the organismal lineages screened for phytochrome homologs. … · stramenopiles chlorophyceae seed...

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


Taiwania cryptomerioides

Buxus sempervirens

Phaseolus vulgaris

Fragaria vesca

Buxus sempervirens

Encephalartos barteri


Laurelia sempervirens

Aquilegia coerulea

Solanum lycopersicum 1



Cucumis sativus 1

Peperomia fraseri

Solanum lycopersicum

Ginkgo biloba

Vitis vinifera

Arabidopsis thaliana D

Cephalotaxus harringtonia

Ginkgo biloba


Buxus sempervirens

Podocarpus rubens


Pinus parviflora

Thuja plicata

Vitis vinifera


Welwitschia mirabilis



Illicium floridanum

Oryza sativa

Ginkgo biloba

Phaseolus vulgaris 1


Aquilegia coerulea


Phaseolus vulgaris


Illicium floridanum

Oryza sativa

Phaseolus vulgaris 2



Fragaria vesca

Pistia stratioides

Cucumis sativus

Pistia stratioides

Peperomia fraseriPistia stratioides

Thuja plicata


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

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66

52

10098

100

10095

55

97

91

100

100

10099

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55

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89

80

98

8381

6460

100

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89

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98

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8191

5657

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68


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


Pseudolycopodiella caroliniana 1

Pteridium aquilinum

Vittaria appalachiana

Equisetum diffusum A

Plagiogyria japonica

Pseudolycopodiella caroliniana 2

Selaginella apoda


Myriopteris rufa

Polypodium hesperium

Cystopteris fragilis

Deparia lobato-crenata

Pilularia globulifera

Marattia attenuata

Equisetum diffusum B

Gaga arizonica


Diplazium wichurae

Gaga arizonica


Huperzia selago 1

Homalosorus pycnocarpos


Athyrium filix-femina

Pteris ensiformis

Equisetum diffusumMarattia howeana

Sceptridium dissectum B


Sceptridium dissectum A

Pityrogramma trifoliata

Dipteris conjugata

Selaginella wallacei

Huperzia lucidula 2

Adiantum capillus-veneris



Blechnum spicant

Cryptogramma acrostichoides

Adiantum raddianum


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


Polypodium hesperium


Selaginella kraussiana

Woodsia ilvensis

Anemia tomentosa

Deparia lobato-crenata

Gymnocarpium dryopteris

Leucostegia immersa

Notholaena montieliae

Botrypus virginianus B

Woodsia scopulina


Woodsia ilvensis

Dipteris conjugata

Blechnum spicant

Psilotum nudum

Blechnum spicant


Selaginella willdenowii

Cystopteris protrusa

Athyrium filix-femina

Osmunda sp

Leucostegia immersa

Isoetes tegetiformans Isoetales PHY

To Fig. 2a(Seed plants)




Fig. 2d neochrome



86

69

62

6670

58

7053

85

93

51

95

10010065

100

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5695

84

57

95

61

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82 100

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84

69

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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


Racomitrium varium E

Loeskeobryum brevirostre D

Physcomitrella patens 1

Physcomitrella patens A


Porella pinnata


Paraphymatoceros hallii


Marchantia paleacea

Loeskeobryum brevirostre

Bazzania trilobata


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


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. 2d neochrome



60

61

7457

96

54

55

63

62

92

75

618851

69

57

52

8177

61

98

93

98

81

94

100

100

9563

9661

91

99

52

77

74

68

99

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91

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91

93

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646398

72

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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


Phaeoceros carolinianus

Mougeotia scalaris 1Mougeotia scalaris 2

Cylindrocystis spCylindrocystis brebissonii

Nothoceros aenigmaticus

Blechnum spicant

Megaceros flagellaris


Fern neochrome

Hornwort neochrome

To Fig. 2c(bryophytes)

Zygnematales neochrome

Hornwort neochrome




Fig. 2d neochrome



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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


Interfilum paradoxum

Penium exiguum

Guillardia theta PHY2

Phymatodocis nordstedtiana

Planotaenium ohtanii

Hemiselmis virescens*

Onychonema laeve

Staurodesmus convergens

Glaucocystis nostochinearum 4


Onychonema laeve

Roya obtusa

Roya obtusa

Gonatozygon kinahanii

Mesostigma viride

Cylindrocystis cushleckae

Chaetosphaeridium globosum


Cryptomonas curvata*

Desmidium aptogonum

Micromonas pusilla

Penium exiguum

Desmidium aptogonum

Cosmarium granatum

Rhodomonas sp*


Cyanoptyche gloeocystis 1

Chlorokybus atmophyticus 2

Mesotaenium caldariorum

Entransia fimbriat


Guillardia theta PHY1


Cosmarium granatum

Zygnemopsis sp

Guillardia theta PEK1

Onychonema laeve

Cosmarium subtumidum

Chaetosphaeridium globosum

Netrium digitus

Penium exiguum

Cylindrocystis sp

Chroomonas sp PEK

Coleochaete irregularis


Mesotaenium kramstae



Coleochaete irregularis

Cyanophora paradoxa 4


Netrium digitusColeochaete irregularis

Klebsormidium subtile






Netrium digitus


Phymatodocis nordstedtiana Gonatozygon kinahanii 1

Chlorokybus atmophyticus 1

Mesotaenium braunii

Tetraselmis astigmatica

Nephroselmis pyriformis

Spirotaenia minuta



Cosmarium granatum

Zygnemopsis sp

Onychonema laeve



Cosmarium granatumCosmarium subtumidum

Desmidium aptogonum

Dolichomastix tenuilepsis

Mougeotia scalaris

Prasinoderma coloniale

Planotaenium ohtanii


Zygnemopsis sp

Monomastix opisthostigma

Penium exiguum

Gonatozygon kinahanii 2

Cylindrocystis sp

Entransia fimbriata

Pyramimonas parkeae



Cylindrocystis cushleckae


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. 2d neochrome



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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





Fig. 2d neochrome



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100

100

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6583

9272

9452

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95

5284

54

52

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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the organismal lineages screened for phytochrome homologs. … · stramenopiles chlorophyceae seed...

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