Table S1Table S1. Gene compositions of red algal plastid genomes.No.Class & SubclassOrderSpeciesSequencingraw dataPlastidgenome(bp)PlastidgenomecoverageGC ontent(%)Coding generDNAsduplicatedrRNAstRNAsIntronAccessionnumberReferences1CyanidiophyceaCyanidialesCyanidioschyzon merolae-149,987-37.632073X310AB002583.1[17]2Galdieria sulphuraria-167,741-28.491846O390NC_024665.1[26]3Cyanidium caldarium-164,921-32.732003X300AF022186.2[16]4Cyanidiaceae sp.-145,533-37.492103X310KJ569775.1unpublished5PorphyridiophyceaePorphyridialesPorphyridium sordidium2.5 Gb259,42982X30.721916O2965KX284720this study6Porphyridium purpureum-217,694-30.342246O3044NC_023133.1[25]7StylonematophyceaeStylonematalesBangiopsis subsimplex2.3 Gb204,784515X29.251943X3038KX284718this study8Rhodosorus marinus (partial plastid)1.2 Gbfragmented--177-----this study9RhodellophyceaeRhodellalesRhodella violacea (partial plastid)1.1 Gbfragmented--166-----this study10Rhodella maculata (partial plastid)2.8 Gbfragmented--166-----this study11CompsopogonophyceaeErythropeltidalesErythrotrichia carnea1.7 Gb210,691943X31.851916O3259KX284721this study12RhodochaetalesRhodochaete parvula1.1 Gb222,94049X28.311956O3162KX284728this study13BangiophyceaeBangialesBangia fuscopurpurea-196,913-33.542066O370KP714733.1unpublished14Pyropia yezoensis-191,975-33.092136O370KC517072.1[24]15Pyropia fucicola (partial plastid)-187,182-32.732093X350KJ776837.1[24]16Pyropia haitanensis-195,597-32.982136O370NC_021189.1[22]17Pyropia kanakaensis (partial plastid)-189,831-32.852113X350KJ776836.1[24]18Pyropia perforata-189,789-32.912103X350KF515973.1[24]19Porphyra purpurea-191,028-32.992096O370U38804.1[15]20Porphyra pulchra-194,175-33.342076O370NC_029861.1[27]21Porphyra umbilicalis (partial plastid)-189,470-32.92086O370JQ408795.1[24]Florideophyceae-22 HildenbrandiophycidaeHildenbrandialesHildenbrandia rivularis2.6 Gb189,725260X32.391843X312KX284723this study23Hildenbrandia rubra2.5 Gb180,141365X31.371903X312KX284724this study24Apophlaea sinclairii859 Mb182,437117X30.451893X312KX284716this study25 NemaliophycidaePalmarialesPalmaria plamata-192,960-33.912046O332KX284726unpublished26BatrachospermalesKumanoa americana-184,025-29.271983X312KX284725unpublished27ThorealesThorea hispida-175,193-28.351933X302KX284714unpublished28 CorallinophycidaeCorallinalesCalliarthron tuberculosum-178,981-29.162013X312NC_021075.1[21]29SporolithalesSporolithon durum-191,465-29.342023X302NC_029857.1[26]30 AhnfeltiophycidaeAhnfeltialesAhnfeltia plicata1.8 Gb190,451185X32.542056O311KX284715this study31 RhodymeniophycidaeBonnemaisonialesAsparagopsis taxiformis1.6 Gb177,0911,254X29.42033X322KX284717this study32GigartinalesChondrus crispus-180,086-28.732043X301NC_020795.1[17]33PeyssonnelialesRiquetophycus sp.2.9 Gb180,384729X28.782025O (parital)301KX284710this study34AcrosymphytalesSchimmelmannia schousboei547 Mb181,030384X28.612023X301KX284711this study35GelidialesGelidium elegans-174,748-30.22023X301NC_029858.1[27]36Gelidium vagum-179,853-29.872013X301NC_029859.1[27]37CeramialesCeramium japonicum545 Mb171,634460X27.811993X281KX284719this study38Vertebrata lanosa-167,158-29.981930X281NC_026523.1[6]39HalymenialesGrateloupia taiwanensis-191,270-30.562353X301KC894740.1[20]40RhodymenialesRhodymenia pseudopalmata1.3 Gb194,153311X32.032016O321KX284709this study41SebdenialesSebdenia flabellata511 Mb192,140134X29.232055O (partial)301KX284713this study42PlocamialesPlocamium cartilagineum538 Mb171,392257X27.211973X291KX284727this study43NemastomatalesSchizymenia dubyi2.3 Gb183,959543X29.972043X301KX284712this study44GracilarialesGracilariopsis chorda3.1 Gb182,459798X27.382013X301KX284722this study45Gracilariopsis lemaneiformis-183,013-27.42073X321KP330491.1unpublished46Gracilaria salicornia-179,757-28.82033X301NC_023785.1[23]47Gracilaria tenuistipitata var. liui-183,883-29.152053X301NC_006137.1[18]48Gracilaria chilensis-185,637-29.342033X301NC_029860.1[27]

