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Supplemental Table 1: NCBI-GenBank accession numbers (unless otherwise noted) used to construct the phylogenetic trees.

Abbreviation Gene name Species Accession number ReferenceCbCRY1 cryptochrome Capsella bursa-pastoris GQ251561 (Slotte et al. 2009)AtCRY1 cryptochrome Arabidopsis thaliana S66907 (Ahmad and Cashmore

1993)CnCRY1 cryptochrome Cardamine nipponica AB517032 (Ikeda and Setoguchi

2010)BnCRY1 cryptochrome Brassica napus AJ704628 (Chatterjee et al. 2006)BrCRY1 cryptochrome Brassica rapa AJ704628 (Chatterjee et al. 2006)

PtCRY1.1 cryptochrome Populus tremula JN235115 (Keller et al. 2011)PtCRY1.2 cryptochrome Populus tremula JN235116 (Keller et al. 2011)PsCRY1-1 cryptochrome Pisum sativum AY508971 (Platten et al. 2005a)SlCRY1 cryptochrome Solanum lycopersicum NM_001247738 (Ninu et al. 1999;

Perrotta et al. 2000)OmCRY1 cryptochrome Orobanche minor AY351861 (Okazawa et al. 2005)AcCRY1 cryptochrome Adiantum capillus-

venerisBAA32807 (Kanegae and Wada

1998)AcCRY2 cryptochrome Adiantum capillus-

venerisAB012627 (Kanegae and Wada

1998)AcCRY4 cryptochrome Adiantum capillus-

venerisBAA88423

OsCRY2 cryptochrome Oryza sativa AB103094 (Hirose et al. 2006)TaCRY2 cryptochrome Triticum aestivum EF601542 (Xu et al. 2009)SlCRY2 cryptochrome Solanum lycopersicum NM_001247316 (Perrotta et al. 2000)

PsCRY2A cryptochrome Pisum sativum AY508972 (Platten et al. 2005b)PsCRY2B cryptochrome Pisum sativum AY508974 (Platten et al. 2005b)AtCRY2 cryptochrome Arabidopsis thaliana AY576267 (Olsen et al. 2004)AtPHH1 cryptochrome Arabidopsis thaliana U62550 (Hoffman et al. 1996)AhCRY2 cryptochrome Arabidopsis halleri

subsp. gemmiferaJQ180280 (Huang et al. 2012)

AlCRY2 Arabidopsis lyrata subsp. Lyrata

JQ180279 (Huang et al. 2012)

PpCRYp plant-like cryptochrome

Physcomitrella patens AB060693 (Imaizumi et al. 2002)

CsCRYp plant-like cryptochrome

Coccomyxa subellipsoidea C-169

EIE22432

VcCRYp plant-like cryptochrome

Volvox carteri XM_002957226 (Prochnik et al. 2010)

CrCRYp plant-like cryptochrome

Chlamydomonas reinhardtii

L07561 (Small et al. 1995)

SbCRY1b cryptochrome Sylvia borin DQ838738 (Liedvogel et al. 2007)GgCRY1 cryptochrome Gallus gallus NM_204245 (Nagy and Csernus

2007; Tu et al. 2004)MmCRY1 cryptochrome Mus musculus NM_007771 (Jeyaraj et al. 2012;

Tong et al. 2012)OaCRY1 cryptochrome Ovis aries NM_001129735 (Dardente et al. 2008;

Fustin et al. 2009)XlCRY1 cryptochrome Xenopus laevis AY049033 (Zhu and Green 2001)XtCRY1 cryptochrome Xenopus tropicalis NM_001017311 (Klein et al. 2002)DrCRY1a cryptochrome Danio rerio BC124762 (Strausberg et al.

