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Virid
iplan
tae St
rept
ophy
tes
Arch
aepl
astid
a*
Hornworts
Prasinophytes
Rhodophytes
Coleochaetales
Zygnematales
Trebouxiphyceae
Lycophytes
Ulvophyceae
Liverworts
Glaucophytes
Mesostigmatales
Charales
Cryptophytes
Klebsormidiales
Desmidiales
Stramenopiles
Chlorophyceae
Seed plants
Mosses
Ferns
Land
plan
tsC
hlor
ophy
tes
Cha
roph
ytes
Pedinophyceae
Haptophytes
Supplementary Figure 1. The organismal lineages screened for phytochrome homologs. Phytochromes were not detected in lineages indicated in grey. *Traditional Archaeplastida does not include cryptophytes.
Pinus parvifloraGnetum montanum
Platanthera clavellata
Oryza sativa
Podocarpus rubens
Vitis vinifera
Capnoides sempervirens 2
Fragaria vesca
Podocarpus rubens
Cucumis sativus
Solanum lycopersicum 2
Arabidopsis thaliana B
Aquilegia coerulea 1
Fragaria vesca 2
Cephalotaxus harringtonia
Cucumis sativus 2
Illicium floridanum
Amborella trichocarpa
Thuja plicata
Welwitschia mirabilis
Fragaria vesca 1
Gnetum montanum
Aquilegia coerulea
Arabidopsis thaliana
Peperomia fraseri
Arabidopsis thaliana
Taiwania cryptomerioides
Buxus sempervirens
Phaseolus vulgaris
Fragaria vesca
Buxus sempervirens
Encephalartos barteri
Taiwania cryptomerioides
Laurelia sempervirens
Aquilegia coerulea
Solanum lycopersicum 1
Taiwania cryptomerioides
Amborella trichocarpa
Cucumis sativus 1
Peperomia fraseri
Solanum lycopersicum
Ginkgo biloba
Vitis vinifera
Arabidopsis thaliana D
Cephalotaxus harringtonia
Ginkgo biloba
Encephalartos barteri
Buxus sempervirens
Podocarpus rubens
Platanthera clavellata
Pinus parviflora
Thuja plicata
Vitis vinifera
Platanthera clavellata
Welwitschia mirabilis
Solanum lycopersicum
Laurelia sempervirens
Illicium floridanum
Oryza sativa
Ginkgo biloba
Phaseolus vulgaris 1
Amborella trichocarpa
Aquilegia coerulea
Encephalartos barteri
Phaseolus vulgaris
Solanum lycopersicum
Illicium floridanum
Oryza sativa
Phaseolus vulgaris 2
Arabidopsis thaliana
Laurelia sempervirens
Fragaria vesca
Pistia stratioides
Cucumis sativus
Pistia stratioides
Peperomia fraseriPistia stratioides
Thuja plicata
Laurelia sempervirens
Illicium floridanum
Aquilegia coerulea 2
Capnoides sempervirens 1
Pinus parviflora
Cucumis sativus
0.1 substitutions/site
Angiosperm PHYA
Gymnosperm PHYN
Angiosperm PHYC
Gymnosperm PHYO
Angiosperm PHYB
Angiosperm PHYE
Gymnosperm PHYP
Supplementary Figure 2. The phylogeny of phytochromes reconstructed from 423 protein sequences. Topology derived from the best maximum likelihood tree. The values associated with branches are maximum likelihood bootstrap support. For better visualization, the complete tree is broken down into six subtrees (a-f) and scaled differently. The inset at the top-left corner shows the map to each subtree. (a) The seed plant phytochrome subtree. Phylogeny continues in Supplementary Fig. 2b.
To Fig. 2b(ferns + lycophytes)
Fig. 2a seed plant PHY
Fig. 2b fern + lycophyte PHY
Fig. 2c bryophyte PHY
Fig. 2d neochrome
Fig. 2e green algae PHY
Fig. 2f prokaryote + stramenopile + fungi PHY
100
100
51
66
52
10098
100
10095
55
97
91
100
100
10099
100100
100
71
55
99
97
89
80
98
8381
6460
100
89
62
100100
89
51
100
100
100
100
100
100100
100
100
100
100100
100
55
62
88
5765
53
98
8889
51
8191
5657
88
89
57
84
68
0.1 substitutions/site
Fern PHY2
Fern PHY4
Fern PHY1
Fern PHY2/4
Lycopodiales PHY
Selaginellales PHY
Supplementary Figure 2. (b) The fern and lycophyte phytochrome subtree. Phylogeny continues in Supplementary Fig. 2a,c. See Fig. 5 for a more extensively sampled and higher resolution phylogeny that was reconstructed from nucleotide dataset.
To Fig. 1c(bryophytes)
Argyrochosma nivea
Pteridium aquilinum
Diplazium wichurae
Polypodium glycyrrhiza
Thyrsopteris elegans
Dendrolycopodium obscurum 1
Polystichum acrostichoides
Blechnum spicant
Alsophila spinulosa
Selaginella moellendorffii
Polystichum acrostichoides
Pseudolycopodiella caroliniana 1
Pteridium aquilinum
Vittaria appalachiana
Equisetum diffusum A
Plagiogyria japonica
Pseudolycopodiella caroliniana 2
Selaginella apoda
Plagiogyria japonica
Myriopteris rufa
Polypodium hesperium
Cystopteris fragilis
Deparia lobato-crenata
Pilularia globulifera
Marattia attenuata
Equisetum diffusum B
Gaga arizonica
Vittaria appalachiana
Diplazium wichurae
Gaga arizonica
Pilularia globulifera
Huperzia selago 1
Homalosorus pycnocarpos
Vittaria appalachiana
Athyrium filix-femina
Pteris ensiformis
Equisetum diffusumMarattia howeana
Sceptridium dissectum B
Polystichum acrostichoides
Sceptridium dissectum A
Pityrogramma trifoliata
Dipteris conjugata
Selaginella wallacei
Huperzia lucidula 2
Adiantum capillus-veneris
Cystopteris fragilis
Pilularia globulifera
Blechnum spicant
Cryptogramma acrostichoides
Adiantum raddianum
Cystopteris fragilis
Pteris ensiformis
Dendrolycopodium obscurum 2
Alsophila spinulosa
Argyrochosma niveaMyriopteris rufa
Selaginella cf pallescens
Osmunda sp.
Woodsia scopulina
Gymnocarpium dryopteris
Botrypus virginianus A
Asplenium platyneuron
Cryptogramma acrostichoides
Pteridium aquilinum
Culcita macrocarpa
Adiantum capillus veneris
Plagiogyria japonica
Polypodium hesperium
Asplenium platyneuron
Selaginella kraussiana
Woodsia ilvensis
Anemia tomentosa
Deparia lobato-crenata
Gymnocarpium dryopteris
Leucostegia immersa
Notholaena montieliae
Botrypus virginianus B
Woodsia scopulina
Asplenium platyneuron
Woodsia ilvensis
Dipteris conjugata
Blechnum spicant
Psilotum nudum
Blechnum spicant
Adiantum capillus-veneris
Selaginella willdenowii
Cystopteris protrusa
Athyrium filix-femina
Osmunda sp
Leucostegia immersa
Isoetes tegetiformans Isoetales PHY
To Fig. 2a(Seed plants)
Fig. 2a seed plant PHY
Fig. 2b fern + lycophyte PHY
Fig. 2c bryophyte PHY
Fig. 2d neochrome
Fig. 2e green algae PHY
Fig. 2f prokaryote + stramenopile + fungi PHY
86
69
62
6670
58
7053
85
93
51
95
10010065
100
50
5695
84
57
95
61
98
100
66
82 100
100100
53
99
84
69
90
99
53
52
98
100
100
100
76
58
100
85
5286
95
69
52
81
100
54
7382
98
97
9099
99
100
100
87
6377
0.1 substitutions/site
Moss PHY5
Moss PHY2_4
Supplementary Figure 2. (c) The bryophyte phytochrome subtree. Phylogeny continues in Supplementary Fig. 2b,d,e. See Fig. 4 for a more extensively sampled and higher resolution phylogeny that was reconstructed from nucleotide dataset.