Tabel S2Table S2. Representative homologous gene sets of red algal plastid genes (present=O and absent=yellow color; rpoC1 and rpoC2 genes were combined as rpoC; see Methods).Homologousgene setsGaldieria sulphurariaCyanidium caldariumCyanidiaceae sp.Cyanidioschyzon merolaePorphyridium sordidumPorphyridium purpureumBangiopsis subsimplexErythrotrichia carneaRhodochaete parvulaPorphyra purpureaPorphyra umbilicalisBangia fuscopurpureaPyropia yezoensisPyropia fucicolaPorphyra pulchraPyropia kanakaensisPyropia perforataPyropia haitanensisHildenbrandia rivularisHildenbrandia rubraApophlaea sinclairiiPalmaria palmataKumanoa americanaThorea hispidaSporolithon durumCalliarthron tuberculosumAhnfeltia plicataAsparagopsis taxiformisChondrus crispusRiquetophycus sp.Schimmelmannia schousboeiVertebrata lanosaCeramium japonicumGelidium elegansGelidium vagumGrateloupia taiwanensisSebdenia flabellataRhodymenia pseudopalmataPlocamium cartilagineumSchizymenia dubyiGracilariopsis chordaGracilariopsis lemaneiformisGracilaria salicorniaGracilaria chilensisGracilaria 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_ORF64ORF12ORF164ORF621

Table S3Table S3. Intron prediction of plastid intronic proteins in red algal 5 basal taxa.No.SpeciesIntron regionIntronPredicted familye-valueIntronic ORFRemarks1Bangiopsis subsimplexacpPintronintron II (domainV) 4.72E-10atpBintron1intron II (domainV) 1.90E-09intron2intron II, derived9.75E-08intron3intron II (domainV) 5.82E-12maturaseintron4intron II (domainV) 4.36E-11intron5intron II (domainV) 1.69E-05maturaseintron6intron II (domainV) 1.11E-11atpGintronintron II (domainV) 6.14E-08atpIintronintron II (domainV) 1.69E-11chlBintron1intron II (domainV) 5.15E-11intron2intron II (domainV) 8.50E-14cpcGintronintron II, derived1.48E-10ilvHintronintron II, derived1.50E-12mntAintron1intron II (domainV) 2.38E-09intron2 intron II (domainV) 1.03E-09nblAintronintron II (domainV) 2.91E-08petBintronintron II, derived5.61E-11psaAintron1intron II (domainV) 2.62E-09intron2intron II (domainV) 1.64E-08intron3intron II (domainV) 3.77E-07psaCintronintron II (domainV) 2.50E-09psaFintronintron II (domainV) 5.09E-10psaLintronintron II (domainV) 1.68E-13psbBintron1unknownintron2intron II (domainV) 1.79E-09intron3intron II, derived1.29E-09rpoZintronintron II (domainV) 1.90E-13rps12intron1intron II, derived4.43E-09intron2intron II (domainV) 1.59E-11maturasesufBintronintron II, derived5.48E-08sufCintronintron II, derived6.98E-11tatCintron1intron II (domainV) 2.79E-11intron2intron II (domainV) 2.79E-11trmMeintronintron II, derived1.04E-08ycf20intronintron II (domainV) 4.71E-09ycf23intronintron II, derived4.36E-12ycf3intronintron II (domainV) 1.80E-11ycf35intronintron II (domainV) 4.58E-092Erythrotrichia carneaapcDintron1Unknownintron2UnknownatpDintronintron II, derived 3.11E-07different regionsintron II, derived 5.12E-09atpFintronintron II, derived 1.42E-03atpIintron1Unknownintron2intron II, derived 2.75E-04bas1intron1intron II, derived 1.55E-05intron2Unknownintron3intron II, derived 2.84E-07car1intronUnknownclpCintronUnknowndnaKintron1Unknownintron2intron II, derived 2.52E-04maturaseintron3intron II, derived 2.81E-04intron4Unknownorf546gltBintronintron II, derived 1.35E-07infCintronUnknownodpBintronintron II, derived 4.46E-04ORF565intronintron II, derived 1.41E-03petGintronUnknownpgmAintronUnknownpsaAintron1intron II, derived 1.55E-04intron2Unknownmat1bpsaEintronUnknownpsaFintron1intron II, derived 1.79E-04intron2UnknownpsaJintronintron II, derived 8.86E-05psaKintronUnknownrpl18intronUnknownrpl2intronintron II, derived 2.32E-06rpl22intronintron II, derived 1.07E-04rpl31intron1Unknownintron2UnknownrpoAintron1intron II, derived 8.17E-05intron2intron II, derived 6.62E-04intron3intron II, derived 4.08E-09intron4intron II, derived 6.98E-04intron5intron II, derived 1.89E-05intron6intron II, derived 1.04E-03intron7UnknownrpoC1intronintron II, derived 4.62E-05rps10intronintron II, derived 3.38E-04rps12intron1Unknownintron2intron II, derived 1.25E-06rps2intronUnknownrps3intronintron II, derived 3.32E-05rps6intronintron II, derived 5.92E-08rps7intronintron II, derived 1.30E-05rps8intronintron II, derived 2.52E-05trxAintron1Unknownintron2intron II, derived 4.34E-04intron3Unknownintron4Unknownintron5intron II, derived 1.59E-05tsfintronUnknownycf20intron1Unknownintron2Unknownycf23intronUnknownycf26intronUnknown3Rhodochaete parvulaycf20Intronintron II, derived4.89E-05bas1Intron1intron