N P Q S L Q G Y H V G D T I D S L D T L A D R L A N R L F D R V F K T K A M S P C A L F S P S I K 0 10 20 30 40 50 60 70 GQFDLVWSLESGEHMPDKSQFLDELARVTAPGGK.... Position Glucose-6-phosphate dehydrogenase >MGD_149202_c0_seq1 SignalP-4.1 prediction (euk networks): MGD_149202_c0_seq1 C-score 1.0 S-score Y-score MSTSRMCRASLNFLICCVAHGHVTNHSQAGWVGGLVDEFA 0.8 GQLVSKLFDRALDAPPLQRAELQRSMLAKPSHVAIPSHTH 0.6 VPLVPLKAHAHSFYSSGALRYQPQQGKAILAQHMRVGQTV Score 0.4 QKSLGNWARQLQSTPSRYADQLQAVDPDFLPSLYGADEDL 0.2 TLVIIGASGDLARKKVFPAIFALYAQGLLPKSTHIVGYAR 0.0 TDLSRDEFIERISEKLMCRIDWDAPDCSDDMDKFLSLTDY M S T S R M C R A S L N F L I C C V A H G H V T N H S Q A G W V G G L V D E F A G Q L V S K L F D R A L D A P P L Q R A E L Q R S M L A K P 0 10 20 30 40 50 60 70 VSGQYDSEADFAKLDAFITQKEVERKAKASNRLF.... Position RED:Signal Peptide predicted by SignalP-4.1 BLUE:Putative mature protein region Photosystem II 13kDa protein (Psb28) >TGD_36373_c0_seq1 SignalP-4.1 prediction (euk networks): TGD_36373_c0_seq1 C-score 1.0 S-score Y-score MCCIRVAILLACIAQVSAKQTAADDAMDKLADRLVDKLAD 0.8 KLSDRLNQASSLHSADMDGTTLGKTSAIAAPQPRAVARAA 0.6 GVAPRMGMPFGMGAAGRVVQQRMPVLANAGASLQFIKGTD Score 0.4 EPDVPEVKLSKSRSSSMGQATFIFENPSVFDLEGPGKDDI 0.2 TGLYMVDDEGEMRTVDVQARFVNGKPAGIIAKYTMQNEAQ 0.0 WDRFMRFMERYAEANDLGFNKAK M C C I R V A I L L A C I A Q V S A K Q T A A D D A M D K L A D R L V D K L A D K L S D R L N Q A S S L H S A D M D G T T L G K T S A I A A 0 10 20 30 40 50 60 70 Position 4-alpha-glucanotransferase >TGD_140644_c0_seq2 SignalP-4.1 prediction (euk networks): TGD_140644_c0_seq2 C-score 1.0 S-score Y-score MLKAAYILLASVSCVDANELVVHDAAFAPAFIDTVVDRLV 0.8 DKLAKRTRSSDLGSTTLGKAVHVATRCRPGSQPCALSTSH 0.6 SMPAWPRTYHVARPMTVPRQTADFEKIFAGVSTKRSLPVV Score 0.4 QAQQAEVAKEAFKFDLKRRAGVLLPVSSLDGQGPIGNLDD 0.2 AERFVDWLAEAGMALWQILPLVPTDSAGSPYSSWSTLSGN 0.0 PDLVGLGGLVAAGLLDKEKTKLPLLTTVNYTVVAAQKRTL M L K A A Y I L L A S V S C V D A N E L V V H D A A F A P A F I D T V V D R L V D K L A K R T R S S D L G S T T L G K A V H V A T R C R P G 0 10 20 30 40 50 60 70 VLEAAQALLDRPDHPLRPALDKFVANAKWATDAA.... Position Nucleoside-diphosphate kinase >TGD_174950_c0_seq1 SignalP-4.1 prediction (euk networks): TGD_174950_c0_seq1 C-score 1.0 S-score Y-score MMSKVAAAVLFVVVAQTFAQQTAVSQYDLANKVADKLAAK 0.8 LLDRMEDANLDDTTLGALLQSSNMQLAGLSPSTQLAFSAG 0.6 PLRTPLAPSRIALNAWESDTCARRAVSAAAVAGVPRMCAA Score 0.4 KEVRALGLRKSQPTHVVQASASAERSYVMIKPDGVQRGLV 0.2 GEIISRFERKGFYLKGLKMFQTPEDLAKEHYKDLSEKPFF 0.0 GDLVEYICSGPVVCMVWEGKGVIKSARKLIGATNPLEAEP M M S K V A A A V L F V V V A Q T F A Q Q T A V S Q Y D L A N K V A D K L A A K L L D R M E D A N L D D T T L G A L L Q S S N M Q L A G L S 0 10 20 30 40 50 60 70 GTIRGDFAVETGRNVIHGSDSIENGEREIGIWF.... Position RED:Signal Peptide predicted by SignalP-4.1 BLUE:Putative mature protein region Synechococcus sp. CC9311 Cyanobacteria Prochlorococcus marinus Cyanophora paradoxa Glaucophyta 98 endosymbiont of Dinophysis norvegica Rhodomonas salina Cryptomonas paramecium Guillardia theta Aureococcus anophagefferens 94 Heterosigma akashiwo Ectocarpus siliculosus Odontella sinensis Kryptoperidinium foliaceum 99 100 98 Durinskia baltica Cyanidium caldarium & Chromera velia