To Fig. 2b(ferns + lycophytes)
Atrichum angustatum
Leucodon brachypus E
Rhynchostegium serrulatum E
Scapania nemorosa
Stereodon subimponens
Hedwigia ciliata
Leucodon brachypus
Anomodon attenuatus
Phaeoceros carolinianus
Racomitrium varium
Metzgeria crassipilis
Andreaea rupestris
Leucodon brachypus D 1
Stereodon subimponens
Atrichum angustatum
Sphaerocarpos texanus
Neckera douglasii E
Syntrichia princeps E
Scouleria aquatica D
Pseudotaxiphyllum elegans E
Physcomitrella patens B
Aulacomnium heterostichum E 2
Syntrichia princeps D
Nothoceros aenigmaticus
Scouleria aquatica
Hedwigia ciliata D
Claopodium rostratum D
Takakia lepidozioides
Odontoschisma prostratum
Physcomitrella patens C
Anomodon attenuatus E
Claopodium rostratum
Bryum argenteum
Scouleria aquatica E
Leucodon brachypus
Pseudotaxiphyllum elegans D
Ceratodon purpureus “PHY3”
Rhynchostegium serrulatum
Loeskeobryum brevirostre
Megaceros flagellaris
Leucodon julaceus
Aulacomnium heterostichum D
Schistochila sp
Leucodon brachypus D
Racomitrium varium
Ceratodon purpureus “PHY2”
Racomitrium varium E
Loeskeobryum brevirostre D
Physcomitrella patens 1
Physcomitrella patens A
Ceratodon purpureus “PHY4”
Porella pinnata
Ceratodon purpureus “PHY1”
Paraphymatoceros hallii
Physcomitrella patens 2
Marchantia paleacea
Loeskeobryum brevirostre
Bazzania trilobata
Physcomitrella patens 4
Racomitrium varium D
Neckera douglasii
Bryum argenteum
Pellia neesiana
Neckera douglasii
Ceratodon purpureus
Rhynchostegium serrulatum
Rhynchostegium serrulatum D
Hedwigia ciliata E
Andreaea rupestris
Aulacomnium heterostichum
Aulacomnium heterostichum
Bryum argenteum D
Leucodon julaceus E
Lunularia cruciata
Loeskeobryum brevirostre E
Leucodon julaceus
Philonotis fontana
Philonotis fontana E
Physcomitrella patens 3
Leucobryum albidum
Anthoceros punctatus
Conocephalum conicum
Hedwigia ciliata
Leucobryum albidum
Aulacomnium heterostichum E 1
Claopodium rostratum
Sphagnum palustre
Leucodon brachypus D 2
Anomodon attenuatus D
Philonotis fontana
Pseudotaxiphyllum elegans
Claopodium rostratum E
Philonotis fontana D
Pseudotaxiphyllum elegans
Ricciocarpos natans
Moss PHY2_4/5
Moss PHY1_3
Liverwort PHY
Hornwort PHY
To Fig. 2d(neochrome)
To Fig. 2e(green algae)
Fig. 2a seed plant PHY
Fig. 2b fern + lycophyte PHY
Fig. 2c bryophyte PHY
Fig. 2d neochrome
Fig. 2e green algae PHY
Fig. 2f prokaryote + stramenopile + fungi PHY
60
61
7457
96
54
55
63
62
92
75
618851
69
57
52
8177
61
98
93
98
81
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100
100
9563
9661
91
99
52
77
74
68
99
56
9960
91
86
91
93
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88
8394
98
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94
68
100
96
9585
646398
72
77
90
87
8054
63
73
0.5 substitutions/site
Supplementary Figure 2. (d) The neochrome subtree. Phylogeny continues in Supplementary Fig. 2c,e. See Fig. 3 for a more extensively sampled and higher resolution phylogeny.
Paraphymatoceros hallii
Zygnemopsis sp
Cylindrocystis sp
Anthoceros punctatus
Dipteris conjugata
Hemidictyum marginatum
Cylindrocystis brebissonii
Adiantum capillus-veneris
Phaeoceros carolinianus
Mougeotia scalaris 1Mougeotia scalaris 2
Cylindrocystis spCylindrocystis brebissonii
Nothoceros aenigmaticus
Blechnum spicant
Megaceros flagellaris
To Fig. 2e(green algae)
Fern neochrome
Hornwort neochrome
To Fig. 2c(bryophytes)
Zygnematales neochrome
Hornwort neochrome
Fig. 2a seed plant PHY
Fig. 2b fern + lycophyte PHY
Fig. 2c bryophyte PHY
Fig. 2d neochrome
Fig. 2e green algae PHY
Fig. 2f prokaryote + stramenopile + fungi PHY
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100
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100
83
8363
100
100
100
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99
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73
0.5 substitutions/site
Desmidiales PHY2C
Supplementary Figure 2. (e) The green algae phytochrome subtree. Green star marks the origin of canonical plant phyto-chrome. Phylogeny continues in Supplementary Fig. 2c,d,f. “*” marks the cryptophyte phytochromes that have incomplete C-terminal end, so that they cannot be determined as PEK or not.
To Fig. 2c (bryophytes)
Gloeochaete wittrockiana 2
Tetraselmis cordiformis
Cylindrocystis brebissonii
Interfilum paradoxum
Penium exiguum
Guillardia theta PHY2
Phymatodocis nordstedtiana
Planotaenium ohtanii
Hemiselmis virescens*
Onychonema laeve
Staurodesmus convergens
Glaucocystis nostochinearum 4
Gloeochaete wittrockiana 3
Onychonema laeve
Roya obtusa
Roya obtusa
Gonatozygon kinahanii
Mesostigma viride
Cylindrocystis cushleckae
Chaetosphaeridium globosum
Phymatodocis nordstedtiana
Cryptomonas curvata*
Desmidium aptogonum
Micromonas pusilla
Penium exiguum
Desmidium aptogonum
Cosmarium granatum
Rhodomonas sp*
Staurodesmus convergens
Cyanoptyche gloeocystis 1
Chlorokybus atmophyticus 2
Mesotaenium caldariorum
Entransia fimbriat
Staurodesmus convergens
Guillardia theta PHY1
Cyanoptyche gloeocystis 2
Cosmarium granatum
Zygnemopsis sp
Guillardia theta PEK1
Onychonema laeve
Cosmarium subtumidum
Chaetosphaeridium globosum
Netrium digitus
Penium exiguum
Cylindrocystis sp
Chroomonas sp PEK
Coleochaete irregularis
Gonatozygon kinahanii
Mesotaenium kramstae
Cosmarium subtumidum
Mesotaenium kramstae
Coleochaete irregularis
Cyanophora paradoxa 4
Glaucocystis nostochinearum 1
Netrium digitusColeochaete irregularis
Klebsormidium subtile
Glaucocystis nostochinearum 2
Cyanophora paradoxa 1
Staurodesmus convergens
Cosmarium subtumidum
Gonatozygon kinahanii
Netrium digitus
Cylindrocystis brebissonii
Phymatodocis nordstedtiana Gonatozygon kinahanii 1
Chlorokybus atmophyticus 1
Mesotaenium braunii
Tetraselmis astigmatica
Nephroselmis pyriformis
Spirotaenia minuta
Mesotaenium kramstae
Cyanoptyche gloeocystis 3
Cosmarium granatum
Zygnemopsis sp
Onychonema laeve
Staurodesmus convergens
Cyanophora paradoxa 2
Cosmarium granatumCosmarium subtumidum
Desmidium aptogonum
Dolichomastix tenuilepsis
Mougeotia scalaris
Prasinoderma coloniale
Planotaenium ohtanii
Gloeochaete wittrockiana 1
Zygnemopsis sp
Monomastix opisthostigma
Penium exiguum
Gonatozygon kinahanii 2
Cylindrocystis sp
Entransia fimbriata
Pyramimonas parkeae
Gloeochaete wittrockiana 4
Phymatodocis nordstedtiana
Cylindrocystis cushleckae
Glaucocystis nostochinearum 3
Guillardia theta PEK2
Guillardia thetaPEK3
Desmidiales PHY2B
Desmidiales PHY2A
Zygnematales PHY2
Coleochaetales PHY2
Klebsormidiales PHY2
Desmidiales PHY1
Klebsormidiales PHY1
Mesostigmatales PHY1/2
Zygnematales PHYX2
Zygnematales PHYX1
To Fig. 2d (neochromes)
Coleochaetales PHYX2
Coleochaetales PHYX1
Glaucophyte GPS
Cryptophyte PHY
CharophytePHY2
Prasinophyte PHY
To Fig. 2f(prokaryotes
stramenopilesfungi)
CharophytePHY1
CharophytePHY1/2
CharophytePHYX2
CharophytePHYX1
Fig. 2a seed plant PHY
Fig. 2b fern + lycophyte PHY
Fig. 2c bryophyte PHY
Fig. 2d neochrome
Fig. 2e green algae PHY
Fig. 2f prokaryote + stramenopile + fungi PHY
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99
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90
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65
7691
63
0.5 substitutions/site
Supplementary Figure 2. (f) The prokaryote + stramenopile + fungi phytochrome subtree. Phylogeny continues in Supple-mentary Fig. 2e.