II, derived3.43E-04Intron2intron II, derived2.10E-06Intron3intron II, derived2.15E-09carAIntronintron II, derived4.49E-06apcDIntron1UnknownIntron2intron II, derived6.08E-05psaFIntron1intron II, derived6.20E-05Intron2intron II, derived4.60E-05psaJIntronintron II, derived7.55E-05psbDIntronUnknownrps6IntronUnknownycf23IntronUnknowngltBIntronintron II, derived1.74E-09apcAIntron1intron II, derived3.22E-04Intron2intron II, derived3.51E-04psaAIntron1UnknownIntron2UnknownMaturasepsaBIntronintron II, derived2.24E-08psaLIntronintron II, derived2.12E-05rpoC1Intronintron II, derived5.39E-08rps2Intronintron II, derived2.87E-05tsfIntronUnknownatpIIntron1intron II, derived5.63E-04Intron2intron II, derived1.91E-05atpFIntronUnknowninfCIntronUnknownycf45Intron1UnknownIntron2intron II, derived2.91E-09petBIntronintron II (domainV)4.30E-14MaturasednaKIntron1intron II, derived1.19E-05Intron2UnknownIntron3intron II, derived6.93E-05MaturaseIntron4intron II (domainV)1.22E-06RVTrpl2Intronintron II, derived1.52E-05rpl22Intronintron II, derived5.68E-09rps3Intronintron II, derived5.14E-04rps8Intronintron II, derived9.47E-08rpl18Intronintron II, derived2.18E-04rpoAIntron1intron II, derived2.96E-04Intron2UnknownIntron3intron II, derived1.63E-04Intron4intron II, derived2.09E-08Intron5intron II, derived4.03E-05Intron6intron II, derived8.69E-07rpl31Intron1UnknownIntron2intron II, derived8.59E-04rps12Intron1intron II, derived1.61E-07Intron2intron II, derived1.92E-07rps7Intronintron II, derived5.53E-05rps10Intronintron II, derived1.62E-04acpPIntron1UnknownIntron2intron II (domainV)3.27E-06trxAIntron1UnknownIntron2UnknownIntron3intron II, derived5.33E-05Intron4UnknownIntron5intron II, derived1.72E-06ycf26Intronintron II (domainV)2.96E-05orf62Intronintron II, derived7.06E-05different regionsintron II, derived7.04E-04ycf33Intronintron II (domainV)6.85E-12Maturase4Porphyridium sordidumapcFintronintron II (domainV)7.93E-11atpAintronintron II (domainV)8.67E-12atpBintron1intron II (domainV)7.89E-08intron2intron II (domainV)1.05E-09intron3intron II (domainV)3.11E-11atpDintronintron II (domainV)5.69E-12atpFintron1intron II (domainV)1.19E-08intron2intron II (domainV)6.61E-07atpGintron1intron II (domainV)2.49E-11intron2intron II (domainV)8.97E-13atpIintron1intron II (domainV)8.35E-09different regionsintron II, derived5.69E-06intron2UnknownclpCintron1intron II (domainV)6.17E-11intron2intron II (domainV)6.17E-11intron3intron II (domainV)4.67E-13intron4intron II (domainV)2.73E-09dnaBintronintron II (domainV)1.02E-11dnaKintron1intron II (domainV)2.18E-10different regionsintron II (domainV)1.80E-10intron2intron II (domainV)8.26E-10intron3Unknownmat1bintron4intron II (domainV)2.42E-12fabHintron1intron II (domainV)4.74E-12intron2intron II (domainV)1.54E-08infCintron1intron II (domainV)1.74E-09intron2Unknownintron3Unknownintron4intron II (domainV)4.86E-10psaAintronintron II, derived9.14E-05psaCintronintron II (domainV)4.54E-10psbEintronintron II (domainV)2.41E-10mat1ipsbJintronUnknownpsbNintronUnknownrpl19intronintron II (domainV)3.16E-11rpl5intronintron II (domainV)3.73E-10rpl9intronUnknownrpoAintronintron II (domainV)2.47E-08rpoBintron1intron II (domainV)1.40E-10intron2intron II (domainV)3.53E-05intron3intron II (domainV)3.63E-12intron4intron II (domainV)1.04E-06intron5intron II (domainV)3.27E-10rpoC1intron1intron II (domainV)1.36E-10intron2intron II (domainV)4.67E-13rpoZintronintron II (domainV)2.75E-05rps6intronintron II (domainV)1.88E-07secGintron1Unknownrps4intron2UnknowntilSintron1Unknownintron2Unknownintron3Unknownintron4Unknowntsfintronintron II (domainV)2.41E-10ycf23intronUnknownycf34intronUnknownycf35intronintron II (domainV)9.67E-08ycf45intron1Unknownintron2intron II, derived4.22E-06intron3Unknownycf46intron1Unknownintron2Unknownintron3Unknownintron4intron II (domainV)9.01E-07intron5intron II (domainV)1.06E-08different regionsintron II, derived2.62E-05ycf55intronUnknownycf56intronintron II (domainV)1.02E-115Porphyridium purpureumatpFintronintron II (domainV)7.81E-12atpGintronintron II (domainV)2.40E-07atpIintron1intron II, derived2.68E-08intron2intron II (domainV)1.49E-14dnaBintronintron II, derived2.65E-05dnaKintron1intron II (domainV)1.93E-10intron2Unknownmat1BgltBintronintron II (domainV)1.49E-14mat1DinfCintron1Unknownintron2Unknownintron3intron II (domainV)1.49E-14mat1CmntAintronintron II (domainV)1.30E-12preAintronintron II (domainV)3.61E-12psaAintronUnknownpsbJintronUnknownpsbNintron1Unknownintron2intron II (domainV)6.44E-11rpl28intronUnknownrpl4intronUnknownrpoAintronUnknownrpoBintron1intron II (domainV)5.75E-05intron2intron II (domainV)1.33E-10rpoC1intronintron II (domainV)3.17E-10rpoC2intron1intron II (domainV)1.49E-14ORF 84intron2intron II (domainV)1.44E-12mat1ErpoZintronintron II, derived2.73E-09rps19intron1Unknownintron2Unknownrps3intronUnknownsecGintronintron II (domainV)4.44E-09tsfintronUnknownycf23intronUnknownycf34intronUnknownycf45intronUnknownycf46intron1Unknownintron2Unknownintron3Unknownintron4intron II (domainV)2.65E-12intron5intron II (domainV)1.99E-06ycf55intronUnknownycf62intron1Unknownintron2intron II (domainV)1.55E-08intron3Unknown

Table S4Table S4. List of 191 red algal plastid protein-coding genes used in the ML tree search.No. of plastidgene setSpeciesGene nameRemarks1Asparagopsis taxiformisaccASchimmelmannia schousboeiaccASebdenia flabellataaccAAhnfeltia plicataaccASchizymenia dubyiaccAGelidium vagumaccAHildenbrandia rivularisaccAPlocamium cartilagineumaccAGracilaria tenuistipitataaccACyanidiaceae sp.accACalliarthron tuberculosumaccASporolithon durumaccAPyropia yezoensisaccAPyropia perforataaccAGracilariopsis lemaneiformisaccAVertebrata lanosaaccAPalmaria palmataaccAGracilaria chilensisaccAPyropia haitanensisaccABangia fuscopurpureaaccAChondrus crispusaccAGaldieria sulphurariaaccAGracilaria salicorniaaccAPorphyra pulchraaccAHildenbrandia rubraaccAPorphyra purpureaaccACyanidioschyzon merolaeaccAPyropia kanakaensisaccAKumanoa americanaaccAApophlaea sinclairiiaccAPyropia fucicolaaccAGrateloupia taiwanensisaccACeramium japonicumaccARhodymenia pseudopalmataaccAThorea hispidaaccAPorphyra umbilicalisaccARiquetophycus sp.accACyanidium caldariumaccAGelidium elegansaccAGracilariopsis chordaaccA2Vertebrata lanosaaccBPyropia yezoensisaccBBangia fuscopurpureaaccBGelidium vagumaccBCeramium japonicumaccBGrateloupia taiwanensisaccBThorea hispidaaccBPyropia fucicolaaccBKumanoa americanaaccBHildenbrandia rivularisaccBGracilaria chilensisaccBPyropia haitanensisaccBCalliarthron tuberculosumaccBHildenbrandia rubraaccBPorphyra umbilicalisaccBPyropia perforataaccBGracilariopsis chordaaccBSchizymenia dubyiaccBGracilaria tenuistipitataaccBRiquetophycus sp.accBPalmaria palmataaccBCyanidiaceae sp.accBGelidium elegansaccBPorphyra purpureaaccBGracilariopsis lemaneiformisaccBGracilaria salicorniaaccBGaldieria sulphurariaaccBCyanidium caldariumaccBPyropia kanakaensisaccBAhnfeltia plicataaccBChondrus crispusaccBPorphyra pulchraaccBSchimmelmannia schousboeiaccBSebdenia flabellataaccBAsparagopsis taxiformisaccBSporolithon durumaccBRhodymenia pseudopalmataaccBApophlaea sinclairiiaccBPlocamium cartilagineumaccBCyanidioschyzon merolaeaccB3Gracilaria tenuistipitataaccDGrateloupia taiwanensisaccDRhodymenia pseudopalmataaccDCyanidiaceae sp.accDChondrus crispusaccDSchizymenia dubyiaccDCyanidium caldariumaccDPorphyra purpureaaccDVertebrata lanosaaccDPyropia haitanensisaccDGracilaria salicorniaaccDAhnfeltia plicataaccDPyropia kanakaensisaccDGracilaria chilensisaccDSporolithon durumaccDPyropia yezoensisaccDPlocamium cartilagineumaccDSchimmelmannia schousboeiaccDPorphyra pulchraaccDCalliarthron tuberculosumaccDSebdenia flabellataaccDBangia fuscopurpureaaccDPyropia fucicolaaccDGelidium elegansaccDCeramium japonicumaccDGaldieria sulphurariaaccDPalmaria palmataaccDPyropia perforataaccDGelidium vagumaccDKumanoa americanaaccDGracilariopsis lemaneiformisaccDCyanidioschyzon merolaeaccDThorea hispidaaccDPorphyra umbilicalisaccDHildenbrandia rivularisaccDAsparagopsis taxiformisaccDGracilariopsis chordaaccDApophlaea sinclairiiaccDHildenbrandia rubraaccDRiquetophycus sp.accD4Hildenbrandia rivularisacpPAsparagopsis taxiformisacpPSchimmelmannia schousboeiacpPGaldieria sulphurariaacpPGracilaria tenuistipitataacpPPlocamium cartilagineumacpPRiquetophycus sp.acpPGracilariopsis lemaneiformisorf8Grateloupia taiwanensisacpPRhodella maculataacpPCyanidium caldariumacpPRhodochaete