2002)PaCRY1a cryptochrome Phreatichthys andruzzii GQ404476 (Cavallari et al. 2011)DlCRY2 cryptochrome Dicentrarchus labrax JX046478 (del Pozo et al. 2012)RnCRY2 cryptochrome Rattus norvegicus EDL79575 (Florea et al. 2005)MmCRY2 cryptochrome Mus musculus NM_009963 (Thresher et al. 1998;

van der Horst et al. 1999)

HsCRY2.1 cryptochrome Homo sapiens NM_021117 (Kume et al. 1999; van der Horst et al. 1999)

DmPhr6-4 photolyase Drosophila melanogaster

BAA12067 (Todo et al. 1996)

Dwil/GK cryptochrome-like Drosophila willistoni XM_002064700 (Clark et al. 2007)CgCRY1 cryptochrome Crassostrea gigas EKC39908 (Zhang et al. 2012)Xl64phr 6-4 photolyase Xenopus laevis NM_001087952 (Klein et al. 2002)DrCRY5 cryptochrome Danio rerio NM_131788 (Weger et al. 2011)SsCRY1 cryptochrome Salmo salar BT058852 (Leong et al. 2010)Vv6-4Ph 6-4 DNA

photolyase-likeVitis vinifera XM_002285291

PtiCRYa cryptochrome-like Populus trichocarpa XM_002304127 (Tuskan et al. 2006)JcCRYa cryptochrome-like Jatropha curcas BAJ53248 (Sato et al. 2011)AtUVR3 6-4 DNA

photolyaseArabidopsis thaliana NM_112432 (Salanoubat et al.

2000)HvCRYa cryptochrome-like Hordeum vulgare subsp.

VulgareAK360897 (Matsumoto et al.

2011)OsCRYa cryptochrome-like Oryza sativa EEC72708 (Yu et al. 2005)ZmCRYa cryptochrome-like Zea mays AFW70620 (Schnable et al. 2009)SbCRYa cryptochrome-like Sorghum bicolor XM_002451702 (Paterson et al. 2009)PpUVR3 UVR3 AtUVR3-

like 6-4 DNAphotolyase

Physcomitrella patens XM_001754022 (Rensing et al. 2008)

CsUVR3 UVR3 AtUVR3-like 6-4 DNA

photolyase

Coccomyxa subellipsoidea C-169

EIE22254

CvCRYa cryptochrome-like Chlorella variabilis EFN51376 (Blanc et al. 2010)Ds6-4Ph 6-4 photolyase,

cryptochrome-likeDunaliella salina AY845324 (Yi et al. 2006)

CrCRYa animal-like cryptochrome


XM_001698002 (Beel et al. 2012; Merchant et al. 2007)

VcCRYa animal-like cryptochrome


XlCRYd DASH cryptochrome

Xenopus laevis NP_001084438 (Daiyasu et al. 2004)

DlCRYd DASH cryptochrome

Dicentrarchus labrax CBN81995 (Kuhl et al. 2011; Tine et al. 2011)

DrCRYd DASH cryptochrome

Danio rerio Q4KML2 (Daiyasu et al. 2004)

DpCRYd DASH cyptochrome

Daphnia pulex EFX86680 (Colbourne et al. 2011)

NvCRYd DASH-like cyptochrome

Nematostella vectensis XM_001623193 (Putnam et al. 2007)

CmPHR5 DASH cryptochrome

Cyanidioschyzon merolae

BAM78760 (Asimgil and Kavakli 2012; Matsuzaki et al.

