91/87/96/+/+ Citrus clememtina† Manihot esculeanta† Vitis vinifera† Solanum lycopersicum† Arabidopsis thaliana† Aquilegia coerulea† Angiosperm PHOT1 Amborella trichopoda† 92/89/91/+/+ Setaria italica† Sorghum bicolor† Oryza sativa† Cunninghamia lanceolata OUOI KJ195049 +/+/99/+/+ Thuja plicata VFYZ KJ195050 Cephalotaxus harringtonia WYAJ KJ195047 Podocarpus rubens XLGK KJ195048 Stangeria eriopus KAWQ KJ195051 Gymnosperm PHOT1 Welwitschia mirabilis TOXE KJ195052 Gnetum montanum GTHK KJ195053 93/89/95/+/+ Arabidopsis thaliana† +/97/+/+/+ 88/83/94/+/+ Citrus clememtina† 87/88/94/+/+ Manihot esculeanta† 92/98/80/+/+ Vitis vinifera† Solanum lycopersicum† Aquilegia coerulea† Angiosperm PHOT2 Sorghum bicolor† +/+/+/98/+ Setaria italica† Oryza sativa† Amborella trichopoda† Thuja plicata VFYZ KJ195057 Cunninghamia lanceolata OUOI KJ195056 Cephalotaxus harringtonia WYAJ KJ195054 98/96/+/+/+ Podocarpus rubens XLGK KJ195055 Gymnosperm PHOT2 Gnetum montanum GTHK KJ195060 70/81/88/+/+ Welwitschia mirabilis TOXE KJ195059 Stangeria eriopus KAWQ KJ195058 98/97/95/+/+ Leucostegia immersa WGTU KJ195062 97/92/96/+/+ Polypodium hesperium GYFU KJ195061 98/98/97/+/+ Cystopteris reevesiana RICC KJ195063 Pteridium aquilinum‡ Adiantum capillus-veneris AB037188 Fern PHOT1 Pilularia globulifera KIIX KJ195065 Osmunda sp. UOMY KJ195066 99/+/95/+/+ +/99/+/+/+ Leucostegia immersa WGTU KJ195068 82/85/+/+/+ Polypodium hesperium GYFU KJ195067 +/+/99/+/+ Cystopteris reevesiana RICC KJ195069 Pteridium aquilinum‡ Adiantum capillus-veneris AB115545 Fern PHOT2 Pilularia globulifera KIIX KJ195071 +/97/99/+/+ Osmunda sp. UOMY KJ195072 Selaginella moellendorffii† XM_002971663 Selaginella kraussiana ZFGK KJ195077 Isoetes tegetiformans PKOX KJ195078 Selaginella kraussiana ZFGK KJ195076 Selaginella moellendorffii† XM_002965438 Lycophyte PHOT Lycopodium deuterodensum PQTO KJ195073 Huperzia lucidula GKAG KJ195075 Pseudolycopodiella caroliniana UPMJ KJ195074 Schistochila sp. LGOW KJ195081 Scapania nemorosa IRBN KJ195079 Porella pinnata UUHD KJ195080 Metzgeria crassipilis NRWZ KJ195082 Pellia neesiana JHFI KJ195083 Liverwort PHOT 99/99/97/+/+ Marchantia polymorpha JPYU KJ195084 +/83/+/+/+ Conocephalum conicum ILBQ KJ195085 +/+/99/+/+ Sphaerocarpos texanus HERT KJ195086 Bryum argenteum JMXW KJ195089 Anomodon rostratus VBMM KJ195087 Timmia austriaca ZQRI KJ195090 Scouleria aquatica BPSG KJ195088 Physcomitrella patens† XM_001774204 Moss PHOTA 93/76/82/+/+ Bryum argenteum JMXW 98/97/+/+/+ Physcomitrella patens† XM_001765356 KJ195092 Polytrichum commune SZYG KJ195091 Sphagnum lescurii GOWD KJ195093 97/97/99/+/+ Anomodon rostratus VBMM KJ195094 Bryum argenteum JMXW KJ195095 97/95/88/+/+ Scouleria aquatica BPSG KJ195096 Timmia austriaca ZQRI KJ195099 97/95/+/+/+ Physcomitrella patens† XM_001766357 Moss PHOTB 95/97/99/+/+ Scouleria aquatica BPSG KJ195098 Anomodon rostratus VBMM KJ195097 Polytrichum commune gametophyte SZYG KJ195100 80/85/99/+/+ Sphagnum lescurii GOWD KJ195101 Go to Fig. S2 Coleochaete scutata VQBJ KJ195103 Coleochaete irregularis QPDY KJ195102 Coleochaetophyceae PHOT Cylindrocystis brebissonii YOXI KJ195116 +/99/+/+/+ Cylindrocystis sp. VAZE KJ195115 Cylindrocystis