parvulaacpPPyropia haitanensisacpPKumanoa americanaacpPRhodosorus marinusacpPPyropia kanakaensisacpPPorphyra purpureaacpPGelidium vagumacpPPyropia fucicolaacpPSporolithon durumacpPCyanidioschyzon merolaeacpPGelidium elegansacpPRhodella violaceaacpPPyropia yezoensisacpPThorea hispidaacpPRhodymenia pseudopalmataacpPPorphyridium sordidumacpPCeramium japonicumacpPCalliarthron tuberculosumacpPAhnfeltia plicataacpPPyropia perforataacpPGracilariopsis chordaacpPBangiopsis subsimplexacpPPorphyra pulchraacpPPorphyra umbilicalisacpPApophlaea sinclairiiacpPGracilaria chilensisacpPErythrotrichia carneaacpPPorphyridium purpureumacpPSchizymenia dubyiacpPPalmaria palmataacpPVertebrata lanosaacpPBangia fuscopurpureaacpPSebdenia flabellataacpPHildenbrandia rubraacpPChondrus crispusacpPGracilaria salicorniaacpPCyanidiaceae sp.acpP5Sebdenia flabellataacsFPorphyra pulchraacsFRhodymenia pseudopalmataacsFPalmaria palmataacsFSporolithon durumacsFRhodella maculataacsFApophlaea sinclairiiacsFPorphyridium purpureumacsFCyanidioschyzon merolaeycf59Gracilaria salicorniaycf59Cyanidium caldariumycf59Gracilaria chilensisacsFPyropia yezoensisycf59Thorea hispidaacsFPorphyra purpureaycf59Pyropia perforataycf59Galdieria sulphurariaacsFRhodochaete parvulaacsFPlocamium cartilagineumacsFGelidium elegansacsFGrateloupia taiwanensisacsFErythrotrichia carneaacsFCeramium japonicumacsFPyropia fucicolaycf59Cyanidiaceae sp.ycf59Bangiopsis subsimplexacsFRhodella violaceaacsFRhodosorus marinusacsFPyropia haitanensisycf59Kumanoa americanaacsFChondrus crispusacsFCalliarthron tuberculosumacsFRiquetophycus sp.acsFGelidium vagumacsFBangia fuscopurpureaycf59Porphyra umbilicalisYcf59Gracilariopsis lemaneiformisycf59Ahnfeltia plicataacsFVertebrata 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sulphurariaftsHRhodella violaceaftsHGrateloupia taiwanensisftsHApophlaea sinclairiiftsHCyanidiaceae sp.ftsHRhodymenia pseudopalmataftsHRhodochaete parvulaftsHBangiopsis subsimplexftsHGracilariopsis chordaftsHHildenbrandia rivularisftsHAhnfeltia plicataftsHPorphyra purpureaftsHPalmaria palmataftsHCyanidioschyzon merolaeftsHSchizymenia dubyiftsHPyropia kanakaensisftsHVertebrata lanosaftsHErythrotrichia carneaftsH40Erythrotrichia carneagltBPorphyra purpureagltBPyropia kanakaensisgltBSebdenia flabellatagltBCyanidiaceae sp.gltBGelidium vagumgltBGracilaria chilensisgltBBangia fuscopurpureagltBSporolithon durumgltBCeramium japonicumgltBBangiopsis subsimplexgltBHildenbrandia rivularisgltBCyanidioschyzon merolaegltBGracilariopsis lemaneiformisgltBPalmaria palmatagltBKumanoa americanagltBPyropia haitanensisgltBCalliarthron tuberculosumgltBAhnfeltia plicatagltBPorphyra pulchragltBPyropia perforatagltBGracilaria tenuistipitatagltBCyanidium caldariumgltBPlocamium cartilagineumgltBGelidium elegansgltBPorphyridium sordidumgltBRiquetophycus sp.gltBGracilariopsis chordagltBPyropia yezoensisgltBGrateloupia taiwanensisgltBSchizymenia dubyigltBGracilaria salicorniagltBAsparagopsis taxiformisgltBRhodymenia pseudopalmatagltBSchimmelmannia schousboeigltBRhodochaete parvulagltBChondrus crispusgltBGaldieria sulphurariagltBPyropia fucicolagltBApophlaea sinclairiigltBPorphyridium purpureumgltBPorphyra umbilicalisgltBVertebrata lanosagltBThorea hispidagltBRhodosorus marinusgltBHildenbrandia rubragltB41Cyanidiaceae sp.groELHildenbrandia rivularisgroELVertebrata lanosagroELChondrus crispusgroELGrateloupia taiwanensisgroELCyanidioschyzon merolaegroELPyropia kanakaensisgroELGracilariopsis lemaneiformisgroELHildenbrandia rubragroELPyropia perforatagroELGracilariopsis chordagroELAsparagopsis taxiformisgroELPlocamium cartilagineumgroELSchimmelmannia schousboeigroELPorphyra pulchragroELPyropia yezoensisgroELRhodymenia pseudopalmatagroELPalmaria palmatagroELAhnfeltia plicatagroELCeramium japonicumgroELRhodella violaceagroELRhodella maculatagroELPyropia fucicolagroELGelidium vagumgroELApophlaea sinclairiigroELCalliarthron tuberculosumgroELKumanoa americanagroELSporolithon durumgroELRhodosorus marinusgroELGracilaria chilensisgroELGracilaria salicorniagroELGelidium elegansgroELGracilaria tenuistipitatagroELPorphyridium sordidumgroELCyanidium caldariumgroELRhodochaete parvulagroELPorphyra