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 KJ195154 Pteridium aquilinum‡ Adiantum capillus-veneris AB016151 91/96/+ Blechnum spicant VITX KJ195153 Fern PHY1 Plagiogyria japonica UWOD KJ195152 Pilularia globulifera KIIX KJ195151 Osmunda sp. UOMY KJ195150

Dendrolycopodium obscurum XNXF KJ195173 Huperzia selago GTUO KJ195174 Dendrolycopodium obscurum XNXF KJ195175 Huperzia lucidula GKAG KJ195176 Lycophyte PHY +/98/+ Selaginella moellendorffii† XM_002991595 Selaginella wallacei JKAA KJ195172 Isoetes tegetiformans PKOX KJ195171

Porella pinnata UUHD KJ195178 Scapania nemorosa IRBN KJ195177 80/95/+ 98/+/+ Schistochila sp. LGOW KJ195179 Metzgeria crassipilis NRWZ KJ195180 96/+/+ Pellia neesiana JHFI KJ195181 Liverwort PHY Conocephalum conicum ILBQ KJ195182 83/+/+ Marchantia paleacea var diptera AB022917 97/+/+ Sphaerocarpos texanus HERT KJ195183

90/+/+ Paraphymatoceros hallii FAJB KJ195198 Phaeoceros carolinianus WCZB KJ195199 84/+/+ Megaceros flagellaris UCRN KJ195197 Hornwort PHY Nothoceros aenigmaticus KJ128384 Tectaria zeylanica KJ195022 Anthoceros punctatus KJ195038 Pronephrium lakhimpurense FJ501966 Hedwigia ciliata YWNF KJ195190 72/+/.91 Blechnum spicant KJ195007 Anomodon rostratus VBMM KJ195189 KJ195021 Bryum argenteum JMXW KJ195191 Matteuccia struthiopteris +/84/+ Physcomitrella patens† XM_001773498 Alsophila podophylla KJ195014 +/99/+ Physcomitrella patens† XM_001782287 Plagiogyria distinctissima FJ501965 Timmia austriaca ZQRI KJ195192 95/+/+ 94/+/+ Anomodon rostratus VBMM KJ195184 Homalosorus pycnocarpos OCZL KJ195008 99/+/+ Hedwigia ciliata YWNF KJ195186 84/97/+ Dennstaedtia punctilobula KJ195016 Fern NEO Timmia austriaca ZQRI KJ195188 93/96/+ 99/+/+ Bryum argenteum JMXW KJ195187 Moss PHY Allantodia dilatata FJ455447 KJ195185 Anomodon rostratus VBMM Dryopteris expansa KJ195015 94/98/+ Physcomitrella patens† XM_001761093 Hedwigia ciliata YWNF KJ195194 Dipteris conjugata MEKP KJ195011 Bryum argenteum JMXW KJ195195 Hemidictyum marginatum KJ195037 Anomodon rostratus VBMM KJ195193 80/98/+ Adiantum capillus-veneris AB012082 93/97/+Physcomitrella patens† XM_001765983 Physcomitrella patens† XM_001778103 Nothoceros aenigmaticus KJ128382 Timmia austriaca ZQRI KJ195196 Megaceros flagellaris UCRN KJ195132 77/98/+ Phymatoceros phymatodes KJ195002 76/93/+ Hornwort NEO Paraphymatoceros hallii FAJB KJ194999

Phaeoceros carolinianus WCZB KJ194998

Anthoceros punctatus KJ194997

Mougeotia scalaris AB206965 Mesotaenium caldariorum U31283 Zygnemopsis sp. MFZO KJ195202 Cylindrocystis brebissonii YOXI KJ195204 98/96/+ Cylindrocystis sp. VAZE KJ195203 Zygnematophyceae PHY 98/99/+ Roya obtusa XRTZ KJ195200 Planotaenium ohtanii SNOX KJ195201 Mesotaenium braunii WSJO KJ195205

94/98/+ 97/99/+ Chaetosphaeridium globosum DRGY KJ195207 Coleochaete irregularis QPDY KJ195206 Coleochaetophyceae PHY

Interfilum paradoxum FPCO KJ195208 Klebsormidium subtile FQLP KJ195209 Klebsormidiophyceae PHY Entransia fimbriata BFIK KJ195210 0.2 substitutions/site Fig. S3. Phylogenetic relationships of land plant and algal phytochrome (PHY) and the corresponding domains from hornwort and fern neochrome (NEO). Topology derived from the best maximum likelihood tree. The three support values associated with branches are maximum likelihood bootstrap values (BS) / aLRT supports under codon model (aLRT) / Bayesian posterior probabilities (PP) from MrBayes; these are only displayed (along with thickened branches) if BS > 70, aLRT > 0.95 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 whole genome sequence data, and “‡” from Pteridium aquilinum transcriptome. For space considerations, the dashed line artificially extends the NEO clade and does not reflect true branch length. The orange and yellow branches represent hornwort neochrome and fern neochrome, respectively. Woodsia scopulina YJJY KJ195215 Blechnum spicant VITX KJ195216 72 Cystopteris fragilis LHLE KJ195214 Polystichum acrostichoides FQGQ KJ195212 80 100 Polypodium glycyrrhiza CJNT KJ195213 Leucostegia immersa WGTU KJ195211 Adiantum aleuticum WCLG KJ195217 90 Alsophila spinulosa GANB KJ195218 99 Pilularia globulifera KIIX KJ195220 Ferns 83 Plagiogyria japonica UWOD KJ195219 Dipteris conjugata MEKP KJ195221 60 Osmunda sp. UOMY KJ195222 Angiopteris evecta NHCM KJ195224 70 Sceptridium dissectum EEAQ KJ195223 Tmesipteris parva ALVQ KJ195225 Equisetum diffusum CAPN KJ195226

Selaginella moellendorffii† XM_002960207 100 Selaginella moellendorffii† XM_002967415 Isoetes sp. FITN KJ195229 Lycophytes 96 Huperzia selago NYBX KJ195228 Lycopodium annotinum ENQF KJ195227

94 Nothoceros vincentianus TCBC KJ195231 85 Nothoceros aenigmaticus DXOU KJ195230 93 Nothoceros aenigmaticus ψ KJ195232 Hornworts Megaceros flagellaris UCRN KJ195233 96 Paraphymatoceros hallii FAJB KJ195235 Phaeoceros carolinianus WCZB KJ195234

50 Polytrichum commune SZYG KJ195240 Bryum argenteum JMXW KJ195238 Timmia austriaca ZQRI KJ195237 99 Hedwigia ciliata YWNF KJ195239 Mosses 58 Anomodon rostratus VBMM KJ195236 78 Physcomitrella patens† XM_001759317 Sphagnum lescurii GOWD KJ195241

96 Scapania nemorosa IRBN KJ195243 86 Porella pinnata UUHD KJ195242 Pellia epiphylla PIUF KJ195244 Liverworts 90 99 Sphaerocarpos texanus HERT KJ195246 Marchantia paleacea IHWO KJ195245

Peperomia fraseri XSZI KJ195248 Illicium parviflorum ROAP KJ195249 Nuphar advena WTKZ KJ195247 Amborella trichopoda† 58 Zea mays† Aquilegia coerulea† Arabidopsis thaliana† Seed Plants Cryptomeria japonica DSXO KJ195250 80 Ephedra sinica VDAO KJ195251 52 Cedrus libani GGEA KJ195252 97 Ginkgo biloba SGTW KJ195253 0.2 substitutions/site Encephalartos barteri GNQG KJ195254