2004)CmPHR2 DASH

cryptochromeCyanidioschyzon

merolaeBAM80259 (Asimgil and Kavakli

2012; Matsuzaki et al. 2004)

AtCRYd DASH cryptochrome

Arabidopsis thaliana Q84KJ5 (Brudler et al. 2003; Kleine et al. 2003; Tabata et al. 2000)

PtiCRY DASH-like cyptochrome

Populus trichocarpa XM_002330784 (Tuskan et al. 2006)

ZmCRYd DASH cyptochrome

Zea mays NP_001146707 (Soderlund et al. 2009)

SbCRYd DASH-like cyptochrome

Sorghum bicolor XM_002438751 (Paterson et al. 2009)

HvCRY DASH-like cyptochrome

Hordeum vulgare AK375185 (Matsumoto et al. 2011)

OsCRYd DASH cyptochrome

Oryza sativa EEE66166 (Yu et al. 2005)

VcCRYd1 DASH cryptochrome


CrCRYd1 DASH cryptochrome


XM_001701819 (Merchant et al. 2007)

CsCRYd cryptochrome Coccomyxa subellipsoidea C-169

EIE22181 (Blanc et al. 2012)

CvCRYd1 DASH cyptochrome

Chlorella variabilis EFN56221 (Blanc et al. 2010)

TpCPF3 DASH-like cyptochrome

Thalassiosira pseudonana

XM_002291289 (Armbrust et al. 2004; Bowler et al. 2008)

ToCRY DASH-like cyptochrome

Thalassiosira oceanica EJK57807

AaCRYd DASH-like cyptochrome

Aureococcus anophagefferens

EGB10801 (Gobler et al. 2011)

Msp.CRYd DASH-like cyptochrome

Micromonas sp. RCC299 XM_002508319 (Worden et al. 2009)

MpCRYd DASH-like cyptochrome

Micromonas pusilla CCMP1545

XP_003062980 (Worden et al. 2009)

OlCRYd DASH-like cyptochrome

Ostreococcus lucimarinus CCE9901

XM_001415659 (Palenik et al. 2007)

OtCRYd DASH-like cyptochrome

Ostreococcus tauri XM_003074649 (Derelle et al. 2006)

VfPhot1B phototropin Vicia faba AB095910 (Kinoshita et al. 2003)PsPhot phototropin Pisum sativum U83281 (Lin et al. 1991)

PvPhot1B phototropin Phaseolus vulgaris AB204873 (Inoue et al. 2005)PvPhot1A phototropin Phaseolus vulgaris AB204872 (Inoue et al. 2005)VvPhot1 Phototropin-like Vitis vinifera XM_002281716PtPhot Phototropin-like Populus trichocarpa XM_002298523 (Tuskan et al. 2006)

AtNph1 phototropin Arabidopsis thaliana AF030864 (Huala et al. 1997)ZmPhot1 phototropin Zea mays NM_001111416 (Gardiner et al. 2004)

OsNPH1-1 phototropin-like Oryza sativa NM_001071765 (Matsumoto et al. 2005)

AsNPH1-1 phototropin Avena sativa AF033096 (Huala et al. 1997)AsNPH1-2 phototropin Avena sativa AAC05084 (Huala et al. 1997)VcPhot1 phototropin Volvox carteri XM_002950419 (Prochnik et al. 2010)CrPhot1 phototropin Chlamydomonas

reinhardtiiAJ416557 (Huang et al. 2002)

CsPhot1 Phototropin-like Coccomyxa subellipsoidea C-169

EIE23763 (Blanc et al. 2012)

CvPhot1 Phototropin-like Chlorella variabilis EFN51280 (Blanc et al. 2010)MspPhot phototropin Micromonas sp. RCC299 XM_002506242MpPhot phototropin Micromonas pusilla

CCMP1545XM_003063488 (Worden et al. 2009)

OtPhot phototropin Ostreococcus tauri XM_003083691 (Derelle et al. 2006)

OlPhot Phototropin-like Ostreococcus lucimarinus CCE9901

XP_001421797 (Palenik et al. 2007)

OspPhot phototropin Ostreococcus sp. RCC809

JGI (Ostreococcus sp. RCC809)

accession numbers: 95946

ChR1 channelrhodopsin-1


AF385748 (Nagel et al. 2002; Sineshchekov et al. 2002; Suzuki et al.