umbilicalisgroELPorphyra purpureagroELSebdenia flabellatagroELRiquetophycus sp.groELBangia fuscopurpureagroELThorea hispidagroELPorphyridium purpureumgroELPyropia haitanensisgroELBangiopsis subsimplexgroELGaldieria sulphurariagroELErythrotrichia carneagroELSchizymenia dubyigroEL42Schimmelmannia schousboeiilvBApophlaea sinclairiiilvBRhodochaete parvulailvBPlocamium cartilagineumilvBGracilaria salicorniailvBSebdenia flabellatailvBPorphyridium purpureumilvBPalmaria palmatailvBSporolithon durumilvBPorphyra purpureailvBRhodosorus marinusilvBPyropia yezoensisilvBGracilariopsis lemaneiformisilvBGelidium vagumilvBCeramium japonicumilvBBangia fuscopurpureailvBGracilaria tenuistipitatailvBPorphyra pulchrailvBBangiopsis subsimplexilvBRiquetophycus sp.ilvBCyanidium caldariumilvBHildenbrandia rivularisilvBKumanoa americanailvBCyanidioschyzon merolaeilvBPyropia kanakaensisilvBGaldieria sulphurariailvBSchizymenia dubyiilvBPyropia haitanensisilvBPyropia perforatailvBAsparagopsis taxiformisilvBThorea hispidailvBChondrus crispusilvBGrateloupia taiwanensisilvBHildenbrandia rubrailvBErythrotrichia carneailvBRhodella violaceailvBPorphyra umbilicalisilvBAhnfeltia plicatailvBPorphyridium sordidumilvBCyanidiaceae sp.ilvBGracilaria chilensisilvBRhodella maculatailvBPyropia fucicolailvBGelidium elegansilvBRhodymenia pseudopalmatailvBCalliarthron tuberculosumilvBGracilariopsis chordailvBVertebrata lanosailvB43Thorea hispidailvHApophlaea sinclairiiilvHSporolithon durumilvHGelidium elegansilvHGracilaria tenuistipitatailvHGrateloupia taiwanensisilvHCeramium japonicumilvHCyanidioschyzon merolaeilvHKumanoa americanailvHRhodosorus marinusilvHGracilariopsis chordailvHSchizymenia dubyiilvHPorphyra purpureailvHPlocamium cartilagineumilvHPyropia perforatailvHPorphyra umbilicalisilvHErythrotrichia carneailvHRhodochaete parvulailvHPyropia haitanensisilvHSebdenia flabellatailvHRhodella maculatailvHPyropia yezoensisilvHHildenbrandia rubrailvHBangiopsis subsimplexilvHGelidium vagumilvHPorphyridium sordidumilvHGracilariopsis lemaneiformisilvHVertebrata lanosailvHRhodella violaceailvHRiquetophycus sp.ilvHCyanidium caldariumilvHChondrus crispusilvHRhodymenia pseudopalmatailvHPorphyra pulchrailvHGracilaria chilensisilvHCalliarthron tuberculosumilvHPorphyridium purpureumilvHCyanidiaceae sp.ilvHSchimmelmannia schousboeiilvHAhnfeltia plicatailvHHildenbrandia rivularisilvHGracilaria salicorniailvHAsparagopsis taxiformisilvHPalmaria palmatailvHPyropia kanakaensisilvHBangia fuscopurpureailvHGaldieria sulphurariailvHPyropia fucicolailvH44Plocamium cartilagineuminfBSporolithon duruminfBPyropia yezoensisinfBGrateloupia taiwanensisinfBBangia fuscopurpureainfBCalliarthron tuberculosuminfBGelidium elegansinfBPyropia kanakaensisinfBRhodymenia pseudopalmatainfBAsparagopsis taxiformisinfBSchimmelmannia schousboeiinfBRiquetophycus sp.infBGelidium vaguminfBPorphyridium sordiduminfBSchizymenia dubyiinfBGracilariopsis chordainfBGracilaria salicorniainfBPalmaria palmatainfBHildenbrandia rivularisinfBBangiopsis subsimplexinfBCeramium japonicuminfBGracilaria tenuistipitatainfBRhodella violaceainfBPorphyra umbilicalisinfBPyropia haitanensisinfBKumanoa americanainfBPyropia fucicolainfBPyropia perforatainfBHildenbrandia rubrainfBGaldieria sulphurariainfBPorphyra pulchrainfBGracilariopsis lemaneiformisinfBRhodosorus marinusinfBErythrotrichia carneainfBPorphyridium purpureuminfBCyanidioschyzon merolaeinfBCyanidiaceae sp.infBAhnfeltia plicatainfBPorphyra purpureainfBThorea hispidainfBRhodella maculatainfBRhodochaete parvulainfBGracilaria chilensisinfBVertebrata lanosainfBApophlaea sinclairiiinfBChondrus crispusinfBSebdenia flabellatainfB45Porphyridium sordiduminfCErythrotrichia carneainfCGelidium vaguminfCHildenbrandia rubrainfCKumanoa americanainfCCyanidioschyzon merolaeinfCSebdenia flabellatainfCRhodella violaceainfCPorphyra purpureainfCSporolithon duruminfCRiquetophycus sp.infCPorphyra pulchrainfCGracilaria chilensisinfCGracilaria salicorniainfCPorphyridium purpureuminfCPyropia haitanensisinfCAhnfeltia plicatainfCPyropia yezoensisinfCHildenbrandia rivularisinfCPlocamium cartilagineuminfCGaldieria sulphurariainfCGelidium elegansinfCRhodochaete parvulainfCSchizymenia