Brown algae PHY
Phaeodactylum tricornutumgiThalassiosira pseudonana
Nodularia spumigena
Tolypothrix sp
Oceanicola granulosus
Ectocarpus siliculosus virus isolate EsV
Nostoc punctiforme
Aspergillus fumigatus
Synechocystis sp
Scytosiphon lomentaria
Ralstonia pickettii
Neurospora crassa
Stenotrophomonas maltophilia
Sclerotinia sclerotiorum
Pseudomonas syringae
Penicillium marneffei
Agrobacterium tumefaciens
Ustilago maydis
Nostoc sp
Synechococcus sp
Ishige okamurai
Rhodopseudomonas palustris
Anabaena variabilis
Feldmannia species virus isolate FsV
Cyanothece sp
Pseudomonas aeruginosaMagnetospirillum magnetotacticum
Microcoleus chthonoplastes
Anabaena variabilis
Ectocarpus siliculosus
Microcystis aeruginosa
Tolypothrix sp
Lyngbya sp
Neurospora crassa
Methylocella silvestris
Petalonia fascia
Cochliobolus heterostrophus
Brown algae virus PHYDiatom PHY
Fungi PHY
Cyanobacteria PHY
Bacteria PHY
Cyanobacteria PAS-less PHY
To Fig. 2e(green algae)
Fig. 2a seed plant PHY
Fig. 2b fern + lycophyte PHY
Fig. 2c bryophyte PHY
Fig. 2d neochrome
Fig. 2e green algae PHY
Fig. 2f prokaryote + stramenopile + fungi PHY
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Source 1KP3+identififerAngiosperm
Amborella+trichocarpa Genome,+Amborella+Genome+Project1 ;Aquilegia+coerulea Genome,+Phytozome2 ;Arabidopsis+thaliana Genome,+Phytozome ;Buxus+sempervirens Transcriptome,+1KP3 IWMWCapnoides+sempervirens Transcriptome,+1KP AUGVCucumis+sativus Genome,+Phytozome ;Fragaria+vesca Genome,+Phytozome ;Illicium+floridanum Transcriptome,+1KP VZCILaurelia+sempervirens Transcriptome,+1KP WAILOryza+sativa Genome,+Phytozome ;Peperomia+fraseri Transcriptome,+1KP XSZIPhaseolus+vulgaris Genome,+Phytozome ;Pistia+stratioides Transcriptome,+1KP MFINPlatanthera+clavellata Transcriptome,+1KP MTHWSolanum+lycopersicum Genome,+Phytozome ;Vitis+vinifera Genome,+Phytozome ;
Gymnosperm
Cephalotaxus+harringtonia Transcriptome,+1KP WYAJEncephalartos+barteri Transcriptome,+1KP GNQGGinkgo+biloba Transcriptome,+1KP SGTWGnetum+montanum Transcriptome,+1KP GTHKPinus+parviflora Transcriptome,+1KP IIOLPodocarpus+rubens Transcriptome,+1KP XLGKTaiwania+cryptomerioides Transcriptome,+1KP QSNJThuja+plicata Transcriptome,+1KP VFYZWelwitschia+mirabilis Transcriptome,+1KP TOXE
Fern
Adiantum+tenerum Transcriptome,+1KP BMJRAnemia+tomentosa Transcriptome,+1KP CQPWArgyrochosma+nivea Transcriptome,+1KP XDDTAsplenium+platyneuron Transcriptome,+1KP KJZGAthyrium+filix;femina Transcriptome,+1KP AFPOAzolla+caroliniana Transcriptome,+1KP CVEGAzolla+filiculoides Transcriptome,+Brouwer+et+al.4+ ;Blechnum+spicant Transcriptome,+1KP VITXBotrypus+virginianus Transcriptome,+1KP BEGMCeratopteris+thalictroides Transcriptome,+1KP PIVWGaga+arizonica Transcriptome,+1KP DCDT
Supplementary3Table31.+List+of+transcriptomes+and+genomes+screened+for+phytochrome+homologs.+";":+not+applicable.
Taxa
Cryptogramma+acrostichoides Transcriptome,+1KP WQMLCulcita+macrocarpa Transcriptome,+1KP PNZOAlsophila+spinulosa Transcriptome,+1KP GANBCystopteris+fragilis Transcriptome,+1KP LHLECystopteris+protrusa Transcriptome,+1KP YOWVDanaea+nodosa Transcriptome,+1KP DFHODeparia+lobato;crenata Transcriptome,+1KP FCHSDiplazium+wichurae Transcriptome,+1KP UFJNDipteris+conjugata Transcriptome,+1KP MEKPEquisetum+diffusum Transcriptome,+1KP CAPNGymnocarpium+dryopteris Transcriptome,+1KP HEGQHomalosorus+pycnocarpos Transcriptome,+1KP OCZLLeucostegia+immersa Transcriptome,+1KP WGTULindsaea+microphylla Transcriptome,+1KP YIXPLonchitis+hirsuta Transcriptome,+1KP VVRNLygodium+japonicum Transcriptome,+1KP PBUUMarattia+attenuata Transcriptome,+1KP UGNKMyriopteris+rufa Transcriptome,+1KP GSXDNotholaena+montieliae Transcriptome,+1KP YCKEOsmunda+javanica Transcriptome,+1KP VIBOOsmunda+sp Transcriptome,+1KP UOMYOsmundastrum+cinnamomeum Transcriptome,+1KP RFMZPilularia+globulifera Transcriptome,+1KP KIIXPityrogramma+trifoliata Transcriptome,+1KP UJTTPlagiogyria+japonica Transcriptome,+1KP UWODPolypodium+glycyrrhiza Transcriptome,+1KP CJNTPolypodium+hesperium Transcriptome,+1KP GYFUPolystichum+acrostichoides Transcriptome,+1KP FQGQPteridium+aquilinum Transcriptome,+Der+et+al.5 ;Pteris+ensiformis Transcriptome,+1KP FLTDSceptridium+dissectum Transcriptome,+1KP EEAQThyrsopteris+elegans Transcriptome,+1KP EWXKVittaria+appalachiana Transcriptome,+1KP NDUVWoodsia+ilvensis Transcriptome,+1KP YQECWoodsia+scopulina Transcriptome,+1KP YJJY
Isoetopsida
Selaginella+cf+pallescens Transcriptome,+1KP ABIJSelaginella+moellendorffii Genome,+Phytozome ;Selaginella+willdenowii Transcriptome,+1KP KJYCSelaginella+kraussiana Transcriptome,+1KP ZFGKSelaginella+wallacei Transcriptome,+1KP JKAASelaginella+apoda Transcriptome,+1KP LGDQ
Isoetes+tegetiformans Transcriptome,+1KP PKOXLycopodiales3
Dendrolycopodium+obscurum Transcriptome,+1KP XNXFHuperzia+selago Transcriptome,+1KP GTUOHuperzia+lucidula Transcriptome,+1KP GKAGPseudolycopodiella+caroliniana Transcriptome,+1KP UPMJ
Moss
Andreaea+rupestris Transcriptome,+1KP WOGBAnomodon+attenuatus Transcriptome,+1KP QMWBClaopodium+rostratum Transcriptome,+1KP VBMMAtrichum+angustatum Transcriptome,+1KP ZTHVAulacomnium+heterostichum Transcriptome,+1KP WNGHBryum+argenteum Transcriptome,+1KP JMXWCeratodon+purpureus Transcriptome,+1KP FFPDHedwigia+ciliata Transcriptome,+1KP YWNFStereodon+subimponens Transcriptome,+1KP LNSFLeucobryum+albidum Transcriptome,+1KP VMXJLeucodon+brachypus Transcriptome,+1KP ZACWNeckera+douglasii Transcriptome,+1KP TMAJPhilonotis+fontana Transcriptome,+1KP ORKSPhyscomitrella+patens Genome,+Phytozome ;Pseudotaxiphyllum+elegans Transcriptome,+1KP QKQORacomitrium+varium Transcriptome,+1KP RDOORhynchostegium+serrulatum Transcriptome,+1KP JADLLoeskeobryum+brevirostre Transcriptome,+1KP WSPMLeucodon+julaceus Transcriptome,+1KP IGUHScouleria+aquatica Transcriptome,+1KP BPSGSphagnum+palustre Transcriptome,+1KP RCBTSyntrichia+princeps Transcriptome,+1KP GRKUTakakia+lepidozioides Transcriptome,+1KP SKQD
Liverwort
Scapania+nemorosa Transcriptome,+1KP IRBNPorella+pinnata Transcriptome,+1KP UUHDSchistochila+sp Transcriptome,+1KP LGOWMetzgeria+crassipilis Transcriptome,+1KP NRWZPellia+neesiana Transcriptome,+1KP JHFIOdontoschisma+prostratum Transcriptome,+1KP YBQNConocephalum+conicum Transcriptome,+1KP ILBQLunularia+cruciata Transcriptome,+1KP TXVBSphaerocarpos+texanus Transcriptome,+1KP HERTRicciocarpos+natans Transcriptome,+1KP WJLOBazzania+trilobata Transcriptome,+1KP WZYK
Hornwort
Nothoceros+aenigmaticus Transcriptome,+1KP DXOUMegaceros+flagellaris Transcriptome,+1KP UCRNParaphymatoceros+hallii Transcriptome,+1KP FAJBPhaeoceros+carolinianus Transcriptome,+1KP WCZBAnthoceros+punctatus Genome,+Li+et+al.6 ;Phaeomegaceros+coriaceus Transcriptome,+1KP AKXBLeiosporoceros+dussii Transcriptome,+1KP ANON
Desmidiales