brebissonii YOXI KJ195114 96/96/95/+/+ Cylindrocystis sp. VAZE KJ195113 77/83/84/+/.99 Cylindrocystis cushleckae JOJQ KJ195118 96/99/94/+/+ 78/76/79/+/+ Zygnemopsis sp. MFZO KJ195117 Zygnemataceae PHOT Mougeotia scalaris AB206964 87/98/80/+/+ 99/98/+/+/+ Cylindrocystis cushleckae JOJQ KJ195120 Zygnemopsis sp. MFZO KJ195119 Mougeotia scalaris AB206963 91/71/90/+/+ Cosmocladium constrictum RQFE KJ195110 99/99/+/+/+ +/99/99/+/+ Desmidium aptogonum DFDS KJ195109 Penium margaritaceum AEKF KJ195112 Desmidaceae PHOT Planotaenium ohtanii SNOX KJ195111 Zygnemataceae NEO Cylindrocystis brebissonii YOXI KJ195044 Cylindrocystis sp. VAZE KJ195043 Cylindrocystis brebissonii YOXI KJ195042 Cylindrocystis sp. VAZE KJ195041 Mougeotia scalaris AB206961 Mougeotia scalaris +/+/+/+/.94 Zygnemopsis sp. MFZO KJ195039 AB206962 94/96/96/+/+ Cylindrocystis cushleckae JOJQ KJ195040 Mesotaenium braunii WSJO KJ195046 Mesotaenium braunii WSJO KJ195045 Mesotaenium braunii WSJO KJ195121 +/99/99/+/+ Zygnemataceae PHOT Klebsormidium subtile FQLP KJ195104 Interfilum paradoxum FPCO KJ195105 Klebsormidiophyceae PHOT Entransia fimbriata BFIK KJ195106 +/+/99/+/+ Mesostigma viride KYIO KJ195108 Chlorokybus atmophyticus AZZW KJ195107 Mesostigmatophyceae PHOT Volvox carteri† 87/74/90/+/+ Chlamydomonas reinhardtii† Chloromonas tughillensi UTRE KJ195124 Chlorophyceae PHOT Oedogonium cardiacum DVYE KJ195125 96/95/97/+/+ Botryococcus terribilis QYXY KJ195130 93/95/99/+/+ Coccomyxa pringsheimii GXBM KJ195129 Trebouxiophyceae PHOT 98/96/95/+/+ Prasiola crispa WCLV KJ195128 Percursaria percursa OAEZ KJ195126 83/94/94/+/+ Bolbocoleon piliferum LSHT KJ195127 Ulvophyceae PHOT Nephroselmis olivacea MMKU KJ195123 Cymbomonas sp XIVI KJ195122 +/99/99/+/+ +/99/+/+/+ Micromonas pusilla† Prasinophyte PHOT 0.3 substitutions/site Ostreococcus tauri† Fig. S1. Phylogenetic relationships of land plant and algal phototropin (PHOT) and the corresponding domains from hornwort, fern, and algal neochrome (NEO). Topology derived from the best maximum likelihood tree. The five support values associated with branches are maximum likelihood bootstrap values (BS) from Garli / BS from nhPhyML / aLRT supports under codon model (aLRT) / Bayesian posterior probabilities (PP) from MrBayes / PP from BEAST; these are only displayed (along with thickened branches) when BS > 70, aLRT > 70 and PP > 0.95. “+” denotes BS = 100, aLRT = 100 or PP = 1.00; thickened branches without numbers are “+/+/+/+/+”. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, or Genbank accessions, or both; “†” indicates the sequence came from genome sequence data, and “‡” from Pteridium aquilinum transcriptome. The blue, orange and yellow branches represent hornwort phototropin, hornwort neochrome and fern neochrome, respectively. Phegopteris hexagonoptera KJ195023 Athyrium filix-femina AFPO KJ195025 Deparia acrostichoides KJ195013 Adiantum aleuticum WCLG KJ195006 Onoclea sensilibis KJ195024 94/96/98/+/+ Thelypteris noveboracensis KJ195034 Macrothelypteris torresiana KJ195012 Homalosorus pycnocarpos OCZL KJ195008 Coniogramme intermedia var glabra FJ501964 Plagiogyria distinctissima FJ501965 Alsophila podophylla KJ195014 Dennstaedtia