dubyiinfCChondrus crispusinfCVertebrata lanosainfCApophlaea sinclairiiinfCBangia fuscopurpureainfCPalmaria palmatainfCGracilaria tenuistipitatainfCCeramium japonicuminfCCalliarthron tuberculosuminfCGrateloupia taiwanensisinfCPyropia perforatainfCPyropia kanakaensisinfCRhodymenia pseudopalmatainfCGracilariopsis lemaneiformisinfCPorphyra umbilicalisinfCRhodosorus marinusinfCCyanidiaceae sp.infCPyropia fucicolainfCThorea hispidainfCSchimmelmannia schousboeiinfCBangiopsis subsimplexinfCAsparagopsis taxiformisinfCCyanidium caldariuminfCGracilariopsis chordainfCRhodella maculatainfC46Pyropia yezoensisORF382Gelidium vagummoeBRhodosorus marinusmoeBBangia fuscopurpureaorf382Cyanidium caldariummoeBRhodella maculatamoeBCalliarthron tuberculosummoeBSchizymenia dubyimoeBPalmaria palmatamoeBErythrotrichia carneaorf383Gracilaria salicorniamoeBGracilariopsis chordamoeBAhnfeltia plicatamoeBCyanidiaceae sp.moeBGracilaria chilensismoeBHildenbrandia rubramoeBHildenbrandia rivularismoeBSebdenia flabellatamoeBApophlaea sinclairiimoeBRhodymenia pseudopalmatamoeBSporolithon durummoeBSchimmelmannia schousboeimoeBPorphyridium purpureummoeBAsparagopsis taxiformismoeBPyropia haitanensisORF382Galdieria sulphurariamoeBPyropia kanakaensismoeBBangiopsis subsimplexmoeBPorphyridium sordidummoeBPorphyra umbilicalisorf383Gracilaria tenuistipitatamoeBPorphyra pulchramoeBRhodella violaceamoeBVertebrata lanosamoeBPyropia fucicolamoeBCeramium japonicummoeBKumanoa americanamoeBPlocamium cartilagineummoeBGracilariopsis lemaneiformismoeBPyropia perforatamoeBChondrus crispusmoeBRhodochaete parvulaorf383Thorea hispidamoeBPorphyra purpureaORF382Cyanidioschyzon merolaemoeBRiquetophycus sp.moeBGelidium elegansmoeBGrateloupia taiwanensismoeB47Hildenbrandia rubranblABangiopsis subsimplexnblAChondrus crispusnblAVertebrata lanosanblAGracilariopsis lemaneiformisnblACyanidioschyzon merolaenblAPorphyra umbilicalisycf18Calliarthron tuberculosumnblAPalmaria palmatanblAAsparagopsis taxiformisnblASchizymenia dubyinblAPyropia fucicolanblAGracilaria salicornianblACyanidiaceae sp.nblARhodymenia pseudopalmatanblAGelidium vagumnblAGracilariopsis chordanblACeramium japonicumnblAThorea hispidanblABangia fuscopurpureaycf18Porphyra purpureaycf18Hildenbrandia rivularisnblAErythrotrichia carneanblARiquetophycus sp.nblASporolithon durumnblAPorphyridium purpureumnblAGaldieria sulphurarianblACyanidium caldariumycf18Porphyridium sordidumnblAGracilaria chilensisnblARhodochaete parvulanblAPorphyra pulchranblARhodosorus marinusnblASebdenia flabellatanblAApophlaea sinclairiinblAGrateloupia taiwanensisnblASchimmelmannia schousboeinblAKumanoa americananblAPyropia haitanensisycf18Gracilaria tenuistipitatanblAGelidium elegansnblAPyropia yezoensisycf18Plocamium cartilagineumnblAPyropia perforatanblAPyropia kanakaensisnblAAhnfeltia plicatanblA48Kumanoa americanantcAPorphyridium purpureumntcABangia fuscopurpureaycf28Gracilaria salicorniantcACyanidioschyzon merolaeycf28Calliarthron tuberculosumntcAGracilariopsis lemaneiformisntcAGaldieria sulphurariantcAGracilaria chilensisntcAChondrus crispusntcAPorphyridium sordidumntcARhodosorus marinusntcARhodochaete parvulantcAThorea hispidantcAErythrotrichia carneantcAPorphyra umbilicalisycf28Pyropia kanakaensisycf28Porphyra purpureaycf28Pyropia fucicolaycf28Vertebrata lanosantcAGracilaria tenuistipitatantcARiquetophycus sp.ntcARhodella maculatantcAPyropia haitanensisycf28Ahnfeltia plicatantcASporolithon durumntcAPlocamium cartilagineumntcARhodymenia pseudopalmatantcAGracilariopsis chordantcARhodella violaceantcAGelidium elegansntcACyanidium caldariumntcAGelidium vagumntcAHildenbrandia rivularisntcASebdenia flabellatantcAPorphyra pulchrantcACyanidiaceae sp.ycf28Ceramium japonicumntcAApophlaea sinclairiintcAPyropia perforataycf28Pyropia yezoensisycf28Asparagopsis taxiformisntcAGrateloupia taiwanensisntcASchimmelmannia schousboeintcAPalmaria palmatantcASchizymenia dubyintcA49Pyropia fucicolaodpASporolithon durumodpAGelidium vagumodpAAsparagopsis taxiformisodpAPorphyra pulchraodpARhodymenia pseudopalmataodpASchimmelmannia schousboeiodpAGracilariopsis chordapdhARhodochaete parvulaodpASchizymenia dubyiodpAGracilaria salicorniaodpAHildenbrandia