Cosmarium+granatum Transcriptome,+1KP MNNMCosmarium+subtumidum Transcriptome,+1KP WDGVDesmidium+aptogonum Transcriptome,+1KP DFDSGonatozygon+kinahanii Transcriptome,+1KP KEYWOnychonema+laeve Transcriptome,+1KP GGWHPenium+exiguum Transcriptome,+1KP YSQTPhymatodocis+nordstedtiana Transcriptome,+1KP RPQVPlanotaenium+ohtanii Transcriptome,+1KP SNOXRoya+obtusa Transcriptome,+1KP XRTZStaurodesmus+convergens Transcriptome,+1KP WCQU
Zygnematales
Cylindrocystis+brebissonii Transcriptome,+1KP YOXICylindrocystis+cushleckae Transcriptome,+1KP JOJQCylindrocystis+sp Transcriptome,+1KP VAZEMesotaenium+braunii Transcriptome,+1KP WSJOMesotaenium+kramstae Transcriptome,+1KP NBYPNetrium+digitus Transcriptome,+1KP FFGRZygnemopsis+sp Transcriptome,+1KP MFZO
Coleochaetales
Coleochaete+irregularis Transcriptome,+1KP QPDYChaetosphaeridium+globosum Transcriptome,+1KP DRGY
Klebsormidiales
Interfilum+paradoxum Transcriptome,+1KP FPCOKlebsormidium+subtile Transcriptome,+1KP FQLPEntransia+fimbriata Transcriptome,+1KP BFIK
Mesostigmatales
Chlorokybus+atmophyticus Transcriptome,+1KP AZZWMesostigma+viride Transcriptome,+1KP KYIOSpirotaenia+minuta Transcriptome,+1KP NNHQ
Charales
Chara+vulgaris Transcriptome,+1KP MWXTTrebouxiophyceae
Botryococcus+braunii Transcriptome,+1KP ETGN
Botryococcus+terribilis Transcriptome,+1KP QYXYCoccomyxa+pringsheimii Transcriptome,+1KP GXBMEremosphaera+viridis Transcriptome,+1KP MNCBGeminella+sp. Transcriptome,+1KP PFUDLeptosira+obovata Transcriptome,+1KP ZNUMMicrothamnion+kuetzigianum Transcriptome,+1KP DXNYNannochloris+atomus Transcriptome,+1KP MFYCNeochloris+oleoabundans Transcriptome,+1KP EEJOParachlorella+kessleri Transcriptome,+1KP AKCRPrasiola+crispa Transcriptome,+1KP WCLVPrototheca+wickerhamii Transcriptome,+1KP BILCStichococcus+bacillaris Transcriptome,+1KP WXRITrebouxia+arboricola Transcriptome,+1KP NKXU
Ulvophyceae
Acrosiphonia+sp. Transcriptome,+1KP JIWJBlastophysa+cf.+rhizopus Transcriptome,+1KP VHIJBolbocoleon+piliferum Transcriptome,+1KP LSHTBryopsis+plumosa Transcriptome,+1KP JTIGCephaleuros+virescens Transcriptome,+1KP YDCQCladophora+glomerata Transcriptome,+1KP VBLHCodium+fragile Transcriptome,+1KP GYBHDesmochloris+halophila Transcriptome,+1KP KSFKEntocladia+endozoica Transcriptome,+1KP OQONHalochlorococcum+marinum Transcriptome,+1KP ALZFHelicodictyon+planctonicum Transcriptome,+1KP AJAUIgnatius+tetrasporus Transcriptome,+1KP KADGOchlochaete+sp. Transcriptome,+1KP CQQPOltmannsiellopsis+viridis Transcriptome,+1KP PZBHOltmannsiellopsis+viridis Transcriptome,+1KP QJYXPercursaria+percursa Transcriptome,+1KP OAEZPlanophila+laetevirens Transcriptome,+1KP CBNGPlanophila+sp. Transcriptome,+1KP LETFPirula+salina Transcriptome,+1KP NQYPPseudoneochloris+marina Transcriptome,+1KP GJIYTrentepohlia+annulata Transcriptome,+1KP NATT
Chlorophyceae
Ankistrodesmus+sp. Transcriptome,+1KP OTQGAphanochaete+repens Transcriptome,+1KP IJMTAsteromonas+gracilis Transcriptome,+1KP NTLEBotryosphaerella+sudetica Transcriptome,+1KP VJDZBrachiomonas+submarina Transcriptome,+1KP GUBDCarteria+crucifera Transcriptome,+1KP VIAU
Carteria+obtusa Transcriptome,+1KP RUIFChaetopeltis+orbicularis Transcriptome,+1KP BAZFChlamydomonas+reinhardtii Genome,+Phytozome ;Chlamydomonas+bilatus Transcriptome,+1KP MULFChlamydomonas+cribrum Transcriptome,+1KP BCYFChlamydomonas+moewusii Transcriptome,+1KP JRGZChlamydomonas+noctigama Transcriptome,+1KP VALZChlamydomonas+sp. Transcriptome,+1KP TSBQChlamydomonas+sp. Transcriptome,+1KP AOUJChlorella+variabilis Genome,+Blanc+et+al.7 ;Chloromonas+oogama Transcriptome,+1KP IHOIChloromonas+perforata Transcriptome,+1KP QRTHChloromonas+reticulata Transcriptome,+1KP LBRPChloromonas+rosae Transcriptome,+1KP AJUWChloromonas+subdivisa Transcriptome,+1KP GFURChloromonas+tughillensis Transcriptome,+1KP UTRECylindrocapsa+geminella Transcriptome,+1KP DZPJDunaliella+salina Transcriptome,+1KP RHVCDunaliella+tertiolecta Transcriptome,+1KP ZDIZEudorina+elegans Transcriptome,+1KP RNATFritschiella+tuberosa Transcriptome,+1KP VFIVGolenkinia+longispicula Transcriptome,+1KP BZSHGonium+pectorale Transcriptome,+1KP KUJUHaematococcus+pluvialis Transcriptome,+1KP ODXIHaematococcus+pluvialis Transcriptome,+1KP AGIOHafniomonas+reticulata Transcriptome,+1KP FXHGHeterochlamydomonas+inaequalis Transcriptome,+1KP IRYHLobochlamys+segnis Transcriptome,+1KP OFUELobomonas+rostrata Transcriptome,+1KP JKKIMicrospora+cf.+tumidula Transcriptome,+1KP FOYQNeodesmus+pupukensis Transcriptome,+1KP MWANNeochlorosarcina+sp. Transcriptome,+1KP USIXOedogonium+cardiacum Transcriptome,+1KP DVYEOedogonium+foveolatum Transcriptome,+1KP SDPCOogamochlamys+gigantea Transcriptome,+1KP XDLLPandorina+morum Transcriptome,+1KP RYJXPediastrum+duplex Transcriptome,+1KP XKWQPediastrum+duplex Transcriptome,+1KP XTONPhacotus+lenticularis Transcriptome,+1KP ZIVZPleurastrum+insigne Transcriptome,+1KP PRIQPteromonas+angulosa Transcriptome,+1KP LNILPteromonas+sp. Transcriptome,+1KP ACRY
Scenedesmus+dimorphus Transcriptome,+1KP PZIFSpermatozopsis+exsultans Transcriptome,+1KP MXDSSpermatozopsis+similis Transcriptome,+1KP ENAUStephanosphaera+pluvialis Transcriptome,+1KP ZLQEStigeoclonium+helveticum Transcriptome,+1KP JMUIUronema+sp. Transcriptome,+1KP ISGTUronema+belkae Transcriptome,+1KP RAWFVitreochlamys+sp. Transcriptome,+1KP QWRAVolvox+carteri Genome,+Phytozome ;Volvox+aureus Transcriptome,+1KP JWGTVolvox+aureus Transcriptome,+1KP WRSLVolvox+globator Transcriptome,+1KP ISPU
Pedinophyceae
Pedinomonas+minor Transcriptome,+1KP RRSVPedinomonas+tuberculata Transcriptome,+1KP PUAN
Red3Algae
Betaphycus+gelatinae Transcriptome,+1KP BWVJCeramium+kondoi Transcriptome,+1KP VZWXChondrus+crispus+ Genome,+Collen+et+al.8 ;Chondrus+crispus Transcriptome,+1KP UGPMChroodactylon+ornatum Transcriptome,+1KP LLXJCyanidioschyzon+merolae+ Genome,+Matsuzaki+et+al.9 ;Dumontia+simplex Transcriptome,+1KP IEHFEucheuma+denticulatum Transcriptome,+1KP JEBKGaldieria+sulphuraria Genome,+Barbier+et+al.10 ;Glaucosphaera+vacuolata Transcriptome,+1KP RSOFGloeopeltis+furcata Transcriptome,+1KP SBLTGracilaria+asiatica Transcriptome,+1KP VNALGracilaria+blodgettii Transcriptome,+1KP LJPNGracilaria+chouae Transcriptome,+1KP FTRPGracilaria+lemaneiformi Transcriptome,+1KP IKWMGrateloupia+filicina Transcriptome,+1KP ZJOJGrateloupia+livida Transcriptome,+1KP IKIZGrateloupia+turuturu Transcriptome,+1KP URSBGrateloupia+chiangii Transcriptome,+1KP PWKQGymnogongrus+ftabelliformis Transcriptome,+1KP CKXFHeterosiphonia+pulchra Transcriptome,+1KP YSBDKappaphycus+alvarezii Transcriptome,+1KP IHJYMazzaella+japonica Transcriptome,+1KP WEJNPolysiphonia+japonica Transcriptome,+1KP XAXWPyropia+yezoensis Genome,+Nakamura+et+al.11 ;Porphyra+yezoensis Transcriptome,+1KP ZULJ