Fig. S4. Phylogenetic relationships of land plant imidazoleglycerol-phosphate dehydratase (IGPD). In the hornwort Nothoceros aenigmaticus, we conducted genome-walking downstream of neochrome and found a IGPD pseudogene (denoted by ψ). In a land plant phylogeny of IGPD our N. aenigmaticus pseudogene is most closely related to other hornwort IGPD. This relationship confirms that our hornwort neochrome sequence data were indeed derived from the hornwort genome, and not from symbiotic algae or fungi. Numbers associated with branches are maximum likelihood bootstrap support values. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, or Genbank accessions, or both; “†” indicates the sequence came from whole genome sequence data. Citrus clememtina Manihot esculeanta Vitis vinifera Solanum lycopersicum Arabidopsis thaliana Aquilegia coerulea Amborella trichopoda Angiosperm PHOT1 Setaria italica 12. Sorghum bicolor Oryza sativa 10. Thuja plicata VFYZ Cunninghamia lanceolata OUOI Cephalotaxus harringtonia WYAJ 14. Podocarpus rubens XLGK Welwitschia mirabilis TOXE Gymnosperm PHOT1 Gnetum montanum GTHK Stangeria eriopus KAWQ Citrus clememtina Arabidopsis thaliana Manihot esculeanta Vitis vinifera Solanum lycopersicum Aquilegia coerulea Setaria italica Angiosperm PHOT2 13. Sorghum bicolor Oryza sativa Amborella trichopoda Cunninghamia lanceolata OUOI 11. Thuja plicata VFYZ Cephalotaxus harringtonia WYAJ 15. Podocarpus rubens XLGK Gnetum montanum GTHK Gymnosperm PHOT2 2. Welwitschia mirabilis TOXE Stangeria eriopus KAWQ Leucostegia immersa WGTU Polypodium hesperium GYFU 8. Cystopteris reevesiana RICC Pteridium aquilinum Adiantum capillus-veneris Fern PHOT1 6. Pilularia globulifera KIIX Osmunda sp. UOMY Leucostegia immersa WGTU 1. 9. Polypodium hesperium GYFU Cystopteris reevesiana RICC Pteridium aquilinum Adiantum capillus-veneris Fern PHOT2 7. Pilularia globulifera KIIX Osmunda sp. UOMY Selaginella kraussiana ZFGK Selaginella moellendorffii Isoetes tegetiformans PKOX Selaginella kraussiana ZFGK Selaginella moellendorffii Lycophyte PHOT Huperzia lucidula GKAG Lycopodium deuterodensum PQTO Pseudolycopodiella caroliniana UPMJ Hedwigia ciliata YWNF Anomodon rostratus VBMM Bryum argenteum JMXW Timmia austriaca ZQRI Physcomitrella patens Polytrichum commune SZYG Moss PHOTA Bryum argenteum JMXW 3. Physcomitrella patens Sphagnum lescurii GOWD Bryum argenteum JMXW Hedwigia ciliata YWNF Anomodon rostratus VBMM Timmia austriaca ZQRI Physcomitrella patens Hedwigia ciliata YWNF Moss PHOTB Anomodon rostratus VBMM 4. Polytrichum commune SZYG Sphagnum lescurii GOWD Scapania nemorosa IRBN Schistochila sp. LGOW Porella pinnata UUHD 5. Metzgeria crassipilis NRWZ Pellia neesiana JHFI Conocephalum conicum ILBQ Liverwort PHOT Marchantia polymorpha JPYU Sphaerocarpos texanus HERT Adiantum aleuticum WCLG Onoclea sensilibis Thelypteris noveboracensis Phegopteris hexagonoptera Athyrium filix-femina AFPO Deparia acrostichoides Macrothelypteris torresiana Homalosorus pycnocarpos OCZL Coniogramme intermedia Pronephrium lakhimpurense Alsophila podophylla Plagiogyria distinctissima Dennstaedtia punctilobula Dryopteris amurensis Fern NEO 81 MYA Allantodia dilatata Diplazium wichurae UFJN Blechnum spicant VITX Plagiogyria japonica UWOD Dipteris conjugata MEKP Adiantum capillus-veneris 179 MYA Lindsaea linearis NOKI Hemidictyum marginatum Hypolepis tenuifolia Adiantum raddianum BMJR Nothoceros aenigmaticus Megaceros flagellaris UCRN Phymatoceros phymatodes Phaeoceros carolinianus WCZB Hornwort NEO Paraphymatoceros hallii FAJB Anthoceros punctatus Nothoceros aenigmaticus Megaceros flagellaris UCRN Phymatoceros phymatodes Paraphymatoceros hallii FAJB Hornwort PHOT Phaeoceros carolinianus WCZB Anthoceros punctatus Coleochaete irregularis QPDY Coleochaete scutata VQBJ Coleochaetophyceae PHOT Cylindrocystis brebissonii YOXI Cylindrocystis sp. VAZE Cylindrocystis brebissonii YOXI Cylindrocystis sp. VAZE Cylindrocystis cushleckae JOJQ Zygnemopsis sp. MFZO Zygnemataceae PHOT Mougeotia scalaris Zygnemopsis sp. MFZO Cylindrocystis cushleckae JOJQ Mougeotia scalaris Cosmocladium constrictum RQFE Desmidium aptogonum DFDS Penium margaritaceum AEKF Desmidaceae PHOT Planotaenium ohtanii SNOX Cylindrocystis brebissonii YOXI Cylindrocystis sp. VAZE Cylindrocystis brebissonii YOXI Cylindrocystis sp. VAZE Zygnemopsis sp. MFZO Cylindrocystis cushleckae JOJQ Zygnemataceae NEO Mougeotia scalaris Mougeotia scalaris Mesotaenium braunii WSJO Mesotaenium braunii WSJO Mesotaenium braunii WSJO Zygnemataceae PHOT Interfilum paradoxum FPCO Klebsormidium subtile FQLP Entransia fimbriata BFIK Klebsormidiophyceae PHOT Chlamydomonas reinhardtii Volvox carteri Chloromonas tughillensi UTRE Chlorophyceae PHOT Oedogonium cardiacum DVYE Coccomyxa pringsheimii GXBM Botryococcus terribilis QYXY Prasiola crispa WCLV Trebouxiophyceae PHOT Percursaria percursa OAEZ Bolbocoleon piliferum LSHT Ulvophyceae PHOT Cymbomonas sp. XIVI Nephroselmis olivacea MMKU Ostreococcus tauri Prasinophyte PHOT Micromonas pusilla Mesostigma viride KYIO Chlorokybus atmophyticus AZZW Mesostigmatophyceae PHOT

1250 1000 750 500 250 0 MYA Fig. S5. Chronogram of land plant and algal phototropin (PHOT) and the corresponding domains from hornwort, fern, and algal neochrome (NEO). A simplified version of this figure is shown in Fig. 1B. Grey bars represent 95% highest posterior density intervals of the age estimates. Italicized numbers adjacent to nodes refer to the fossil or secondary time calibrations detailed in Table S2. Two divergence time estimates are highlighted: one marks the HGT event (179 MYA) and the other marks the split of Gleicheniales (blue taxon), Cyatheales (green taxa) and other neochromes (81 MYA). Gene Tree Species Tree Deparia lancea Deparia lancea Deparia lobato-crenata Deparia lobato-crenata Deparia acrostichoides Deparia acrostichoides Onoclea sensilibis Diplazium wichurae Adiantum tetraphyllum Diplazium bombonasae Pronephrium lakhimpurense Allantodia dilatata Thelypteris noveboracensis Athyrium filix-femina Athyrium filix-femina Doodia media Phegopteris hexagonoptera Blechnum spicant Matteuccia struthiopteris Homalosorus pycnocarpos Matteuccia struthiopteris Macrothelypteris torresiana Onoclea sensilibis Coniogramme intermedia Thelypteris noveboracensis Tectaria zeylanica Pronephrium lakhimpurense 94/+/.99 Didymochlaena truncatula Macrothelypteris torresiana Plagiogyria distinctissima Phegopteris hexagonoptera Alsophila podophylla Homalosorus pycnocarpos Dennstaedtia punctilobula Hemidictyum marginatum Adiantum aleuticum Dryopteris expansa Adiantum pedatum Dryopteris amurensis Adiantum andicola Dryopteris filix-mas 95/+/+ Deparia acrostichoides Bolbitis auriculata Deparia lancea 98/95/+ Tectaria zeylanica Dryopteris expansa Didymochlaena truncatula 98/97/+ Dryopteris amurensis Adiantum aleuticum Dryopteris filix-mas 99/+/+ Adiantum pedatum Diplazium wichurae Adiantum andicola Diplazium bombonasae Adiantum capillus-veneris Allantodia dilatata Blechnum spicant Adiantum tetraphyllum Plagiogyria japonica Adiantum hispidulum Plagiogyria formosana Adiantum raddianum Dipteris conjugata Coniogramme intermedia Polypodiales Hypolepis punctata Adiantum raddianum Hypolepis tenuifolia Doodia media Dennstaedtia punctilobula 99/97/+ Adiantum hispidulum Lindsaea linearis Bolbitis auriculata

