Supplemental Table 1: NCBI-GenBank accession numbers (unless otherwise noted) used to construct the phylogenetic trees.
Abbreviation / Gene name / Species / Accession number / ReferenceCbCRY1 / cryptochrome / Capsellabursa-pastoris / GQ251561 / (Slotte et al. 2009)
AtCRY1 / cryptochrome / Arabidopsisthaliana / S66907 / (Ahmad and Cashmore 1993)
CnCRY1 / cryptochrome / Cardaminenipponica / AB517032 / (Ikeda and Setoguchi 2010)
BnCRY1 / cryptochrome / Brassicanapus / AJ704628 / (Chatterjee et al. 2006)
BrCRY1 / cryptochrome / Brassicarapa / AJ704628 / (Chatterjee et al. 2006)
PtCRY1.1 / cryptochrome / Populustremula / JN235115 / (Keller et al. 2011)
PtCRY1.2 / cryptochrome / Populustremula / JN235116 / (Keller et al. 2011)
PsCRY1-1 / cryptochrome / Pisumsativum / AY508971 / (Platten et al. 2005a)
SlCRY1 / cryptochrome / Solanum lycopersicum / NM_001247738 / (Ninu et al. 1999; Perrotta et al. 2000)
OmCRY1 / cryptochrome / Orobancheminor / AY351861 / (Okazawa et al. 2005)
AcCRY1 / cryptochrome / Adiantumcapillus-veneris / BAA32807 / (Kanegae and Wada 1998)
AcCRY2 / cryptochrome / Adiantumcapillus-veneris / AB012627 / (Kanegae and Wada 1998)
AcCRY4 / cryptochrome / Adiantumcapillus-veneris / BAA88423
OsCRY2 / cryptochrome / Oryzasativa / AB103094 / (Hirose et al. 2006)
TaCRY2 / cryptochrome / Triticumaestivum / EF601542 / (Xu et al. 2009)
SlCRY2 / cryptochrome / Solanum lycopersicum / NM_001247316 / (Perrotta et al. 2000)
PsCRY2A / cryptochrome / Pisumsativum / AY508972 / (Platten et al. 2005b)
PsCRY2B / cryptochrome / Pisumsativum / AY508974 / (Platten et al. 2005b)
AtCRY2 / cryptochrome / Arabidopsisthaliana / AY576267 / (Olsen et al. 2004)
AtPHH1 / cryptochrome / Arabidopsisthaliana / U62550 / (Hoffman et al. 1996)
AhCRY2 / cryptochrome / Arabidopsishallerisubsp.gemmifera / JQ180280 / (Huang et al. 2012)
AlCRY2 / Arabidopsislyratasubsp.Lyrata / JQ180279 / (Huang et al. 2012)
PpCRYp / plant-likecryptochrome / Physcomitrellapatens / AB060693 / (Imaizumi et al. 2002)
CsCRYp / plant-likecryptochrome / CoccomyxasubellipsoideaC-169 / EIE22432
VcCRYp / plant-likecryptochrome / Volvox carteri / XM_002957226 / (Prochnik et al. 2010)
CrCRYp / plant-likecryptochrome / Chlamydomonasreinhardtii / L07561 / (Small et al. 1995)
SbCRY1b / cryptochrome / Sylvia borin / DQ838738 / (Liedvogel et al. 2007)
GgCRY1 / cryptochrome / Gallusgallus / 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 / Ovisaries / NM_001129735 / (Dardente et al. 2008; Fustin et al. 2009)
XlCRY1 / cryptochrome / Xenopuslaevis / AY049033 / (Zhu and Green 2001)
XtCRY1 / cryptochrome / Xenopustropicalis / NM_001017311 / (Klein et al. 2002)
DrCRY1a / cryptochrome / Daniorerio / BC124762 / (Strausberg et al. 2002)
PaCRY1a / cryptochrome / Phreatichthysandruzzii / GQ404476 / (Cavallari et al. 2011)
DlCRY2 / cryptochrome / Dicentrarchuslabrax / JX046478 / (del Pozo et al. 2012)
RnCRY2 / cryptochrome / Rattusnorvegicus / 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 / Drosophilamelanogaster / BAA12067 / (Todo et al. 1996)
Dwil/GK / cryptochrome-like / Drosophilawillistoni / XM_002064700 / (Clark et al. 2007)
CgCRY1 / cryptochrome / Crassostreagigas / EKC39908 / (Zhang et al. 2012)
Xl64phr / 6-4 photolyase / Xenopuslaevis / NM_001087952 / (Klein et al. 2002)
DrCRY5 / cryptochrome / Daniorerio / NM_131788 / (Weger et al. 2011)
SsCRY1 / cryptochrome / Salmosalar / BT058852 / (Leong et al. 2010)
Vv6-4Ph / 6-4 DNA photolyase-like / Vitisvinifera / XM_002285291