Porphyridium+cruentum Transcriptome,+1KP OBUYPorphyridium+purpureum Genome,+Bhattacharya+et+al.12 ;Porphyridium+purpureum Transcriptome,+1KP PVGPRhodella+violacea Transcriptome,+1KP RTLCRhodochaete+parvula Transcriptome,+1KP JJZRSinotubimorpha+guangdongensis Transcriptome,+1KP PYDBSymphyocladia+latiuscula Transcriptome,+1KP UYFR
Prasinophyte
Monomastix+opisthostigma Transcriptome,+1KP BTFMPyramimonas+parkeae Transcriptome,+1KP TNAWTetraselmis+cordiformis Transcriptome,+1KP DUMA
Cryptophyte
Chroomonas+sp Transcriptome,+1KP ROZZCryptomonas+curvata Transcriptome,+1KP BAKFGuillardia+theta Genome,+Curtis+et+al.13 ;Hemiselmis+virescens Transcriptome,+1KP MJMQRhodomonas+sp Transcriptome,+1KP IAYV
Glaucophyte
Cyanophora+paradoxa Genome,+Price+et+al.14 ;Cyanoptyche+gloeocystis Transcriptome,+1KP JKHAGlaucocystis+nostochinearum Transcriptome,+1KP POOW
Haptophytes
Isochrysis+sp. Transcriptome,+1KP BAJWPavlova+lutheri Transcriptome,+1KP NMAKPrymnesium+parvum Transcriptome,+1KP LXRN
Stramenopiles3H3Chrysophytes
Mallomonas+sp. Transcriptome,+1KP BOGTOchromonas+sp. Transcriptome,+1KP EBWISynura+petersenii Transcriptome,+1KP DBYDSynura+sp. Transcriptome,+1KP VKVG
Stramenopiles3H3Brown3algae
Ishige+okamurae Transcriptome,+1KP APTPPetalonia+fascia Transcriptome,+1KP VRGZScytosiphon+lomentaria Transcriptome,+1KP JCXF
Source 1KP3+identififer GenBank+accessionAngiosperm+PHYA
Arabidopsis+thaliana Genome,+Phytozome2 @ @Fragaria+vesca Genome,+Phytozome @ @Phaseolus+vulgaris+1 Genome,+Phytozome @ @Phaseolus+vulgaris+2 Genome,+Phytozome @ @Cucumis+sativus+1 Genome,+Phytozome @ @Cucumis+sativus+2 Genome,+Phytozome @ @Vitis+vinifera Genome,+Phytozome @ @Solanum+lycopersicum Genome,+Phytozome @ @Buxus+sempervirens Transcriptome,+1KP2 IWMW KT071960Aquilegia+coerulea Genome,+Phytozome @ @Oryza+sativa Genome,+Phytozome @ @Platanthera+clavellata Transcriptome,+1KP MTHW KT071961Pistia+stratioides Transcriptome,+1KP MFIN KT071962Laurelia+sempervirens Transcriptome,+1KP WAIL KT071963Peperomia+fraseri Transcriptome,+1KP XSZI KT071964Illicium+floridanum Transcriptome,+1KP VZCI KT071965Amborella+trichocarpa Genome,+Amborella+Genome+Project1 @ @
Gymnosperm+PHYNCephalotaxus+harringtonia Transcriptome,+1KP WYAJ KT071966Podocarpus+rubens Transcriptome,+1KP XLGK KJ195161Thuja+plicata Transcriptome,+1KP VFYZ KT071967Taiwania+cryptomerioides Transcriptome,+1KP QSNJ KJ195162Pinus+parviflora Transcriptome,+1KP IIOL KJ195163Welwitschia+mirabilis Transcriptome,+1KP TOXE KJ195164Gnetum+montanum Transcriptome,+1KP GTHK KJ195165Ginkgo+biloba Transcriptome,+1KP SGTW KT071968Encephalartos+barteri Transcriptome,+1KP GNQG KJ195166
Angiosperm+PHYCArabidopsis+thaliana Genome,+Phytozome @ @Fragaria+vesca Genome,+Phytozome @ @Cucumis+sativus Genome,+Phytozome @ @Vitis+vinifera Genome,+Phytozome @ @Solanum+lycopersicum Genome,+Phytozome @ @Buxus+sempervirens Transcriptome,+1KP IWMW KT071969Aquilegia+coerulea Genome,+Phytozome @ @Oryza+sativa Genome,+Phytozome @ @Platanthera+clavellata Transcriptome,+1KP MTHW KT071970Pistia+stratioides Transcriptome,+1KP MFIN KT071971Laurelia+sempervirens Transcriptome,+1KP WAIL KT071972Peperomia+fraseri Transcriptome,+1KP XSZI KT071973Illicium+floridanum Transcriptome,+1KP VZCI KT071974Amborella+trichocarpa Genome,+Amborella+Genome+Project @ @
Gymnosperm+PHYOPodocarpus+rubens Transcriptome,+1KP XLGK KJ195167Thuja+plicata Transcriptome,+1KP VFYZ KT071975Taiwania+cryptomerioides Transcriptome,+1KP QSNJ KJ195168Pinus+parviflora Transcriptome,+1KP IIOL KJ195169Ginkgo+biloba Transcriptome,+1KP SGTW KT071976Encephalartos+barteri Transcriptome,+1KP GNQG KJ195170
Supplementary+Table+2.+GenBank+accessions+of+the+phytochromes+used+in+phylogenetic+analyses.+"@":+not+applicable.
Phytochrome
Angiosperm+PHYBArabidopsis+thaliana+D Genome,+Phytozome @ @Arabidopsis+thaliana+B Genome,+Phytozome @ @Fragaria+vesca Genome,+Phytozome @ @Phaseolus+vulgaris Genome,+Phytozome @ @Cucumis+sativus Genome,+Phytozome @ @Vitis+vinifera Genome,+Phytozome @ @Solanum+lycopersicum+1 Genome,+Phytozome @ @Solanum+lycopersicum+2 Genome,+Phytozome @ @Buxus+sempervirens Transcriptome,+1KP IWMW KT071977Aquilegia+coerulea Genome,+Phytozome @ @Oryza+sativa Genome,+Phytozome @ @Platanthera+clavellata Transcriptome,+1KP MTHW KT071978Pistia+stratioides Transcriptome,+1KP MFIN KT071979Laurelia+sempervirens Transcriptome,+1KP WAIL KT071980Peperomia+fraseri Transcriptome,+1KP XSZI KT071981Illicium+floridanum Transcriptome,+1KP VZCI KT071982Amborella+trichocarpa Genome,+Amborella+Genome+Project @ @
Angiosperm+PHYEArabidopsis+thaliana Genome,+Phytozome @ @Fragaria+vesca+1 Genome,+Phytozome @ @Fragaria+vesca+2 Genome,+Phytozome @ @Phaseolus+vulgaris Genome,+Phytozome @ @Cucumis+sativus Genome,+Phytozome @ @Solanum+lycopersicum Genome,+Phytozome @ @Capnoides+sempervirens+1 Transcriptome,+1KP AUGV KT071983Aquilegia+coerulea+1 Genome,+Phytozome @ @Capnoides+sempervirens+2 Transcriptome,+1KP AUGV KT071984Aquilegia+coerulea+2 Genome,+Phytozome @ @Laurelia+sempervirens Transcriptome,+1KP WAIL KT071985Illicium+floridanum Transcriptome,+1KP VZCI KT071986
Gymnosperm+PHYPThuja+plicata Transcriptome,+1KP VFYZ KT071987Taiwania+cryptomerioides Transcriptome,+1KP QSNJ KJ195155Cephalotaxus+harringtonia Transcriptome,+1KP WYAJ KT071988Podocarpus+rubens Transcriptome,+1KP XLGK KJ195156Pinus+parviflora Transcriptome,+1KP IIOL KJ195157Gnetum+montanum Transcriptome,+1KP GTHK KJ195158Welwitschia+mirabilis Transcriptome,+1KP TOXE KJ195159Ginkgo+biloba Transcriptome,+1KP SGTW KT071989Encephalartos+barteri Transcriptome,+1KP GNQG KJ195160
Fern+PHY1Equisetum+diffusum Transcriptome,+1KP CAPN KT071819Marattia+howeana Cloning,+this+study @ KP872700Osmunda+sp Transcriptome,+1KP UOMY KJ195150Dipteris+conjugata Transcriptome,+1KP MEKP KT071820Pilularia+globulifera Transcriptome,+1KP KIIX KJ195151Plagiogyria+japonica Transcriptome,+1KP UWOD KJ195152Adiantum+capillus@veneris GenBank @ AB016151Pteridium+aquilinum Transcriptome,+Der+et+al.5 @ SRX423244Cystopteris+protrusa Transcriptome,+1KP YOWV KT071821Blechnum+spicant Transcriptome,+1KP VITX KJ195153Polypodium+glycyrrhiza Transcriptome,+1KP CJNT KJ195154
Asplenium+platyneuron Transcriptome,+1KP KJZG KT071822Alsophila+spinulosa Transcriptome,+1KP GANB KT071823Woodsia+scopulina Transcriptome,+1KP YJJY KT071824Deparia+lobato@crenata Transcriptome,+1KP FCHS KT071825Vittaria+appalachiana Transcriptome,+1KP NDUV KT071826Danaea+nodosa Transcriptome,+1KP DFHO KT071827Azolla+filiculoides Transcriptome,+Brouwer+et+al.4+ @ @Thyrsopteris+elegans Transcriptome,+1KP EWXK KT071828Ceratopteris+thalictroides Transcriptome,+1KP PIVW KT071829Lonchitis+hirsuta Transcriptome,+1KP VVRN KT071830