NEO Plagiogyria japonica Hypolepis tenuifolia Hornwort Plagiogyria formosana Hypolepis punctata Plagiogyria distinctissima Cyatheales Lindsaea linearis Alsophila podophylla Adiantum capillus-veneris Hemidictyum marginatum Dipteris conjugata Gleicheniales 0.02 substitutions/site

Fig. S6. Phylogenetic incongruence between fern neochrome gene tree and fern species tree. The gene tree topology is derived from the best maximum likelihood tree based on the nucleotide dataset, and the species tree summarized from Schuettpelz and Pryer (1), Kuo et al (2), Rothfels and Schuettpelz (3), and Rothfels et al (4). Tree inference based on codon models, 1st + 2nd and 3rd codon positions yielded similar topologies (Fig. S7). Closely related species/genera are coded with the same color. The neochrome gene tree is rooted with hornwort neochromes (not shown). Numbers above branches are maximum likelihood bootstrap values (BS) / aLRT supports under codon model (aLRT) / Bayesian posterior probabilities from MrBayes (PP), and are only displayed (along with thickened branches) if BS > 70, aLRT > 70 and PP > 0.95. “+” denotes BS = 100, aLRT = 100 or PP = 1.00; thickened branches without numbers are “+/+/+”. Arrowheads point to the two divergent neochrome copies found in Deparia spp. Arrows point to neochromes from Gleicheniales and Cyatheales that appear nested among Polypodiales neochromes.

1. Schuettpelz E, Pryer KM (2007) Fern phylogeny inferred from 400 leptosporangiate species and three plastid genes. Taxon 56:1037–1050. 2. Kuo LY, Li FW, Chiou WL, Wang CN (2011) First insights into fern matK phylogeny. Mol Phylogenet Evol 59:556–566. 3. Rothfels CJ, Schuettpelz E (2013) Accelerated rate of molecular evolution for vittarioid ferns is strong but not driven by selection. Syst Biol 63:31–54. 4. Rothfels CJ et al. (2013) Transcriptome-mining for single-copy nuclear markers in ferns. PLoS ONE 8:e76957. Deparia lancea Deparia lancea Deparia lancea A Deparia lobato-crenata B Deparia lobato-crenata C Deparia lobato-crenata codon model Deparia acrostichoides 1st + 2nd position Deparia acrostichoides 3rd position Deparia acrostichoides Athyrium filix-femina Onoclea sensilibis Thelypteris noveboracensis Phegopteris hexagonoptera Athyrium filix-femina Pronephrium lakhimpurense Matteuccia struthiopteris Phegopteris hexagonoptera Adiantum tetraphyllum Adiantum tetraphyllum Matteuccia struthiopteris Onoclea sensilibis Pronephrium lakhimpurense Deparia lancea Macrothelypteris torresiana Onoclea sensilibis Deparia acrostichoides Homalosorus pycnocarpos Deparia lancea Thelypteris noveboracensis Athyrium filix-femina Deparia acrostichoides Pronephrium lakhimpurense Phegopteris hexagonoptera Thelypteris noveboracensis Adiantum tetraphyllum Matteuccia struthiopteris Macrothelypteris torresiana Adiantum aleuticum Deparia lancea Homalosorus pycnocarpos Adiantum pedatum Deparia acrostichoides Coniogramme intermedia Adiantum andicola Coniogramme intermedia Tectaria zeylanica Macrothelypteris torresiana Tectaria zeylanica Didymochlaena truncatula Homalosorus pycnocarpos Didymochlaena truncatula Dennstaedtia punctilobula Coniogramme intermedia Dennstaedtia punctilobula Alsophila podophylla Alsophila podophylla Alsophila podophylla Plagiogyria japonica Plagiogyria distinctissima Plagiogyria distinctissima Adiantum pedatum Dennstaedtia punctilobula Adiantum aleuticum Adiantum aleuticum Tectaria zeylanica Adiantum pedatum Adiantum andicola Didymochlaena truncatula Adiantum andicola Dryopteris amurensis Dryopteris amurensis Dipteris conjugata Dryopteris expansa Dryopteris expansa Plagiogyria japonica Dryopteris filix-mas Dryopteris filix-mas Plagiogyria formosana Diplazium bombonasae Diplazium bombonasae Blechnum spicant Diplazium wichurae Diplazium wichurae Dryopteris amurensis Allantodia dilatata Allantodia dilatata Dryopteris expansa Blechnum spicant Blechnum spicant Dryopteris filix-mas Plagiogyria formosana Plagiogyria formosana Allantodia dilatata Plagiogyria distinctissima Plagiogyria japonica Diplazium bombonasae Dipteris conjugata Dipteris conjugata Diplazium wichurae Doodia media Adiantum raddianum Doodia media Adiantum raddianum Adiantum hispidulum Adiantum hispidulum Adiantum hispidulum Doodia media Adiantum raddianum NEO NEO Bolbitis auriculata Bolbitis auriculata Bolbitis auriculata Horwort Horwort Hypolepis punctata Hypolepis punctata NEO Hypolepis punctata

Hypolepis tenuifolia Hypolepis tenuifolia Horwort Hypolepis tenuifolia Lindsaea linearis Adiantum capillus-veneris Adiantum capillus-veneris Adiantum capillus-veneris Lindsaea linearis Lindsaea linearis Hemidictyum marginatum Hemidictyum marginatum Hemidictyum marginatum 0.3 substitutions/site 0.05 substitutions/site 0.3 substitutions/site

D E

Alsophila podophylla 1.0 Plagiogyria japonica Purifying selection Dennstaedtia punctilobula

Didymochlaena truncatula 0.8 Neutral or nearly neutral Tectaria zeylanica Positive selection Deparia acrostichoides Deparia lancea Adiantum andicola 0.6 Adiantum aleuticum Adiantum pedatum 0.4 Deparia lancea GC Content Deparia lobato-crenata Deparia acrostichoides

Onoclea sensilibis 0.2 Thelypteris noveboracensis Pronephrium lakhimpurense

Adiantum tetraphyllum 0.0 Matteuccia struthiopteris Phegopteris hexagonoptera 0 500 1000 1500 2000 2500 3000 3500 Athyrium filix-femina Window position (bp) Coniogramme intermedia Homalosorus pycnocarpos Macrothelypteris torresiana Allantodia dilatata Diplazium wichurae Diplazium bombonasae Dryopteris filix-mas Dryopteris amurensis Dryopteris expansa Blechnum spicant Plagiogyria formosana Plagiogyria distinctissima Dipteris conjugata Hypolepis tenuifolia Hypolepis punctata Bolbitis auriculata Adiantum hispidulum Adiantum raddianuum Doodia media Hemidictyum marginatum Lindsaea linearis Adiantum capillus-veneris Phymatoceros phymatodes Megaceros flagellaris Nothoceros vincentianus Nothoceros aenigmaticus Paraphymatoceros hallii Phaeoceros carolinianus Anthoceros punctatus 0.02 substitutions/site

Fig. S7. Phylogeny, selection profile and GC content of fern neochromes. Maximum likelihood reconstructions of gene phylogeny based on (A) codon model, (B) first and second codon positions, and (C) third codon position. Thickened branches indicate aLRT supports (in A) or bootstrap supports (in B, C) > 70. (D) Selection profile displayed along phylogenetic branches for fern and hornwort neochromes. Tree topology derived from the best maximum likelihood tree (Fig. S6). The width of each color along a branch is proportional to the number of codon sites in the corresponding selection class. Thickened branches have experienced significant episodic positive selection (P < 0.05). (E) Sliding window analysis of GC content for fern neochrome. Each line displays the GC content for each neochrome sequence. None of the ferns in our study were deviant in base composition for neochrome. Each window is 400bp in size and the window slides every 50bp. A