PtiCRYa / cryptochrome-like / Populustrichocarpa / XM_002304127 / (Tuskan et al. 2006)
JcCRYa / cryptochrome-like / Jatrophacurcas / BAJ53248 / (Sato et al. 2011)
AtUVR3 / 6-4 DNA photolyase / Arabidopsisthaliana / NM_112432 / (Salanoubat et al. 2000)
HvCRYa / cryptochrome-like / Hordeumvulgaresubsp.Vulgare / AK360897 / (Matsumoto et al. 2011)
OsCRYa / cryptochrome-like / Oryzasativa / 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 DNA
photolyase / Physcomitrellapatens / XM_001754022 / (Rensing et al. 2008)
CsUVR3 / UVR3 AtUVR3-like 6-4 DNA
photolyase / CoccomyxasubellipsoideaC-169 / EIE22254
CvCRYa / cryptochrome-like / Chlorellavariabilis / EFN51376 / (Blanc et al. 2010)
Ds6-4Ph / 6-4 photolyase, cryptochrome-like / Dunaliellasalina / AY845324 / (Yi et al. 2006)
CrCRYa / animal-likecryptochrome / Chlamydomonasreinhardtii / XM_001698002 / (Beel et al. 2012; Merchant et al. 2007)
VcCRYa / animal-likecryptochrome / Volvox carteri / XM_002945880 / (Prochnik et al. 2010)
XlCRYd / DASH cryptochrome / Xenopuslaevis / NP_001084438 / (Daiyasu et al. 2004)
DlCRYd / DASH cryptochrome / Dicentrarchuslabrax / CBN81995 / (Kuhl et al. 2011; Tine et al. 2011)
DrCRYd / DASH cryptochrome / Daniorerio / Q4KML2 / (Daiyasu et al. 2004)
DpCRYd / DASHcyptochrome / Daphnia pulex / EFX86680 / (Colbourne et al. 2011)
NvCRYd / DASH-likecyptochrome / Nematostellavectensis / XM_001623193 / (Putnam et al. 2007)
CmPHR5 / DASH cryptochrome / Cyanidioschyzonmerolae / BAM78760 / (Asimgil and Kavakli 2012; Matsuzaki et al. 2004)
CmPHR2 / DASH cryptochrome / Cyanidioschyzonmerolae / BAM80259 / (Asimgil and Kavakli 2012; Matsuzaki et al. 2004)
AtCRYd / DASH cryptochrome / Arabidopsisthaliana / Q84KJ5 / (Brudler et al. 2003; Kleine et al. 2003; Tabata et al. 2000)
PtiCRY / DASH-likecyptochrome / Populustrichocarpa / XM_002330784 / (Tuskan et al. 2006)
ZmCRYd / DASH cyptochrome / Zea mays / NP_001146707 / (Soderlund et al. 2009)
SbCRYd / DASH-likecyptochrome / Sorghum bicolor / XM_002438751 / (Paterson et al. 2009)
HvCRY / DASH-likecyptochrome / Hordeumvulgare / AK375185 / (Matsumoto et al. 2011)
OsCRYd / DASHcyptochrome / Oryzasativa / EEE66166 / (Yu et al. 2005)
VcCRYd1 / DASH cryptochrome / Volvox carteri / XM_002953647 / (Prochnik et al. 2010)
CrCRYd1 / DASH cryptochrome / Chlamydomonasreinhardtii / XM_001701819 / (Merchant et al. 2007)
CsCRYd / cryptochrome / CoccomyxasubellipsoideaC-169 / EIE22181 / (Blanc et al. 2012)
CvCRYd1 / DASHcyptochrome / Chlorellavariabilis / EFN56221 / (Blanc et al. 2010)
TpCPF3 / DASH-likecyptochrome / Thalassiosirapseudonana / XM_002291289 / (Armbrust et al. 2004; Bowler et al. 2008)
ToCRY / DASH-likecyptochrome / Thalassiosiraoceanica / EJK57807
AaCRYd / DASH-likecyptochrome / Aureococcusanophagefferens / EGB10801 / (Gobler et al. 2011)
Msp.CRYd / DASH-likecyptochrome / Micromonassp. RCC299 / XM_002508319 / (Worden et al. 2009)
MpCRYd / DASH-likecyptochrome / MicromonaspusillaCCMP1545 / XP_003062980 / (Worden et al. 2009)
OlCRYd / DASH-likecyptochrome / OstreococcuslucimarinusCCE9901 / XM_001415659 / (Palenik et al. 2007)
OtCRYd / DASH-likecyptochrome / Ostreococcustauri / XM_003074649 / (Derelle et al. 2006)
VfPhot1B / phototropin / Viciafaba / AB095910 / (Kinoshita et al. 2003)
PsPhot / phototropin / Pisumsativum / U83281 / (Lin et al. 1991)
PvPhot1B / phototropin / Phaseolusvulgaris / AB204873 / (Inoue et al. 2005)
PvPhot1A / phototropin / Phaseolusvulgaris / AB204872 / (Inoue et al. 2005)