Fern+PHY2/4Equisetum+diffusum+A Transcriptome,+1KP CAPN KJ195136Equisetum+diffusum+B Transcriptome,+1KP CAPN KT071831Botrypus+virginianus+A Transcriptome,+1KP BEGM KJ195137Sceptridium+dissectum+A Transcriptome,+1KP EEAQ KT071832Botrypus+virginianus+B Transcriptome,+1KP BEGM KT071833Sceptridium+dissectum+B Transcriptome,+1KP EEAQ KT071834Psilotum+nudum GenBank QVMR X74930Marattia+attenuata Transcriptome,+1KP UGNK KT071835Osmunda+sp+A Transcriptome,+1KP UOMY KJ195138Dipteris+conjugata Transcriptome,+1KP MEKP KJ195139Danaea+nodosa Transcriptome,+1KP DFHO KT071836Osmundastrum+cinnamomeum+A Transcriptome,+1KP RFMZ KT071837Osmunda+javanica+A Transcriptome,+1KP VIBO KT071838Osmundastrum+cinnamomeum+B Transcriptome,+1KP RFMZ KT071839Osmunda+javanica+B Transcriptome,+1KP VIBO KT071840
Fern+PHY2Anemia+tomentosa Transcriptome,+1KP CQPW KJ195140Pilularia+globulifera Transcriptome,+1KP KIIX KJ195142Plagiogyria+japonica Transcriptome,+1KP UWOD KJ195141Adiantum+capillus@veneris GenBank @ AB016232Pteridium+aquilinum Transcriptome,+Der+et+al. @ SRX423244Polystichum+acrostichoides Transcriptome,+1KP FQGQ KT071841Cystopteris+fragilis Transcriptome,+1KP LHLE KT071842Blechnum+spicant Transcriptome,+1KP VITX KJ195143Leucostegia+immersa Transcriptome,+1KP WGTU KT071843Polypodium+hesperium Transcriptome,+1KP GYFU KJ195144Gymnocarpium+dryopteris Transcriptome,+1KP HEGQ KT071844Homalosorus+pycnocarpos Transcriptome,+1KP OCZL KT071845Athyrium+filix@femina Transcriptome,+1KP AFPO KT071846Diplazium+wichurae Transcriptome,+1KP UFJN KT071847Deparia+lobato@crenata Transcriptome,+1KP FCHS KT071848Asplenium+platyneuron Transcriptome,+1KP KJZG KT071849Woodsia+scopulina Transcriptome,+1KP YJJY KT071850Woodsia+ilvensis Transcriptome,+1KP YQEC KT071851Vittaria+appalachiana Transcriptome,+1KP NDUV KT071852Pityrogramma+trifoliata Transcriptome,+1KP UJTT KT071853Pteris+ensiformis Transcriptome,+1KP FLTD KT071854Myriopteris+rufa Transcriptome,+1KP GSXD KT071855Gaga+arizonica Transcriptome,+1KP DCDT KT071856Argyrochosma+nivea Transcriptome,+1KP XDDT KT071857Notholaena+montieliae Transcriptome,+1KP YCKE KT071858Cryptogramma+acrostichoides Transcriptome,+1KP WQML KT071859
Thyrsopteris+elegans Transcriptome,+1KP EWXK KT071860Culcita+macrocarpa Transcriptome,+1KP PNZO KT071861Lindsaea+microphylla Transcriptome,+1KP YIXP KT071862Lonchitis+hirsuta Transcriptome,+1KP VVRN KT071863Ceratopteris+thalictroides Transcriptome,+1KP PIVW KT071864
Fern+PHY4APlagiogyria+japonica Transcriptome,+1KP UWOD KJ195145Pilularia+globulifera Transcriptome,+1KP KIIX KJ195146Adiantum+tenerum Transcriptome,+1KP BMJR KJ195147Polystichum+acrostichoides Transcriptome,+1KP FQGQ KT071865Cystopteris+fragilis Transcriptome,+1KP LHLE KT071866Blechnum+spicant Transcriptome,+1KP VITX KJ195148Leucostegia+immersa Transcriptome,+1KP WGTU KT071867Polypodium+hesperium Transcriptome,+1KP GYFU KJ195149Adiantum+capillus@veneris GenBank @ AB003364Asplenium+platyneuron Transcriptome,+1KP KJZG KT071868Gaga+arizonica Transcriptome,+1KP DCDT KT071869Myriopteris+rufa Transcriptome,+1KP GSXD KT071870Argyrochosma+nivea Transcriptome,+1KP XDDT KT071871Vittaria+appalachiana Transcriptome,+1KP NDUV KT071872Pteris+ensiformis Transcriptome,+1KP FLTD KT071873Cryptogramma+acrostichoides Transcriptome,+1KP WQML KT071874Alsophila+spinulosa Transcriptome,+1KP GANB KT071875Azolla+caroliniana Transcriptome,+1KP CVEG KT071876Lonchitis+hirsuta Transcriptome,+1KP VVRN KT071877Ceratopteris+thalictroides Transcriptome,+1KP PIVW KT071878Anemia+tomentosa+A Transcriptome,+1KP CQPW KT071879Anemia+tomentosa+B Transcriptome,+1KP CQPW KT071880Lindsaea+microphylla Transcriptome,+1KP YIXP KT071881Lygodium+japonicum Transcriptome,+1KP PBUU KT071882Thyrsopteris+elegans Transcriptome,+1KP EWXK KT071883
Fern+PHY4BPteridium+aquilinum Transcriptome,+Der+et+al. @ SRX423244Cystopteris+fragilis Transcriptome,+1KP LHLE KT071884Blechnum+spicant Transcriptome,+1KP VITX KT071885Polystichum+acrostichoides Transcriptome,+1KP FQGQ KT071886Gymnocarpium+dryopteris Transcriptome,+1KP HEGQ KT071887Woodsia+ilvensis Transcriptome,+1KP YQEC KT071888Athyrium+filix@femina Transcriptome,+1KP AFPO KT071889Diplazium+wichurae Transcriptome,+1KP UFJN KT071890
Isoetopsida+PHYSelaginella+cf+pallescens Transcriptome,+1KP ABIJ KT071891Selaginella+moellendorffii Genome,+Phytozome @ XM_002991595Selaginella+willdenowii Transcriptome,+1KP KJYC KT071892Selaginella+kraussiana Transcriptome,+1KP ZFGK KT071893Selaginella+wallacei Transcriptome,+1KP JKAA KJ195172Selaginella+apoda Transcriptome,+1KP LGDQ KT071894Isoetes+tegetiformans Transcriptome,+1KP PKOX KJ195171
Lycopodiales+PHY1Dendrolycopodium+obscurum Transcriptome,+1KP XNXF KJ195173Huperzia+selago Transcriptome,+1KP GTUO KJ195174Pseudolycopodiella+caroliniana Transcriptome,+1KP UPMJ KT071895
Lycopodiales+PHY2
Dendrolycopodium+obscurum Transcriptome,+1KP XNXF KJ195175Huperzia+lucidula Transcriptome,+1KP GKAG KJ195176Pseudolycopodiella+caroliniana Transcriptome,+1KP UPMJ KT071896
Moss+PHY1_3Andreaea+rupestris Transcriptome,+1KP WOGB KT071897Rhynchostegium+serrulatum Transcriptome,+1KP JADL KT071898Aulacomnium+heterostichum Transcriptome,+1KP WNGH KT071899Hedwigia+ciliata Transcriptome,+1KP YWNF KJ195194Philonotis+fontana Transcriptome,+1KP ORKS KT071900Ceratodon+purpureus+A GenBank @ U72993Ceratodon+purpureus+B GenBank @ U87632Leucobryum+albidum Transcriptome,+1KP VMXJ KT071901Physcomitrella+patens+1 Genome,+Phytozome @ XM_001765983Physcomitrella+patens+3 Genome,+Phytozome @ XM_001778103Racomitrium+varium Transcriptome,+1KP RDOO KT071902Leucodon+julaceus Transcriptome,+1KP IGUH KT071903Leucodon+brachypus Transcriptome,+1KP ZACW KT071904Pseudotaxiphyllum+elegans Transcriptome,+1KP QKQO KT071905Neckera+douglasii Transcriptome,+1KP TMAJ KT071906Stereodon+subimponens Transcriptome,+1KP LNSF KT071907Loeskeobryum+brevirostre Transcriptome,+1KP WSPM KT071908Cladopodium+rostratum Transcriptome,+1KP VBMM KJ195193Bryum+argenteum Transcriptome,+1KP JMXW KJ195195
Moss+PHY2_4/5Andreaea+rupestris Transcriptome,+1KP WOGB KT071909Sphagnum+palustre Transcriptome,+1KP RCBT KT071910Takakia+lepidozioides Transcriptome,+1KP SKQD KT071911
Moss+PHY2_4Atrichum+angustatum Transcriptome,+1KP ZTHV KT071912Physcomitrella+patens+4 Genome,+Phytozome @ XM_001773498Physcomitrella+patens+2 Genome,+Phytozome @ XM_001782287Rhynchostegium+serrulatum Transcriptome,+1KP JADL KT071913Aulacomnium+heterostichum Transcriptome,+1KP WNGH KT071914Hedwigia+ciliata Transcriptome,+1KP YWNF KJ195190Philonotis+fontana Transcriptome,+1KP ORKS KT071915Ceratodon+purpureus Transcriptome,+1KP FFPD KT071916Leucobryum+albidum Transcriptome,+1KP VMXJ KT071917Racomitrium+varium Transcriptome,+1KP RDOO KT071918Scouleria+aquatica Transcriptome,+1KP BPSG KT071919Bryum+argenteum Transcriptome,+1KP JMXW KJ195191Loeskeobryum+brevirostre Transcriptome,+1KP WSPM KT071920Neckera+douglasii Transcriptome,+1KP TMAJ KT071921Cladopodium+rostratum Transcriptome,+1KP VBMM KJ195189Leucodon+brachypus Transcriptome,+1KP ZACW KT071922Leucodon+julaceus Transcriptome,+1KP IGUH KT071923Pseudotaxiphyllum+elegans Transcriptome,+1KP QKQO KT071924Anomodon+attenuatus Transcriptome,+1KP QMWB KT071925Stereodon+subimponens Transcriptome,+1KP LNSF KT071926