B

Fig. S8. Hornwort chloroplasts (arrowhead) contract under strong light. (A) Before irradiation, chloroplasts of Nothoceros aenigmaticus occupy most of the cellular space. (B) After irradiation of blue light (57 μmol m-2 s-1) for 2 hours, chloroplasts evidently reduced in size. Scale bar = 40 μm. TableDiphasiastrum)digitatum)WAFT Chaetosphaeridium)globosum)DRGY Aphanochaete)repens)IJMT Cymbomonas)sp.)XIVI Arabidopsis)lyrata* Anemia)tomentosa)CQPW Huperzia)lucidula)GKAG Chara)vulgaris)MWXT Asteromonas)gracilis)NTLE Dolichomastix)tenuilepis)XOAL Arabidopsis)thaliana* Angiopteris)evecta)NHCM Huperzia)myrisinites)CBAE Chlorokybus)atmophyticus)AZZW Brachiomonas)submarina)GUBD Mantoniella)squamata)QXSZ Brachypodium)distachyon* Argyrochosma)nivea)XDDT Huperzia)selago)GTUO Closterium)lunula)DRFX Carteria)crucifera)VIAU Micromonas)pusilla* Capsella)rubella* Asplenium)nidus)PSKY Huperzia)selago)NYBX Coleochaete)irregularis)QPDY Carteria)obtusa)RUIF Monomastix)opisthostigma)BTFM Carica)papaya* Asplenium)platyneuron)KJZG Huperzia)squarrosa)GAON Coleochaete)scutata)VQBJ Chaetopeltis)orbicularis)BAZF Nephroselmis)olivacea)MMKU Citrus)clementina* Azolla)caroliniana)CVEG Lycopodiella)apressa)ULKT Cosmarium)broomei)HIDG Chlamydomonas)reinhardtii* Nephroselmis)pyriformis)ISIM Citrus)sinensis* Athyrium)filixVfemina)URCP Lycopodium)annotinum)ENQF Cosmarium)granatum)MNNM Chlamydomonas)bilatus)MULF Ostreococcus)tauri* Cucumis)sativus* Athyrium)filixVfemina)AFPO Lycopodium)deuterodensum)PQTO Cosmarium)ochthodes)HJVM Chlamydomonas)cribrum)BCYF Ostreococcus)lucimarinus* Eucalyptus)grandis* Blechnum)spicant)VITX Phylloglossum)drummondii)ZZEI Cosmarium)ochthodes)STKJ Chlamydomonas)moewusii)JRGZ Picocystis)salinarum)TGNL Fragaria)vesca* Bolbitis)repanda)JBLI Pseudolycopodiella)caroliniana)UPMJ Cosmarium)subtumidum)WDGV Chlamydomonas)noctigama)VALZ Prasinococcus)capsulatus)XMCL Glycine)max* Botrypus)virginianus)BEGM Selaginella)moellendorffii*) Cosmarium)tinctum)BHBK Chlamydomonas)sp.)TSBQ Prasinoderma)coloniale)HYHN Gossypium)raimondii* Cibotium)glaucum)ORJE Selaginella)acanthonota)ZYCD Cosmocladium)cf.)constrictum)RQFE Chlamydomonas)sp.)AOUJ Pseudoscourfieldia)marina)JMTE Linum)usitatissimum* Crepidomanes)venosum)TWFZ Selaginella)apoda)LGDQ Cylindrocystis)brebissonii)YOXI Chloromonas)oogama)IHOI Pycnococcus)provasolii)MXEZ Malus)domestica* Cryptogramma)acrostichoides)WQML Selaginella)kraussiana)ZFGK Cylindrocystis)brebissonii)RPGL Chloromonas)perforata)QRTH Pyramimonas)parkeae)TNAW Manihot)esculenta* Culcita)macrocarpa)PNZO Selaginella)lepidophylla)ABIJ Cylindrocystis)cushleckae)JOJQ Chloromonas)reticulata)LBRP Scherffelia)dubia)FMVB Medicago)truncatula* Cyathea)spinulosa)GANB Selaginella)selaginoides)KUXM Cylindrocystis)sp.)VAZE Chloromonas)rosae)AJUW Tetraselmis)chui)HVNO Mimulus)guttatus* Cystopteris)fragilis)XXHP Selaginella)stauntoniana)ZZOL Desmidium)aptogonum)DFDS Chloromonas)subdivisa)GFUR Tetraselmis)cordiformis)DUMA Oryza)sativa* Cystopteris)fragilis)LHLE Selaginella)wallacei)JKAA Entransia)fimbriata)BFIK Chloromonas)tughillensis)UTRE Tetraselmis)striata)HHXJ Panicum)virgatum* Cystopteris)protrusa)YOWV Selaginella)willdenowii)KJYC Euastrum)affine)GYRP Chlorosarcinopsis)halophila)KSFK coccoid)prasinophyte)XJGM Phaseolus)vulgaris* Cystopteris)reevesiana)RICC Isoetes)sp.)PYHZ Gonatozygon)kinahanii)KEYW Dunaliella)salina)RHVC Glaucophyta Populus)trichocarpa* Cystopteris)utahensis)HNDZ Isoetes)sp.)FITN Interfilum)paradoxum)FPCO Dunaliella)tertiolecta)ZDIZ Cyanophora)paradoxa)QFND Prunus)persica* Davallia)fejeensis)OQWW Isoetes)tegetiformans)PKOX Klebsormidium)subtile)FQLP Eudorina)elegans)RNAT Cyanophora)paradoxa)YTYU Ricinus)communis* Dennstaedtia)davallioides)MTGC Hornworts Mesostigma)viride)KYIO Fritschiella)tuberosa)VFIV Cyanoptyche)gloeocystis)JKHA Setaria)italica* Deparia)lobatoVcrenata)FCHS Anthoceros)punctatus*2 Mesotaenium)braunii)WSJO Golenkinia)longispicula)BZSH Glaucocystis)cf.)nostochinearum)POOW) Solanum)lycopersicum* Didymochlaena)truncatula)RFRB Megaceros)flagellaris)UCRN Mesotaenium)caldariorum)HKZW Gonium)pectorale)KUJU Gloeochaete)wittrockiana)PQED Solanum)tuberosum* Diplazium)wichurae)UFJN Nothoceros)vincentianus)TCBC Mesotaenium)endlicherianum)WDCW Haematococcus)pluvialis)ODXI RedGymnosperms Gymnocarpium)dryopteris)HEGQ Bazzania)trilobata)WZYK Nucleotaenium)eifelense)KMNX Lobochlamys)segnis)OFUE Dumontia)simplex)IEHF Austrotaxus)spicata)BTTS Hemionitis)arifolia)ZXJO Blasia)sp.)AEXY Onychonema)laeve)GGWH Lobomonas)rostrata)JKKI Eucheuma)denticulatum)JEBK Callitris)macleayana)RMMV Homalosorus)pycnocarpos)OCZL Calypogeia)fissa)RTMU Penium)exiguum)YSQT Microspora)cf.)tumidula)FOYQ Glaucosphaera)vacuolata)RSOF Cathaya)agryrophylla)NPRL Hymenophyllum)bivalve)QIAD Conocephalum)conicum)ILBQ Penium)margaritaceum)AEKF Neochloris)oleoabundans)EEJO Gloeopeltis)furcata)SBLT Cedrus)libani)GGEA Hymenophyllum)cupressiforme)TRPJ Frullania)sp.)CHJJ Phymatodocis)nordstedtiana)RPQV Neochloris)sp.)GJIY Gracilaria)asiatica)VNAL Cephalotaxus)harringtonia)WYAJ Leucostegia)immersa)WGTU Frullania)sp.)TGKW Planotaenium)ohtanii)SNOX Neochlorosarcina)sp.)USIX Gracilaria)blodgettii)LJPN Cryptomeria)japonica)DSXO Lindsaea)linearis)NOKI Lunularia)cruciata)TXVB Pleurotaenium)trabecula)MOYY Oedogonium)cardiacum)DVYE Gracilaria)chouae)FTRP Cunninghamia)lanceolata)OUOI Lindsaea)microphylla)YIXP Marchantia)emarginata)TFYI Roya)obtusa)XRTZ Oedogonium)foveolatum)SDPC Gracilaria)lemaneiformi)IKWM Cupressus)dupreziana)QNGJ Lygodium)japonicum)PBUU Marchantia)paleacea)IHWO Spirogyra)sp.)HAOX Oogamochlamys)gigantea)XDLL Grateloupia)filicina)ZJOJ Cycas)micholitzii)XZUY Marattia)sp.)UXCS Marchantia)paleacea)HMHL Spirotaenia)minuta)NNHQ Pandorina)morum)RYJX Grateloupia)livida)IKIZ Dioon)edule)WLIC