punctilobula KJ195016 Pronephrium lakhimpurense FJ501966 97/97/98/+/+ Dryopteris amurensis KJ195017 Fern NEO Allantodia dilatata FJ455447 86/83/96/+/+ Diplazium wichurae UFJN KJ195009 Blechnum spicant KJ195007 95/93/96/+/+ Plagiogyria japonica UWOD KJ195018 Dipteris conjugata MEKP KJ195011 +/+/98/+/+ Lindsaea linearis NOKI KJ195004 Go to 99/99/96/+/+ Adiantum capillus-veneris AB012082 87/85/93/+/+ Hemidictyum marginatum KJ195037 Fig. S1 Hypolepis tenuifolia KJ195036 Adiantum raddianum BMJR KJ195003 99/99/95/+/+ Nothoceros aenigmaticus KJ128382 Megaceros flagellaris UCRN KJ195000 93/93/98/+/+ 94/89/95/+/+ Phymatoceros phymatodes KJ195002 Paraphymatoceros hallii FAJB KJ194999 Hornwort NEO 99/+/98/+/+ Phaeoceros carolinianus WCZB KJ194998 Anthoceros punctatus KJ194997 +/+/99/+/+ Nothoceros aenigmaticus KJ128383 Megaceros flagellaris UCRN KJ195132 +/99/+/+/+ 87/89/88/+/+ Phymatoceros phymatodes KJ195135 Paraphymatoceros hallii FAJB KJ195133 Hornwort PHOT Phaeoceros carolinianus WCZB KJ195134 Anthoceros punctatus KJ195131 0.3 substitutions/site Fig. S2. Phylogenetic relationships of fern neochrome (NEO), hornwort neochrome and phototropin (PHOT). This figure is continued from Fig. S1 and follows the same conventions. Citrus clememtina† 96/+/+ Arabidopsis thaliana† 83/97/+ Solanum lycopersicum† Vitis vinifera† 89/98/+ Aquilegia coerulea† Setaria italica† Angiosperm PHYA Sorghum bicolor† Oryza sativa† 73/85/.98 Amborella trichopoda† Encephalartos barteri GNQG KJ195166 Welwitschia mirabilis TOXE KJ195164 Gnetum montanum GTHK KJ195165 Pinus parviflora IIOL KJ195163 Gymnosperm PHYN Podocarpus rubens XLGK KJ195161 Taiwania cryptomerioides QSNJ KJ195162 Solanum lycopersicum† Arabidopsis thaliana† Citrus clememtina† Vitis vinifera† Aquilegia coerulea† Angiosperm PHYC 99/+/+ Setaria italica† Sorghum bicolor† Oryza sativa† 92/91/+ Podocarpus rubens XLGK KJ195167 96/+/.97 Taiwania cryptomerioides QSNJ KJ195168 Pinus parviflora IIOL KJ195169 Gymnosperm PHYO Encephalartos barteri GNQG KJ195170 Arabidopsis thaliana† Arabidopsis thaliana† Citrus clememtina† 93/98/+ 99/+/+ Solanum lycopersicum† Solanum lycopersicum† Angiosperm PHYB Vitis vinifera† Aquilegia coerulea† Amborella trichopoda† Citrus clememtina† Arabidopsis thaliana† Solanum lycopersicum† Angiosperm PHYE Aquilegia coerulea† 96/97/+ Aquilegia coerulea† Welwitschia mirabilis TOXE KJ195159 75/96/+ Gnetum montanum GTHK KJ195158 Pinus parviflora IIOL KJ195157 95/99/.99 Podocarpus rubens XLGK KJ195156 Gymnosperm PHYP Taiwania cryptomerioides QSNJ KJ195155 Encephalartos barteri GNQG KJ195160 Blechnum spicant VITX KJ195143 93/+/+ Polypodium hesperium GYFU KJ195144 Pteridium aquilinum‡ Adiantum capillus-veneris AB016232 Fern PHY2 Plagiogyria japonica UWOD KJ195141 Pilularia globulifera KIIX KJ195142 82/+/+ Blechnum spicant VITX KJ195148 99/+/+ Polypodium hesperium GYFU KJ195149 97/+/+ Adiantum tenerum BMJR KJ195147 Pilularia globulifera KIIX KJ195146 Fern PHY4 98/+/+ Plagiogyria japonica UWOD KJ195145 Anemia tomentosa CQPW KJ195140 Dipteris conjugata MEKP KJ195139 97/+/+ Osmunda sp. UOMY KJ195138 Botrypus virginianus BEGM KJ195137 Fern PHY2/4 Equisetum diffusum CAPN KJ195136 Polypodium glycyrrhiza CJNT