Moss+PHY5Atrichum+angustatum Transcriptome,+1KP ZTHV KT071927Physcomitrella+patens+A Genome,+Phytozome @ XM_001761093Physcomitrella+patens+B Genome,+Phytozome @ XM_001767172Physcomitrella+patens+C Genome,+Phytozome @ XM_001754314
Rhynchostegium+serrulatum+D Transcriptome,+1KP JADL KT071928Aulacomnium+heterostichum+D Transcriptome,+1KP WNGH KT071929Hedwigia+ciliata+D Transcriptome,+1KP YWNF KT071930Philonotis+fontana+D Transcriptome,+1KP ORKS KT071931Leucobryum+albidum+D Transcriptome,+1KP VMXJ KT071932Ceratodon+purpureus+D GenBank @ AY123149Scouleria+aquatica+D Transcriptome,+1KP BPSG KT071933Racomitrium+varium+D Transcriptome,+1KP RDOO KT071934Syntrichia+princeps+D Transcriptome,+1KP GRKU KT071935Bryum+argenteum+D Transcriptome,+1KP JMXW KJ195187Leucodon+brachypus+D Transcriptome,+1KP ZACW KT071936Anomodon+attenuatus+D Transcriptome,+1KP QMWB KT071937Cladopodium+rostratum+D Transcriptome,+1KP VBMM KJ195185Loeskeobryum+brevirostre+D Transcriptome,+1KP WSPM KT071938Pseudotaxiphyllum+elegans+D Transcriptome,+1KP QKQO KT071939Racomitrium+varium+E Transcriptome,+1KP RDOO KT071940Scouleria+aquatica+E Transcriptome,+1KP BPSG KT071941Syntrichia+princeps+E Transcriptome,+1KP GRKU KT071942Hedwigia+ciliata+E Transcriptome,+1KP YWNF KJ195186Philonotis+fontana+E Transcriptome,+1KP ORKS KT071943Leucobryum+albidum+E Transcriptome,+1KP VMXJ KT071944Ceratodon+purpureus+E GenBank @ EU122393Rhynchostegium+serrulatum+E Transcriptome,+1KP JADL KT071945Aulacomnium+heterostichum+E+1 Transcriptome,+1KP WNGH KT071946Aulacomnium+heterostichum+E+2 Transcriptome,+1KP WNGH KT071947Anomodon+attenuatus+E Transcriptome,+1KP QMWB KT071948Neckera+douglasii+E Transcriptome,+1KP TMAJ KT071949Pseudotaxiphyllum+elegans+E Transcriptome,+1KP QKQO KT071950Cladopodium+rostratum+E Transcriptome,+1KP VBMM KJ195184Loeskeobryum+brevirostre+E Transcriptome,+1KP WSPM KT071951Leucodon+julaceus+E Transcriptome,+1KP IGUH KT071952Leucodon+brachypus+E Transcriptome,+1KP ZACW KT071953
Liverwort+PHYScapania+nemorosa Transcriptome,+1KP IRBN KJ195177Porella+pinnata Transcriptome,+1KP UUHD KJ195178Schistochila+sp Transcriptome,+1KP LGOW KJ195179Metzgeria+crassipilis Transcriptome,+1KP NRWZ KJ195180Pellia+neesiana Transcriptome,+1KP JHFI KJ195181Odontoschisma+prostratum Transcriptome,+1KP YBQN KT071954Marchantia+paleacea GenBank @ AB022917Conocephalum+conicum Transcriptome,+1KP ILBQ KJ195182Lunularia+cruciata Transcriptome,+1KP TXVB KT071955Sphaerocarpos+texanus Transcriptome,+1KP HERT KJ195183Ricciocarpos+natans Transcriptome,+1KP WJLO KT071956Bazzania+trilobata Transcriptome,+1KP WZYK KT071957
Hornwort+PHYNothoceros+aenigmaticus Cloning,+Li+et+al.6 DXOU KJ128384Megaceros+flagellaris Transcriptome,+1KP UCRN KJ195197Paraphymatoceros+hallii Transcriptome,+1KP FAJB KJ195198Phaeoceros+carolinianus Transcriptome,+1KP WCZB KJ195199Anthoceros+punctatus Genome,+Li+et+al.6 @ KJ195038Phaeomegaceros+coriaceus Transcriptome,+1KP AKXB KT071958Leiosporoceros+dussii Transcriptome,+1KP ANON KT071959
Hornwort+NEONothoceros+aenigmaticus Transcriptome,+1KP DXOU KJ128382Megaceros+flagellaris Transcriptome,+1KP UCRN KJ195132Paraphymatoceros+hallii Transcriptome,+1KP FAJB KJ194999Phaeoceros+carolinianus Transcriptome,+1KP WCZB KJ194998Anthoceros+punctatus Cloning,+Li+et+al. @ KJ194997
Fern+NEOAdiantum+capillus@veneris GenBank @ AB012082Dipteris+conjugata Cloning,+Li+et+al. @ KJ195011Blechnum+spicant Cloning,+Li+et+al. @ KJ195007Hemidictyum+marginatum Cloning,+Li+et+al. @ KJ195037
Zygnematales+NEOMougeotia+scalaris+1 GenBank @ AB206961Mougeotia+scalaris+2 GenBank @ AB206962Cylindrocystis+brebissonii+1 Transcriptome,+1KP YOXI KJ195042Cylindrocystis+sp+1 Transcriptome,+1KP VAZE KJ195043Cylindrocystis+brebissonii+2 Transcriptome,+1KP YOXI KJ195044Cylindrocystis+sp+2 Transcriptome,+1KP VAZE KJ195041Zygnemopsis+sp Transcriptome,+1KP MFZO KJ195039
Desmidiales+PHY2CDesmidium+aptogonum Transcriptome,+1KP DFDS KT071990Onychonema+laeve Transcriptome,+1KP GGWH KT071991Cosmarium+granatum+1 Transcriptome,+1KP MNNM KT071992Staurodesmus+convergens+1 Transcriptome,+1KP WCQU KT071993Cosmarium+subtumidum Transcriptome,+1KP WDGV KT071994Staurodesmus+convergens+2 Transcriptome,+1KP WCQU KT071995Cosmarium+granatum+2 Transcriptome,+1KP MNNM KT071996Phymatodocis+nordstedtiana Transcriptome,+1KP RPQV KT071997Penium+exiguum Transcriptome,+1KP YSQT KT071998Gonatozygon+kinahanii+1 Transcriptome,+1KP KEYW KT071999Gonatozygon+kinahanii+2 Transcriptome,+1KP KEYW KT072000
Desmidiales+PHY2BDesmidium+aptogonum Transcriptome,+1KP DFDS KT072001Onychonema+laeve Transcriptome,+1KP GGWH KT072002Cosmarium+subtumidum Transcriptome,+1KP WDGV KT072003Staurodesmus+convergens Transcriptome,+1KP WCQU KT072004Phymatodocis+nordstedtiana Transcriptome,+1KP RPQV KT072005Penium+exiguum Transcriptome,+1KP YSQT KT072006Gonatozygon+kinahanii Transcriptome,+1KP KEYW KT072007
Desmidiales+PHY2ADesmidium+aptogonum Transcriptome,+1KP DFDS KT072008Cosmarium+subtumidum Transcriptome,+1KP WDGV KT072009Cosmarium+granatum Transcriptome,+1KP MNNM KT072010Onychonema+laeve Transcriptome,+1KP GGWH KT072011Staurodesmus+convergens Transcriptome,+1KP WCQU KT072012Phymatodocis+nordstedtiana Transcriptome,+1KP RPQV KT072013Penium+exiguum Transcriptome,+1KP YSQT KT072014Gonatozygon+kinahanii Transcriptome,+1KP KEYW KT072015Roya+obtusa Transcriptome,+1KP XRTZ KJ195200Planotaenium+ohtanii Transcriptome,+1KP SNOX KJ195201
Zygnematales+PHY2Mougeotia+scalaris Genbank @ AB206965Mesotaenium+kramstae Transcriptome,+1KP NBYP KT072016
Mesotaenium+caldariorum Genbank @ U31283Zygnemopsis+sp Transcriptome,+1KP MFZO KJ195202Cylindrocystis+sp Transcriptome,+1KP VAZE KJ195203Cylindrocystis+brebissonii Transcriptome,+1KP YOXI KJ195204Mesotaenium+braunii Transcriptome,+1KP WSJO KJ195205Netrium+digitus Transcriptome,+1KP FFGR KT072017
Coleochaetales+PHY2Coleochaete+irregularis Transcriptome,+1KP QPDY KJ195206Chaetosphaeridium+globosum Transcriptome,+1KP DRGY KJ195207
Klebsormidiales+PHY2Interfilum+paradoxum Transcriptome,+1KP FPCO KJ195208Klebsormidium+subtile Transcriptome,+1KP FQLP KJ195209Entransia+fimbriata Transcriptome,+1KP BFIK KJ195210
Desmidiales+PHY1Cosmarium+granatum Transcriptome,+1KP MNNM KT072018Cosmarium+subtumidum Transcriptome,+1KP WDGV KT072019Staurodesmus+convergens Transcriptome,+1KP WCQU KT072020Onychonema+laeve Transcriptome,+1KP GGWH KT072021Phymatodocis+nordstedtiana Transcriptome,+1KP RPQV KT072022Penium+exiguum Transcriptome,+1KP YSQT KT072023Gonatozygon+kinahanii Transcriptome,+1KP KEYW KT072024Roya+obtusa Transcriptome,+1KP XRTZ KT072025Planotaenium+ohtanii Transcriptome,+1KP SNOX KT072026
Klebsormidiales+PHY1Entransia+fimbriata Transcriptome,+1KP BFIK KT072027