Myriopteris)eatonii)GSXD Marchantia)polymorpha)JPYU Spirotaenia)sp.)TPHT Pediastrum)duplex)XKWQ Grateloupia)turuturu)URSB Encephalartos)barteri)GNQG Nephrolepis)exaltata)NWWI Metzgeria)crassipilis)NRWZ Staurastrum)sebaldi)ISHC Pediastrum)duplex)XTON Grateloupia)chiangii)PWKQ Ephedra)sinica)VDAO Notholaena)montieliae)YCKE Odontoschisma)prostratum)YBQN Staurodesmus)convergens)WCQU Phacotus)lenticularis)ZIVZ Gymnogongrus)ftabelliformis)CKXF Ginkgo)biloba)SGTW Onoclea)sensibilis)HTFH Pallavicinia)lyellii)YFGP Staurodesmus)omearii)RPRU Pirula)salina)NQYP Heterosiphonia)pulchra)YSBD Glyptostrobus)pensilis)OXGJ Ophioglossum)petiolatum)QHVS Pellia)epiphylla)PIUF Xanthidium)antilopaeum)GBGT Pleurastrum)insigne)PRIQ Kappaphycus)alvarezii)IHJY Gnetum)montanum)GTHK Ophioglossum)petiolatum)WTJG Pellia)neesiana)JHFI Zygnemopsis)sp.)MFZO Pteromonas)angulosa)LNIL Mazzaella)japonica)WEJN Juniperus)scopulorum)XMGP Osmunda)javanica)VIBO Plagiochila)asplenioides)NWQC Trebouxiophyceae Pteromonas)sp.)ACRY Polysiphonia)japonica)XAXW Keteleeria)evelyniana)JUWL Osmunda)regalis)YKSS Porella)navicularis)KRUQ Botryococcus)braunii)ETGN Scenedesmus)dimorphus)PZIF Porphyra)yezoensis)ZULJ Larix)speciosa)WVWN Osmunda)regalis)UOMY Porella)pinnata)UUHD Botryococcus)sudeticus)VJDZ Scourfieldia)sp.)EGNB Porphyridium)cruentum)OBUY Nothotsuga)longibracteata)AREG Osmundastrum)cinnamomeum)BIVQ Radula)lindenbergia)BNCU Botryococcus)terribilis)QYXY Spermatozopsis)exsultans)MXDS Porphyridium)purpureum)PVGP Phyllocladus)hypohyllus)JRNA Pilularia)globulifera)KIIX Riccia)berychiana)WJLO Chlorella)minutissima)MWAN Spermatozopsis)similis)ENAU Rhodella)violacea)RTLC Picea)engelmanii)AWQB Pityrogramma)trifoliata)UJTT Scapania)nemorosa)IRBN Coccomyxa)pringsheimii)GXBM Stephanosphaera)pluvialis)ZLQE Rhodochaete)parvula)JJZR Pinus)jeffreyi)MFTM Plagiogyria)japonica)UWOD Schistochila)sp.)LGOW Eremosphaera)viridis)MNCB Stigeoclonium)helveticum)JMUI Sinotubimorpha)guangdongensis)PYDB Pinus)parviflora)IIOL Pleopeltis)polypodioides)UJWU Sphaerocarpos)texanus)HERT Geminella)sp.)PFUD Uronema)sp.)ISGT Chromista Pinus)ponderosa)JBND Polypodium)amorphum)YLJA Mosses Leptosira)obovata)ZNUM Uronema)belkae)RAWF Chroomonas)sp.)ROZZ Pinus)radiata)DZQM Polypodium)glycyrrhiza)CJNT Anomodon)attenuatus)QMWB Microthamnion)kuetzigianum)DXNY Vitreochlamys)sp.)QWRA Colpomenia)sinuosa)QLMZ Podocarpus)coriaceus)SCEB Polypodium)hesperium)GYFU Anomodon)rostratus)VBMM Nannochloris)atomus)MFYC Volvox)carteri* Cryptomonas)curvata)BAKF Podocarpus)rubens)XLGK Polypodium)hesperium)IXLH Atrichum)angustatum)ZTHV Parachlorella)kessleri)AKCR Volvox)aureus)JWGT Desmarestia)viridis)FSQE Pseudolarix)amabilis)AQFM Phlebodium)pseudoaureum)ZQYU Aulacomnium)heterostichum)WNGH Pedinomonas)minor)RRSV Volvox)aureus)WRSL Dictyopteris)undulata)LIRF Pseudotaxus)chienii)YLPM Polystichum)acrostichoides)FQGQ Bryum)argenteum)JMXW Pedinomonas)tuberculata)PUAN Volvox)globator)ISPU Hemiselmis)virescens)MJMQ Pseudotsuga)menziesii)IOVS Psilotum)nudum)QVMR Buxbaumia)aphylla)HRWG Prasiola)crispa)WCLV Ulvophyceae Ishige)okamurai)APTP Sciadopitys)verticillata)YFZK Pteridium)aquilinum1< Ceratodon)purpureus)FFPD Prototheca)wickerhamii)BILC Acrosiphonia)sp.)JIWJ Isochrysis)sp.)BAJW Stangeria)eriopus)KAWQ Pteris)ensiformis)FLTD Dicranum)scoparium)NGTD Stichococcus)bacillaris)WXRI Blastophysa)cf.)rhizopus)VHIJ Kjellmaniella)crassifolia)RAPY Taiwania)cryptomerioides)QSNJ Pteris)vittata)POPJ Funaria)sp.)XWHK Trebouxia)arboricola)NKXU Bolbocoleon)piliferum)LSHT Laminaria)japonica)OGZM Taxus)baccata)WWSS Sceptridium)dissectum)EEAQ Hedwigia)ciliata)YWNF Bryopsis)plumosa)JTIG Laminaria)japonica)QDTV Taxus)cuspidata)ZYAX Sticherus)lobatus)XDVM Hypnum)subimponens)LNSF Cephaleuros)virescens)YDCQ Mallomonas)sp.)BOGT Thuja)plicata)VFYZ Thelypteris)acuminata)MROH Leucobryum)albidum)VMXJ Cladophora)glomerata)VBLH Nannochloropsis)oculata)JQFK Thujopsis)dolabrata)NKIN Thyrsopteris)elegans)EWXK Leucobryum)glaucum)RGKI Codium)fragile)GYBH Ochromonas)sp.)EBWI Torreya)nucifera)HQOM Tmesipteris)parva)ALVQ Leucodon)sciuroides)ZACW Cylindrocapsa)geminella)DZPJ Pavlova)lutheri))LLEN Torreya)taxifolia)EFMS Vittaria)appalachiana)NDUV Neckera)douglasii)TMAJ Entocladia)endozoica)OQON Pavlova)lutheri))NMAK Tsuga)heterophylla)GAMH Vittaria)lineata)SKYV Orthotrichum)lyellii)CMEQ Halochlorococcum)marinum)ALZF Pavlova)lutheri)RFAD Welwitschia)mirabilis)TOXE Woodsia)ilvensis)YQEC Philonotis)fontana)ORKS Ignatius)tetrasporus)KADG Petalonia)fascia)VRGZ Widdringtonia)cedarbergensis)AUDE Woodsia)scopulina)YJJY Physcomitrella)patens*) Ochlochaete)sp.)CQQP Prorocentrum)micans)TZJQ Wollemia)nobilis)RSCE Physcomitrium)pyrimorfe)YEPO Oltmannsiellopsis)viridis)PZBH Proteomonas)sulcata)IRZA Plagiomnium)insigne)BGXB Oltmannsiellopsis)viridis)QJYX Prymnesium)parvum)LXRN Polytrichum)commune)SZYG Percursaria)percursa)OAEZ Punctaria)latifolia)ASZK Pseudotaxiphyllum)elegans)QKQO Planophila)laetevirens)CBNG Rhodomonas)sp.)IAYV Racomitrium)varium)RDOO Planophila)terrestris)LETF Sargassum)horneri)RWXW Rhynchostegium)serrulatum)JADL Trentepohlia)annulata)NATT Sargassum)thunbergii)YRMA Rhytidiadelphus)loreus)WSPM Sargassum)vachellianum)HFIK Scouleria)aquatica)BPSG Sargassum)fusiforme)LDRY Schwetschkeopsis)fabronia)IGUH Sargassum)hemiphyllum)VYER Sphagnum)lescurii)GOWD Sargassum)henslowianum)FIKG Sphagnum)palustre)RCBT Sargassum)integerrimum)FOMH Sphagnum)recurvatum)UHLI Sargassum)muticum)JGGD Syntrichia)princeps)GRKU Scytosiphon)lomentaria)JCXF Takakia)lepidozioides)SKQD Scytosiphon)dotyo)ULXR Thuidium)delicatulum)EEMJ Symphyocladia)latiuscula)UYFR Timmia)austriaca)ZQRI Synura)petersenii)DBYD Synura)sp.)VKVG Undaria)pinnatifida)FIDQ Excavata Euglena)sp.)UNBZ 1P.G.)Wolf)923)(UTC);)Norwich,)UK. 2D.G.)Long)s.n.)(OXF);)Edinburgh,)UK ! !