Cyanidioschyzon merolae Gracilaria tenuistipitata Rhodophyta Pyropia yezoensis 100 Porphyra purpurea Pavlova gyrans red alga-derived plastids Gyrodinium aureolum 100 Karenia brevis 94 Karlodinium veneficum Chrysochromulina polylepis Isochrysis sp. 98 Emiliania huxleyi Nephroselmis olivacea Monomastix sp. 86 Pyramimonas parkeae Mesostigma viride Chlorokybus atmophyticus Chara vulgaris Staurastrum punctulatum 96 82 Nicotiana tabacum 100 Oryza sativa Pycnococcus provasolii Picocystis salinarum Oocystis solitaria 100 Chlorella vulgaris Parachlorella kessleri 100 TGD Dinophyceae MGD 99 Lepidodinium chlorophorum NIES-1868 Pedinomonas sp. UTEX1026 Pedinomonas minor Pedinophyceae (Pedinomonadales) & Pedinomonas sp. M2079/1 89 Pedinomonas tuberculata Virideplantae Resultor mikron Marsupiomonas sp. NIES-1410 Pedinophyceae (Marsupinomonadales) Marsupiomonas pelliculata 100 Oltmannsiellopsis viridis green alga-derived plastids Acutodesmus obliquus Chlamydomonas reinhardtii 99 Oedogonium cardiacum Stigeoclonium helveticum Leptosira terrestris Bigelowiella natans Tetraselmis striata Bryopsis hypnoides Prasinophyceae sp. CCMP1205 Euglena gracilis Prasinococcus capsulatus Pterosperma cristatum Pseudendoclonium akinetum 100 Ostreococcus tauri Micromonas sp. 0.2 substitutions/site 0.4 substitutions/site Perkinsus_andrewsi Chromera velia Takayama acrotrocha Karlodinium australe 99 / 0.99 Karenia papilionacea Brachidinium capitatum Adenoides eludens Ensiculifera cf. loeblichii Scrippsiella sp. Chimonodinium lomnickii - / 0.93 Pseudopfiesteria shumwayae 95 / 0.90 Cryptoperidiniopsis brodyi 88 / 0.98 Pfiesteria piscicida - / 0.95 Gyrodinium lebouriae Pernambugia tuberosa Tintinnophagus acutus Duboscquodinium collinii Calciodinellum albatrosianum Leonella granifera Peridiniopsis borgei 1 Pentapharsodinium dalei Kryptoperidinium foliaceum Durinskia baltica Gloeodinium montanum Vulcanodinium rugosum Peridinium bipes f. occultatum - / 0.99 Archaeperidinium saanichi Protoperidinium monovelum Diplopsalis lenticula Diplopsalopsis bomba Rhinodinium broomense Amphidinium semilunatum Katodinium glaucum Akashiwo sanguinea Heterocapsa niei TGD MGD Cochlodinium fulvescens Peridinella catenata Peridiniella sp. Amphidoma languida Prorocentrum lima Lingulodinium polyedrum 86 / 0.99 Amylax triacantha Gonyaulax verior Metaphalacroma skogsbergii Nematodinium sp. 96 / 0.99 Warnowia sp. Lepidodinium chlorophorum Dissodinium pseudolunula Polykrikos lebourae 93 / 0.99 Spiniferodinium galeiforme Pheopolykrikos hartmannii Gymnodinium fuscum Gymnodinium catenatum Pyrodinium bahamense var. compressum 1 Thecadinium kofoidii Apicoporus glaber Baldinia anauniensis 100 / 0.96 Woloszynskia halophila Biecheleria cincta - / 0.98 Polarella glacialis 100 / 1 Pelagodinium beii Protodinium simplex Symbiodinium microadriaticum Borghiella dodgei Sphaerodinium cracoviense Histioneis milneri 100 / 0.99 Citharistes regius 99 / 0.99 Ornithocercus magnificus Dinophysis caudata Oxyphysis oxytoxoides 87 / 0.97 Phalacroma mitra Amphisolenia bidentata Jadwigia applanata Glenodiniopsis steinii Protoceratium reticulatum 0.1 Azadinium caudatum var. margalefii .