2003)ChR2 channelrhodopsin-

2Chlamydomonas

reinhardtiiAAM15777 (Nagel et al. 2003;

Sineshchekov et al. 2002; Suzuki et al.

2003)VchR1 channelrhodopsin-

1Volvox carteri ABZ90900 (Kianianmomeni et al.

2009; Zhang et al. 2008)

VchR2 channelrhodopsin-2

Volvox carteri ABZ90903 (Kianianmomeni et al. 2009)

PsChR1 channelrhodopsin-1

Pleodorina starri JQ249903 (Zhang et al. 2011)

PsChR2 channelrhodopsin-2


PgChR1 channelrhodopsin-1

Pyramimonas gelidicola JQ241366 (Zhang et al. 2011)

MChR1 channelrhodopsin-1

Mesostigma viride JF922293 (Govorunova et al. 2011)

HpChR1channelrhodopsin-

1Haematococcus pluvialis JN596950 (Hou et al. 2012)

DchR1channelrhodopsin-

1Dunaliella salina JQ241364 (Zhang et al. 2011)

CyChR1 channelrhodopsin-1

Chlamydomonas yellowstonensis

JN596948 (Hou et al. 2012)

CaChR1channelrhodopsin-

1Chlamydomonas

augustaeJN596951 (Hou et al. 2012)

CrChR2 channelrhodopsin-2

Chlamydomonas raudensis

JN596949 (Hou et al. 2012)

CrHKR1 histidine kinase rhodopsin-1


AAQ16277 (Kateriya et al. 2004; Luck et al. 2012)



XP_001698789 (Kateriya et al. 2004; Merchant et al. 2007)



Phytozome (Chlamydomonas

v5.3.1) Locus name:

Cre01.g038050.t1.2

(Kateriya et al. 2004; Merchant et al. 2007)



XM_001700643 (Merchant et al. 2007)

VcHKR1 histidine kinase rhodopsin-1

Volvox carteri XP_002954798 (Prochnik et al. 2010)


Volvox carteri XP_002957065 (Prochnik et al. 2010)





PsHKR1 histidine kinase rhodopsin-1


PsHKR2 histidine kinase rhodopsin-2


MpHKRa histidine kinase rhodopsin

Micromonas pusilla CCMP1545

XM_003060208 (Worden et al. 2009)

Msp.HKRa histidine kinase rhodopsin

Micromonas sp. RCC299 XM_002505317 (Worden et al. 2009)

BpHKR1 histidine kinase rhodopsin

Bathycoccus prasinos FO082273 (Moreau et al. 2012)

OtHKR histidine kinase rhodopsin

Ostreococcus tauri XM_003083844 (Derelle et al. 2006)

AaRh rhodopsin Acetabulariaacetabulum

AAY82897 (Tsunoda et al. 2006)

CvRh rhodopsin Chlorella vulgaris JQ255360 (Zhang et al. 2011)CsRh rhodopsin Cryptomonas sp. S2 ABA08439 (Sineshchekov et al.

2005)Gt1Rh rhodopsin 1 Guillardia theta ABA08437 (Sineshchekov et al.

2005)Gt2Rh rhodopsin 2 Guillardia theta ABA08438 (Sineshchekov et al.

2005)GtR3 rhodopsin 3 Guillardia theta JQ241365 (Gradinaru et al. 2010)

CpOps1 opsin-1 Cyanophora paradoxa ACV05065 (Frassanito et al. 2010)CpOps2 opsin-2 Cyanophora paradoxa GU138075

ASR sensory rhodopsin Anabaena sp. 1XIO_A (Vogeley et al. 2004)

CrCop1 chlamyopsin-1 Chlamydomonas reinhardtii

Z48968 (Deininger et al. 1995)

CrCop2 chlamyopsin-2 Chlamydomonas reinhardtii

AF295371 (Fuhrmann et al. 2003)

Vop volvoxopsin Volvox carteri Y11204 (Ebnet et al. 1999)

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