Table&S2.!The!calibrations!used!in!dating!the!divergences!within!the!phototropin!gene!family. No. Clade Calibration Date&(MYA) Prior Reference Justification 1 Tracheophyta Zosterophyllum-sp. 416 lognormal!(mean:!3.5,!STD:!1,!offset:!416) 70,!74 Oldest!unequivocal!record!of!total!group!of!lycoposid;!see!Ref.!72!for!detailed!justifications 2 Euphyllophyta Ibyka-sp. 388.2 lognormal!(mean:!3.5,!STD:!1,!offset:!388.2) 70,!75 Oldest!unequivocal!record!of!monilophyte!based!on!protoxylem!morphology;!see!Ref.!72!for!detailed!justifications 3 Bryophyta!PHOTA "type!III"!fragment 330.9V346.7 lognormal!(mean:!1.5,!STD:!1,!offset:!330.9) 71 Oldest!unequivocal!record!of!crown!Bryophyta;!the!fibrils!and!pores!similar!to!those!of!Sphagnum!waterVstorage!cells 4 Bryophyta!PHOTB "type!III"!fragment 330.9V346.7 lognormal!(mean:!1.5,!STD:!1,!offset:!330.9) 71 Oldest!unequivocal!record!of!crown!Bryophyta;!the!fibrils!and!pores!similar!to!those!of!Sphagnum!waterVstorage!cells 5 Jungermanniopsida Riccardiothallus-devonicus 407V411 lognormal!(mean:!1.5,!STD:!1,!offset:!407) 72 Oldest!unequivocal!record!of!crown!Jungermanniopsida;!gross!morphology!similar!to!the!extant!Riccardia!species 6 Polypodiopsida!PHOT1 Rastropteris-pirtgquanensis 296 lognormal!(mean:!1.5,!STD:!1,!offset:!296) 8,!76 Oldest!unequivocal!record!of!Osmundaceae!stem;!see!Ref.!8!for!detailed!justifications 7 Polypodiopsida!PHOT2 Rastropteris-pirtgquanensis 296 lognormal!(mean:!1.5,!STD:!1,!offset:!296) 8,!76 Oldest!unequivocal!record!of!Osmundaceae!stem;!see!Ref.!8!for!detailed!justifications 8 Eupolypod!PHOT1 imported!secondary!date 116.7 Normal!(mean:!116.7,!STD:!35.01) 8 A!wellVestablished!time!estimate!for!the!divergence!of!Eupolypods 9 Eupolypod!PHOT2 imported!secondary!date 116.7 Normal!(mean:!116.7,!STD:!35.01) 8 A!wellVestablished!time!estimate!for!the!divergence!of!Eupolypods 10 Spermatophyta!PHOT1 Cordaixylon-iowensis 306.2 lognormal!(mean:!2.5,!STD:!1,!offset:!306.2) 70,!77 Oldest!unequivocal!record!of!Acrogymnospermae;!see!Ref.!72!for!detailed!justifications 11 Spermatophyta!PHOT2 Cordaixylon-iowensis 306.2 lognormal!(mean:!2.5,!STD:!1,!offset:!306.2) 70,!77 Oldest!unequivocal!record!of!Acrogymnospermae;!see!Ref.!72!for!detailed!justifications 12 Grass!PHOT1 phytoliths!in!dinosaur!coprolites 65V67 lognormal!(mean:!1.5,!STD:!1,!offset:!65) 73 Oldest!unequivocal!record!of!PACMAD!or!BEP!of!grass;!phytoliths!morphology!similar!to!subclades!in!PACMAD!or!in!BEP 13 Grass!PHOT2 phytoliths!in!dinosaur!coprolites 65V67 lognormal!(mean:!1.5,!STD:!1,!offset:!65) 73 Oldest!unequivocal!record!of!PACMAD!or!BEP!of!grass;!phytoliths!morphology!similar!to!subclades!in!PACMAD!or!in!BEP 14 Coniferae!PHOT1 Araucaria-mirabilis 147 lognormal!(mean:!1.5,!STD:!1,!offset:!147) 70 Oldest!unequivocal!record!of!Cupressophyta!crown;!see!Ref.!72!for!detailed!justifications 15 Coniferae!PHOT2 Araucaria-mirabilis 147 lognormal!(mean:!1.5,!STD:!1,!offset:!147) 70 Oldest!unequivocal!record!of!Cupressophyta!crown;!see!Ref.!72!for!detailed!justifications ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! Table&S3.!The!primers!and!PCR!protocols!used!in!this!study.!See!Table!S4!for!primer!sequences. Taxa Gene Primary&PCR&primers Secondary&PCR&primers1 PCR&program 2 Specimen&voucher ! Hornworts: Phymatoceros!phymatodes neochrome neoF65!+!neoR2818 neoF430!+!neoR2776 a/a J.!Pittermann!s.n.!(DUKE) ! Phymatoceros!phymatodes neochrome neoF65!+!neoR4110 neoF2367!+!neoR3456 a/a J.!Pittermann!s.n.!(DUKE) Phymatoceros!phymatodes neochrome neoF65!+!neoR4110 neoF3230!+!neoR4110 a/a J.!Pittermann!s.n.!(DUKE) ! Phymatoceros!phymatodes phototropin neoF65!+!neoR4110 neoF2367!+!neoR3456 a/a J.!Pittermann!s.n.!(DUKE) ! Phymatoceros!phymatodes phototropin photF1856!+!photR2508 photF1970!+!photR2245 a/a J.!Pittermann!s.n.!(DUKE) Phymatoceros!phymatodes phototropin photF2774!+!photR4339 O a J.!Pittermann!s.n.!(DUKE) ! Megaceros!flagellaris neochrome neoF65!+!neoR902 O b B.!CrandallOStotler!s.n.!(ABSH) Megaceros!flagellaris neochrome neoF649!+!neoR1950 O b B.!CrandallOStotler!s.n.!(ABSH) ! Megaceros!flagellaris neochrome neoF1844!+!neoR2361 O c B.!CrandallOStotler!s.n.!(ABSH) Megaceros!flagellaris neochrome neoF2239!+!neoR3300 O b B.!CrandallOStotler!s.n.!(ABSH) ! Megaceros!flagellaris neochrome neoF2361!+!neoR4110 O c B.!CrandallOStotler!s.n.!(ABSH) Megaceros!flagellaris phototropin photF1856!+!photR4339 photF1970!+!photR4339 a/a B.!CrandallOStotler!s.n.!(ABSH) ! Nothoceros!aenigmaticus neochrome F5!+!R1_T1 F565!+!R1_T1 d/d F.W.!Li!1291!(DUKE) Nothoceros!aenigmaticus neochrome3 neoF4018!+!AP1 neoF4110!+!AP2 e/f F.W.!Li!1569!(DUKE) ! Nothoceros!aenigmaticus neochrome3 neoR429!+!AP1 R3re_phyN!+!AP2 e/f F.W.!Li!1569!(DUKE) Nothoceros!aenigmaticus neochrome3 NaNEO_3O1_GM1!+!AP1 NaNEO_3O1_GM2!+!AP2 e/f F.W.!Li!1569!(DUKE) ! Nothoceros!aenigmaticus phototropin 5upF1!+!R7 5upF2!