Mesostigmatales+PHY1/2Mesostigma+viride Transcriptome,+1KP KYIO KT072028Chlorokybus+atmophyticus+1 Transcriptome,+1KP AZZW KT072029Chlorokybus+atmophyticus+2 Transcriptome,+1KP AZZW KT072030Spirotaenia+minuta Transcriptome,+1KP NNHQ KT072031
Zygnematales+PHYX2Zygnemopsis+sp+ Transcriptome,+1KP MFZO KT072032Cylindrocystis+cushleckae Transcriptome,+1KP JOJQ KT072033Mesotaenium+kramstae Transcriptome,+1KP NBYP KT072034Netrium+digitus Transcriptome,+1KP FFGR KT072035
Coleochaetales+PHYX2Coleochaete+irregularis Transcriptome,+1KP QPDY KT072036Chaetosphaeridium+globosum Transcriptome,+1KP DRGY KT072037
Zygnematales+PHYX1Zygnemopsis+sp Transcriptome,+1KP MFZO KT072038Mesotaenium+kramstae Transcriptome,+1KP NBYP KT072039Cylindrocystis+cushleckae Transcriptome,+1KP JOJQ KT072040Cylindrocystis+brebissonii Transcriptome,+1KP YOXI KT072041Cylindrocystis+sp Transcriptome,+1KP VAZE KT072042Netrium+digitus Transcriptome,+1KP FFGR KT072043
Coleochaetales+PHYX1Coleochaete+irregularis Transcriptome,+1KP QPDY KT072044
Prasinophyte+PHYMonomastix+opisthostigma Transcriptome,+1KP BTFM @Pyramimonas+parkeae Transcriptome,+1KP TNAW @Tetraselmis+cordiformis Transcriptome,+1KP DUMA @Dolichomastix+tenuilepsis GenBank @ KF876183Tetraselmis+astigmatica GenBank @ KF876182
Prasinoderma+coloniale GenBank @ KF876180Nephroselmis+pyriformis GenBank @ KF876181Micromonas+pusilla GenBank @ KF754357
Cryptophyte+PHYHemiselmis+virescens Transcriptome,+1KP MJMQ KT013280Cryptomonas+curvata Transcriptome,+1KP BAKF KT013281Rhodomonas+sp Transcriptome,+1KP IAYV KT013282Guillardia+theta+1 Genome,+Curtis+et+al.13 @ @Guillardia+theta+2 Genome,+Curtis+et+al. @ @Chroomonas+sp Transcriptome,+1KP ROZZ KT013283Guillardia+theta+PEK1 Genome,+Curtis+et+al. @ @Guillardia+theta+PEK2 Genome,+Curtis+et+al. @ @Guillardia+theta+PEK3 Genome,+Curtis+et+al. @ @
Glaucophyte+PHYCyanophora+paradoxa+1 Genome,+Price+et+al.14 @ KF597305Cyanophora+paradoxa+2 Genome,+Price+et+al. @ KF615870Cyanophora+paradoxa+4 Genome,+Price+et+al. @ @Gloeochaete+wittrockiana+GPS2 Transcriptome,+Duanmu+et+al.15 @ @Gloeochaete+wittrockiana+GPS4 Transcriptome,+Duanmu+et+al. @ @Gloeochaete+wittrockiana+GPS3 Transcriptome,+Duanmu+et+al. @ @Gloeochaete+wittrockiana+GPS1 Transcriptome,+Rockwell+et+al.16 @ KF894953Cyanoptyche+gloeocystis+1 Transcriptome,+1KP JKHA KT013284Cyanoptyche+gloeocystis+2 Transcriptome,+1KP JKHA KT013285Cyanoptyche+gloeocystis+3 Transcriptome,+1KP JKHA KT013286Glaucocystis+nostochinearum+1 Transcriptome,+1KP POOW KT013287Glaucocystis+nostochinearum+2 Transcriptome,+1KP POOW KT013288Glaucocystis+nostochinearum+3 Transcriptome,+1KP POOW KT013289Glaucocystis+nostochinearum+4 Transcriptome,+1KP POOW KT013290
Diatom+PHYThalassiosira+pseudonana GenBank @ XM_002290775Phaeodactylum+tricornutum GenBank @ XM_002179026
Brown+algae+PHYPetalonia+fascia Transcriptome,+1KP VRGZ KT003814Scytosiphon+lomentaria Transcriptome,+1KP JCXF KT003815Ishige+okamurai Transcriptome,+1KP APTP KT003816Ectocarpus+siliculosus GenBank @ FN649030Feldmannia+species+virus+isolate+FsV GenBank @ EU916176Ectocarpus+siliculosus+virus+isolate+EsV GenBank @ AF204951
Fungi+PHYAspergillus+fumigatus GenBank @ DS499603Ustilago+maydis GenBank @ AACP01000210Cochliobolus+heterostrophus GenBank @ AY456024Neurospora+crassa+1 GenBank @ BK004087Neurospora+crassa+2 GenBank @ DQ128077Penicillium+marneffei GenBank @ XM_002144684
Cyanobacteria+PHYMicrocystis+aeruginosa GenBank @ AP009552Nodularia+spumigena GenBank @ AAVW01000039Synechocystis+sp GenBank @ BA000022Anabaena+variabilis GenBank @ NC_007413Cyanothece+sp GenBank @ ABVE01000001Nostoc+sp GenBank @ BA000019Tolypothrix+sp+1 GenBank @ AF309559
Tolypothrix+sp+2 GenBank @ AF309560Cyanobacteria+PASQless+PHY
Microcoleus+chthonoplastes GenBank @ DS989848Lyngbya+sp GenBank @ AAVU01000002Nostoc+punctiforme GenBank @ CP001037Anabaena+variabilis GenBank @ CP000117Synechococcus+sp GenBank @ ABD00881
Bacteria+PHYAgrobacterium+tumefaciens GenBank @ C58AE007869Pseudomonas+aeruginosa GenBank @ CH482383Pseudomonas+syringae GenBank @ AE016853Ralstonia+pickettii GenBank @ CP001068Stenotrophomonas+maltophilia GenBank @ AM743169Rhodopseudomonas+palustris GenBank @ BX572602Oceanicola+granulosus GenBank @ AAOT01000028Methylocella+silvestris GenBank @ CP001280Sclerotinia+sclerotiorum GenBank @ CH476645Magnetospirillum+magnetotacticum GenBank @ AAAP01003476
Supplementary,references,,1Amborella*Genome*Project.*The*Amborella*genome*and*the*evolution*of*flowering*plants.*Science*342,*1241089*(2013).*2Goodstein,*D.*M.*et.al.*Phytozome:*a*comparative*platform*for*green*plant*genomics.*Nucleic.Acids.Res.*40,*D1178–86*(2012).*3Matasci,*N.*et.al.*Data*access*for*the*1,000*Plants*(1KP)*project.*GigaScience*3,*17*(2014).*4Brouwer,*P.*et.al.*Azolla*domestication*towards*a*biobased*economy?*New.Phytol*202,*1069–1082*(2014).*5Der,*J.*P.,*Barker,*M.*S.,*Wickett,*N.*J.,*Depamphilis,*C.*W.*&*Wolf*P.*G.*De*novo*characterization*of*the*gametophyte*transcriptome*in*bracken*fern,*Pteridium.aquilinum.*BMC.Genomics*12,*99*(2011).*6Li,*F.[W.*et.al.*Horizontal*transfer*of*an*adaptive*chimeric*photoreceptor*from*bryophytes*to*ferns.*Proc..Natl..Acad..Sci..USA.111,*6672–6677*(2014).*7Blanc,*G.*et.al.*The*Chlorella.variabilis*NC64A*genome*reveals*adaptation*to*photosymbiosis,*coevolution*with*viruses,*and*cryptic*sex.*Plant.Cell*22,*2943–2955*(2010).*8Collen,*J.*et.al.*Genome*structure*and*metabolic*features*in*the*red*seaweed*Chondrus.crispus*shed*light*on*evolution*of*the*Archaeplastida.*Proc..Natl..Acad..Sci..USA.110,*5247–5252*(2013).*9Matsuzaki,*M.*et.al.*Genome*sequence*of*the*ultrasmall*unicellular*red*alga*Cyanidioschyzon.merolae*10D.*Nature*428,*653–657*(2004).*10Barbier,*G.*et.al.*Comparative*genomics*of*two*closely*related*unicellular*thermo[acidophilic*red*algae,*Galdieria.sulphuraria*and*Cyanidioschyzon.merolae,*reveals*the*molecular*basis*of*the*metabolic*flexibility*of*Galdieria*sulphuraria*and*significant*differences*in*carbohydrate*metabolism*of*both*algae.*Plant.Physiology*137,*460–474*(2005).*11Nakamura,*Y.*et.al.*The*first*symbiont[free*genome*sequence*of*marine*red*alga,*Susabi[nori*(Pyropia.yezoensis).*PLoS.ONE*8,*e57122*(2013).*12Bhattacharya,*D..et.al.*Genome*of*the*red*alga*Porphyridium.purpureum.*Nat.Comms*4,*1941*(2013).*13Curtis,*B.*A.*et.al.*Algal*genomes*reveal*evolutionary*mosaicism*and*the*fate*of*nucleomorphs.*Nature.492,*59–65*(2012).**14Price,*D.*C.*et.al.*Cyanophora.paradoxa.genome*elucidates*origin*of*photosynthesis*in*algae*and*plants.*Science*335,*843–847*(2012).*15Duanmu,*D.*et.al.*Marine*algae*and*land*plants*share*conserved*phytochrome*signaling*systems.*Proc..Natl..Acad..Sci..USA*111,*15827–15832*(2014).*16Rockwell,*N.*C.*et.al.*Eukaryotic*algal*phytochromes*span*the*visible*spectrum.*Proc..Natl..Acad..Sci..USA*111,*3871–3876*(2014).*
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