rivularisodpAGracilaria chilensisodpARhodella maculataodpAGrateloupia taiwanensisodpARhodosorus marinusodpACalliarthron tuberculosumpdhAPyropia perforataodpACyanidioschyzon merolaeodpAKumanoa americanapdhAHildenbrandia rubraodpAPorphyridium purpureumodpABangiopsis subsimplexodpACeramium japonicumodpARhodella violaceaodpAVertebrata lanosaodpAGelidium elegansodpABangia fuscopurpureaodpAPlocamium cartilagineumodpAPorphyra purpureaodpAPyropia haitanensisodpAThorea hispidapdhACyanidiaceae sp.odpAPyropia yezoensisodpAChondrus crispuspdhAApophlaea sinclairiiodpAPyropia kanakaensisodpAGracilariopsis lemaneiformisodpAGracilaria tenuistipitataodpAPorphyra umbilicalisodpAAhnfeltia plicataodpAGaldieria sulphurariaodpAErythrotrichia carneaodpACyanidium caldariumodpASebdenia flabellataodpAPalmaria palmatapdhARiquetophycus sp.odpAPorphyridium sordidumodpA50Pyropia haitanensisodpBGracilaria chilensisodpBCyanidioschyzon merolaeodpBRhodosorus marinuspdhBCyanidiaceae sp.odpBCyanidium caldariumodpBRhodella violaceaodpBPyropia kanakaensisodpBGelidium vagumodpBRhodymenia 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americanaorf761Pyropia yezoensisORF621Bangiopsis subsimplexorf751Gracilaria salicorniahypothetical proteinPorphyra purpureaORF621Gracilaria chilensisORF220Grateloupia taiwanensisORF621Plocamium cartilagineumorf227Ceramium japonicumorf621Calliarthron tuberculosumORF700Porphyra pulchraORF621Gelidium elegansORF621Rhodella violaceaORF428Pyropia kanakaensisorf621Rhodymenia pseudopalmataorf621Chondrus crispusCcr_ORF745Pyropia fucicolaorf621Rhodochaete parvulaorf721Rhodosorus marinusorf751Riquetophycus sp.ORF621Rhodella maculataORF428Sporolithon durumORF408Gelidium vagumORF614Palmaria palmataorf621Asparagopsis taxiformisorf621Pyropia perforataorf621Gracilariopsis lemaneiformisorf12Sebdenia flabellataorf62153Porphyra purpureapbsARiquetophycus sp.pbsAAhnfeltia plicatapbsARhodosorus marinuspbsAChondrus crispuspbsAPyropia haitanensispbsAPyropia perforatapbsASporolithon durumpbsACeramium japonicumpbsAPyropia fucicolapbsARhodella violaceapbsAGracilaria salicorniapbsAVertebrata lanosapbsASchimmelmannia schousboeipbsACalliarthron tuberculosumpbsAPorphyridium purpureumpbsAPlocamium cartilagineumpbsAGracilaria tenuistipitatapbsARhodella maculatapbsAGelidium eleganspbsAPalmaria palmatapbsASchizymenia dubyipbsAPyropia yezoensispbsAAsparagopsis taxiformispbsAErythrotrichia carneapbsAGelidium vagumpbsAGracilariopsis chordapbsAPyropia kanakaensispbsAGrateloupia taiwanensispbsAPorphyra umbilicalispbsARhodymenia pseudopalmatapbsAPorphyra pulchrapbsASebdenia flabellatapbsABangia fuscopurpureapbsARhodochaete parvulapbsAGracilariopsis lemaneiformispbsABangiopsis subsimplexpbsAPorphyridium sordidumpbsA54Calliarthron tuberculosumpetAPorphyridium purpureumpetACyanidium caldariumpetAGrateloupia taiwanensispetASchimmelmannia schousboeipetABangiopsis subsimplexpetAPyropia fucicolapetAGracilaria tenuistipitatapetAKumanoa americanapetARhodella maculatapetARhodella violaceapetARhodosorus marinuspetAPyropia kanakaensispetASporolithon durumpetAPlocamium cartilagineumpetAPalmaria 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purpureumpetBRhodella maculatapetBGracilaria chilensispetBGaldieria sulphurariapetBRiquetophycus sp.petBSchizymenia dubyipetBSchimmelmannia schousboeipetBAsparagopsis taxiformispetBHildenbrandia rivularispetBPorphyra purpureapetBSporolithon durumpetBCalliarthron tuberculosumpetBGracilaria salicorniapetBPyropia haitanensispetBPyropia kanakaensispetBThorea hispidapetBPlocamium cartilagineumpetBPyropia yezoensispetBPalmaria palmatapetBCyanidium caldariumpetBApophlaea sinclairiipetBVertebrata lanosapetBGelidium eleganspetBRhodochaete parvulapetBSebdenia flabellatapetBChondrus crispuspetBPorphyra umbilicalispetBGracilariopsis chordapetBAhnfeltia plicatapetBRhodella violaceapetBPyropia perforatapetBBangiopsis subsimplexpetBBangia fuscopurpureapetBGracilaria tenuistipitatapetBErythrotrichia carneapetBGelidium vagumpetBPyropia fucicolapetBGrateloupia taiwanensispetB56Vertebrata lanosapetDGelidium eleganspetDPorphyridium purpureumpetDGracilaria tenuistipitatapetDGracilariopsis 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