+!R7 c/g F.W.!Li!1291!(DUKE) Nothoceros!aenigmaticus phototropin4 F565!+!I_R1 I_F2!+!I_R2 d/d F.W.!Li!1291!(DUKE) ! Nothoceros!aenigmaticus phytochrome FO200_Maphy!+!R4850_Maphy FO3_Maphy!+!R4450_Maphy h/h F.W.!Li!1291!(DUKE) Phaeoceros!carolinianus neochrome neoF65!+!neoR877 O c B.!CrandallOStotler!s.n.!(ABSH) ! Phaeoceros!carolinianus neochrome neoF649!+!neoR1950 O b B.!CrandallOStotler!s.n.!(ABSH) ! Phaeoceros!carolinianus neochrome neoF1576!+!neoR4104 O a B.!CrandallOStotler!s.n.!(ABSH) Anthoceros!punctatus neochrome neoF67!+!neoR832 O c D.!Chamberlain!s.n.!(E) ! Anthoceros!punctatus neochrome neoF428!+!neoR3049 neoF812!+!neoR2938 a/g D.!Chamberlain!s.n.!(E) Anthoceros!punctatus neochrome neoF2938!+!neoR4104O2 neoF3049!+!neoR4104O2 a/a D.!Chamberlain!s.n.!(E) ! Ferns: ! Adiantum!andicola neochrome neoF20!+!neoR4242 neoF20!+!neoR2336 i/c C.J.!Rothfels!2641,!DB55495!(DUKE) Adiantum!hispidulum neochrome neoF58!+!neoR4238 neoF651!+!neoR3718 c/c L.!Huiet!s.n.,!DB9529!(DUKE) ! Adiantum!hispidulum neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c L.!Huiet!s.n.,!DB9529!(DUKE) Adiantum!pedatum neochrome neoF20!+!neoR4242 neoF20!+!neoR2336 i/c C.J.Rothfels!3839,!DB7517!(DUKE) ! Adiantum!pedatum neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c C.J.Rothfels!3839,!DB7517!(DUKE) Adiantum!tetraphyllum neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c L.!Huiet!105,!DB2505!(UC) ! Adiantum!tetraphyllum neochrome neoF20!+!neoR4242 neoF20!+!neoR2236 i/c L.!Huiet!105,!DB2505!(UC) Adiantum!tetraphyllum neochrome neoF1108!+!neoR3065 O k L.!Huiet!105,!DB2505!(UC) ! Alsophila!podophylla neochrome neoF20!+!neoR4242 neoF20!+!neoR2336 i/l E.!Schuettpelz!1201A,!DB4948!(DUKE) Alsophila!podophylla neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/l E.!Schuettpelz!1201A,!DB4948!(DUKE) ! Alsophila!podophylla neochrome neoF20!+!neoR4242 neoF538!+!neoR4000 i/l E.!Schuettpelz!1201A,!DB4948!(DUKE) Bolbitis!auriculata neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c F.!!Rakotondrainibe,!DB3504!(P) ! Dennstaedtia!punctilobula neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c C.J.!Rothfels!4167,!DB8975!(DUKE) Dennstaedtia!punctilobula neochrome neoF20!+!neoR4242 neoF20!+!neoR2336 i/l C.J.!Rothfels!4167,!DB8975!(DUKE) ! Dennstaedtia!punctilobula neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/l C.J.!Rothfels!4167,!DB8975!(DUKE) ! Deparia!acrostichoides neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c C.J.!Rothfels!3894,!DB7797!(DUKE) Deparia!acrostichoides neochrome neoF20!+!neoR4242 neoF20!+!neoR2336 i/c C.J.!Rothfels!3894,!DB7797!(DUKE) ! Deparia!acrostichoides neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/c C.J.!Rothfels!3894,!DB7797!(DUKE) Deparia!lancea neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c E.!Schuettpelz!298,!DB2558!(DUKE) ! Deparia!lancea neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/c E.!Schuettpelz!298,!DB2558!(DUKE) Didymochlaena!truncatula neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c E.!Schuettpelz!267,!DB2435!(DULE) ! Diplazium!bombonasae neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/c R.C.!Moran!7493,!DB3764!(DUKE) Doodia!media neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c E.!Schuettpelz!295,!DB2555!(DUKE) ! Dryopteris!amurensis neochrome neoF20!+!neoR4242 neoF20!+!neoR2336 i/c A.!Uchida!1392,!DB7982!(TNS) Dryopteris!amurensis neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/c A.!Uchida!1392,!DB7982!(TNS) ! Dryopteris!expansa neochrome neoF20!+!neoR4242 neoF20!+!neoR2336 i/c A.!Ebihara!TH2007O507,!DB7977!(TNS) Dryopteris!expansa neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/c A.!Ebihara!TH2007O507,!DB7977!(TNS) ! Hemidictyum!marginatum neochrome neoF20!+!neoR4242 neoF20!+!neoR2336 i/j M.!Christenhusz!2476,!DB3054!(CAY) Hemidictyum!marginatum neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/j M.!Christenhusz!2476,!DB3054!(CAY) ! Hemidictyum!marginatum neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/j M.!Christenhusz!2476,!DB3054!(CAY) Hemidictyum!marginatum neochrome neoF1108!+!neoR3065 O k M.!Christenhusz!2476,!DB3054!(CAY) ! Hypolepis!tenuifolia neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/c E.!Schuettpelz!286,!DB2574!(DUKE) Macrothelypteris!torresiana neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c Schuettpelz!335,!DB2980!(DUKE) ! Macrothelypteris!torresiana neochrome neoF20!+!neoR4242 neoF20!+!neoR2336 i/c Schuettpelz!335,!DB2980!(DUKE) Macrothelypteris!torresiana neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/c Schuettpelz!335,!DB2980!(DUKE) ! Matteuccia!struthiopteris neochrome neoF20!+!neoR786 O b A.!Larsson!258,!DB7946!(DUKE) Matteuccia!struthiopteris neochrome neoF649!+!neoR1950 O b A.!Larsson!258,!DB7946!(DUKE) ! Matteuccia!struthiopteris neochrome neoF1530!+!neoR2300 O m A.!Larsson!258,!DB7946!(DUKE) ! Matteuccia!struthiopteris neochrome neoF2239!+!neoR3300 O m A.!Larsson!258,!DB7946!(DUKE) Matteuccia!struthiopteris neochrome neoF2935!+!neoR3720 O m A.!Larsson!258,!DB7946!(DUKE) ! Matteuccia!struthiopteris neochrome neoF58!+!neoR4238 neoF651!+!neoR3718 c/c A.!Larsson!258,!DB7946!(DUKE) Onoclea!sensilibis neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c E.!Schuettpelz!353,!DB2998!(DUKE) ! Onoclea!sensilibis neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/c E.!Schuettpelz!353,!DB2998!(DUKE) Phegopteris!hexagonoptera neochrome neoF20!+!neoR4242 neoF651!+!neoR3718 i/c M.!Christenhusz!3844,!DB2731!(TUR) ! Phegopteris!hexagonoptera neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/c M.!Christenhusz!3844,!DB2731!(TUR) Plagiogyria!formosana neochrome neoF20!+!neoR786 O b E.!Schuettpelz!1083A,!DB4826!(DUKE) ! Plagiogyria!formosana neochrome neoF649!+!neoR1950 O b E.!Schuettpelz!1083A,!DB4826!(DUKE) Plagiogyria!formosana neochrome neoF1530!+!neoR2300 O m E.!Schuettpelz!1083A,!DB4826!(DUKE) ! Plagiogyria!formosana neochrome neoF2935!+!neoR3720 O m E.!Schuettpelz!1083A,!DB4826!(DUKE) Tectaria!zeylanica neochrome neoF20!+!neoR4242 O i E.!Schuettpelz!514,!DB3569!(GOET) ! Thelypteris!noveboracensis neochrome neoF20!+!neoR4242 neoF2115!+!neoR4242 i/l C.J.!Rothfels!4164,!DB8972!(DUKE) 1The!primer!pair!for!secondary!PCR!in!nested!PCR!reaction.!"O"!indicates!no!nested!PCR!was!conducted. a!98:30s,!(98:10s,!70:30s,72:90s)x35,!72:600s! ! 2The!PCR!program!used!(primary!PCR/secondary!PCR,!if!nested!PCR!was!used). b!98:30s,!(98:10s,!60:30s,72:90s)x35,!72:600s! 3Genome!walking!using!Clontech!Genome!Walker!kit. c!98:30s,!(98:10s,!72:120s)x35,!72:600s! ! 4Genome!walking!using!Inverse!PCR. d!98:30s,!(98:10s,!72:180s)x35,!72:600s! ! 5Fern!DNA!Database!number!(http://fernlab.biology.duke.edu). e!(94:25s,!72:180s)x7,!(94:25s,!67:180s)x32,!67:420s f!(94:25s,!72:180s)x5,!(94:25s,!67:180s)x20,!67:420s ! g!98:30s,!(98:10s,!67:30s,72:90s)x35,!72:600s! h!98:30s,!(98:10s,!67:30s,72:150s)x35,!72:600s! i!98:30s,!(98:10s,!68:30s,72:120s)x35,!72:600s! j!94:300s,!(94:60s,!60:60,72:120s)x35,!72:600s! k!94:300s,!(94:60s,!56:60,72:240s)x35,!72:600s! l!98:30s,!(98:10s,!70:30s,72:120s)x35,!72:600s! m!98:30s,!(98:10s,!55:30s,72:90s)x35,!72:600s! ! ! Table&S4.!The!primer!sequences. Primer Sequence&(5'53') ! 5upF1 ATTCACAAATGTTGCCCGATGTGC 5upF2 CTGCACTCCTACTCGTTACCG ! AP1 GTAATACGACTCACTATAGGGC! ! AP2 ACTATAGGGCACGCGTGGT F7200_Maphy AGCGTGTAGCCTTGTCCTGTAC ! F73_Maphy GCGACAGCGGCAAAGTTGAAG ! F5 GCGGCAGGCTGCTCAACTACAG F565 TACACCGAAGGCTACAAGGCTAATG ! I_F2 CAAGTGCAATCCAATGATGCCGC I_R1 TTCTGTAGTTGAGCAGCCTGCC ! I_R2 GAGGAGTAGCCGGTCATGGTGAAG ! NaNEO_371_GM1 TGTGGAACAAAGGCAACTTGGGACGAA NaNEO_371_GM2 ATGTGAAGCCTCAAGCAAATGTTACAAGT ! neoF1108 GTGCAGCTCAACATKGAGCTGGA ! neoF1530 TCBTRTTTTGGTTYAGGTCRCAYACTGC neoF1576 CTGGACAGGGACGACGACTCTCG ! neoF1844 CATTGAGGGACAAGGAGGAGTTACCAGG neoF20 CCAAGACGAAGCACAGCGTG ! neoF2115 GGAGGTGATTGGAGSCAACTGC ! neoF2239 AGGAAAGATGGYAGCWRYTTYTGGAA neoF2300 GCTRGAGGTDASCAAGTACACDGAGGG ! neoF2361 CGGCACCAGGACAAGGTTTCTG ! neoF2367 CAGTCSCTCATCAAGTACGAYGT neoF2935 GTKCAGCTYATCCGAGATGCAGT ! neoF2938 CTGTCCCTGGAGATCGTGAACTACACC neoF3049 CAACAGAAGGTGGCGGATTATGTTCC ! neoF3230 CAGACCATCTATGGGTGCGGCATTC ! neoF4018 ATCTTGCTCTACGAGATGCTCTATGGC neoF4110 TACATTCCCAACCAGCATCCCAGTGAG ! neoF428 GYACGGATSTGCGGATGCTCTTCAC ! neoF430 ACGGATSTGCGGATGCTCTTCAC neoF58 AGBGCNGATGCMAGRCTYCATGC ! neoF649 GATCGDGTGATGGCBTACAARTTYCA neoF649 GATCGDGTGATGGCBTACAARTTYCA ! neoF65 ATGCGAGGCTKAATGCGGCGTTTGAG ! neoF651 TCGGGTGATGGCCTACAAGTTCCA neoF67 GCGAGGCTGMATGCGGYGTTYGAG ! neoF812 ACAAGTTYCAYGAGGACGAGCACG ! neoR1950 CCYCGAAYNGCYTCCATCCAYTCCTG neoR2236 AGAAGYTGCTGCCRTCTTTCCTGTA ! neoR2361 CRGAAACCTTGTCCTGGTGCCG neoR2776 GCGAAGATGATGGGGTTGTCCG ! neoR2818 GCACCTCCTCCCTGCTGTACTCTGTCAG ! neoR2938 GGTGTAGTTCACGATCTCCAGGGACAG neoR3049 GGAACATAATCCGCCACCTTCTGTTG ! neoR3065 CTGHACTCCGATGAAGTACTGGA ! neoR3300 GYARCCTSGGATCTGWGATCAC neoR3456 AGCATCATSGCCTTGTCCATG ! neoR3718 TGACVCCCATGCAGTGGAGGTACTC neoR3720 GTTCTCBGGCTTSAGRTCBCGGTAGATG ! neoR4104 ATGCTGGTKGGGAATGTRAGCTCCTTG ! neoR410472 AYGCTGSTSGGGAAKGTGAGCTCCTTG neoR4110 AGGCTCACTGGGATGCTGGTTGGG ! neoR4238 CGGATRAGAGGCCAGTYGATKYCTYGGA ! neoR4242 CGGATGAGAGGCCAGTCGATKYCT neoR429 GAGTGAACAGCATCCGCACATCCGTG ! neoR786 GGTARTGCARGCCVAGRTAHGGCTCC neoR832 GAGGCTGATCGGCTGGTGGAGC neoR877 ATGTACTGCGTGTGGCAACCGTGC neoR902 GACGAGACGGAGCCCATGTTGC photF1856 CTGGTGSTCAAGGAGGAGCTGG photF1970 GCTCTCCWCCTTCCAGCAGACG photF2645 CTTCGCCTCYGACCAYTTCCTGG photF2774 GGAGAGACGGGACATCACTGTGC photR2508 AGCAGCGACAGAAATCCCGAGGAC photR2901 GCTCGTACTCGCTSCCRTCCAG photR4102 ATGCTGSTSGGRAATGTGAGCTCCTTGTT photR4339 TCYKCCTCGTCCCACTCCAGRTC R1_T1 ACCCAGGATCAAAACACATCGCTG R3re GACGCATTCTCGCTCATTGCCAGGAT R4450_Maphy CCATCCACCACAGGTTCTGAACAC R4850_Maphy AAAATGTCCAGGACCGTCAGGTTC R7 AGAGTGGTGGCCAAGTCAATTCC