VvPhot1 / Phototropin-like / Vitisvinifera / XM_002281716
PtPhot / Phototropin-like / Populustrichocarpa / XM_002298523 / (Tuskan et al. 2006)
AtNph1 / phototropin / Arabidopsisthaliana / AF030864 / (Huala et al. 1997)
ZmPhot1 / phototropin / Zea mays / NM_001111416 / (Gardiner et al. 2004)
OsNPH1-1 / phototropin-like / Oryzasativa / NM_001071765 / (Matsumoto et al. 2005)
AsNPH1-1 / phototropin / Avenasativa / AF033096 / (Huala et al. 1997)
AsNPH1-2 / phototropin / Avenasativa / AAC05084 / (Huala et al. 1997)
VcPhot1 / phototropin / Volvox carteri / XM_002950419 / (Prochnik et al. 2010)
CrPhot1 / phototropin / Chlamydomonasreinhardtii / AJ416557 / (Huang et al. 2002)
CsPhot1 / Phototropin-like / CoccomyxasubellipsoideaC-169 / EIE23763 / (Blanc et al. 2012)
CvPhot1 / Phototropin-like / Chlorellavariabilis / EFN51280 / (Blanc et al. 2010)
MspPhot / phototropin / Micromonassp. RCC299 / XM_002506242
MpPhot / phototropin / MicromonaspusillaCCMP1545 / XM_003063488 / (Worden et al. 2009)
OtPhot / phototropin / Ostreococcustauri / XM_003083691 / (Derelle et al. 2006)
OlPhot / Phototropin-like / OstreococcuslucimarinusCCE9901 / XP_001421797 / (Palenik et al. 2007)
OspPhot / phototropin / Ostreococcus sp. RCC809 / JGI (Ostreococcus sp. RCC809) accession numbers: 95946
ChR1 / channelrhodopsin-1 / Chlamydomonasreinhardtii / AF385748 / (Nagel et al. 2002; Sineshchekov et al. 2002; Suzuki et al. 2003)
ChR2 / channelrhodopsin-2 / Chlamydomonasreinhardtii / AAM15777 / (Nagel et al. 2003; Sineshchekov et al. 2002; Suzuki et al. 2003)
VchR1 / channelrhodopsin-1 / Volvoxcarteri / ABZ90900 / (Kianianmomeni et al. 2009; Zhang et al. 2008)
VchR2 / channelrhodopsin-2 / Volvoxcarteri / ABZ90903 / (Kianianmomeni et al. 2009)
PsChR1 / channelrhodopsin-1 / Pleodorinastarri / JQ249903 / (Zhang et al. 2011)
PsChR2 / channelrhodopsin-2 / Pleodorinastarri / JQ249904 / (Zhang et al. 2011)
PgChR1 / channelrhodopsin-1 / Pyramimonasgelidicola / JQ241366 / (Zhang et al. 2011)
MChR1 / channelrhodopsin-1 / Mesostigmaviride / JF922293 / (Govorunova et al. 2011)
HpChR1 / channelrhodopsin-1 / Haematococcuspluvialis / JN596950 / (Hou et al. 2012)
DchR1 / channelrhodopsin-1 / Dunaliellasalina / JQ241364 / (Zhang et al. 2011)
CyChR1 / channelrhodopsin-1 / Chlamydomonasyellowstonensis / JN596948 / (Hou et al. 2012)
CaChR1 / channelrhodopsin-1 / Chlamydomonasaugustae / JN596951 / (Hou et al. 2012)
CrChR2 / channelrhodopsin-2 / Chlamydomonasraudensis / JN596949 / (Hou et al. 2012)
CrHKR1 / histidinekinase rhodopsin-1 / Chlamydomonasreinhardtii / AAQ16277 / (Kateriya et al. 2004; Luck et al. 2012)
CrHKR2 / histidinekinase rhodopsin-2 / Chlamydomonasreinhardtii / XP_001698789 / (Kateriya et al. 2004; Merchant et al. 2007)
CrHKR3 / histidinekinase rhodopsin-3 / Chlamydomonasreinhardtii / Phytozome(Chlamydomonas v5.3.1)Locus name: Cre01.g038050.t1.2 / (Kateriya et al. 2004; Merchant et al. 2007)
CrHKR4 / histidinekinase rhodopsin-4 / Chlamydomonasreinhardtii / XM_001700643 / (Merchant et al. 2007)
VcHKR1 / histidinekinase rhodopsin-1 / Volvoxcarteri / XP_002954798 / (Prochnik et al. 2010)
VcHKR2 / histidinekinase rhodopsin-2 / Volvoxcarteri / XP_002957065 / (Prochnik et al. 2010)
VcHKR3 / histidinekinase rhodopsin-3 / Volvoxcarteri / XM_002953903 / (Prochnik et al. 2010)
VcHKR4 / histidinekinase rhodopsin-4 / Volvoxcarteri / XM_002952553 / (Prochnik et al. 2010)
PsHKR1 / histidinekinase rhodopsin-1 / Pleodorinastarri / JQ249905 / (Zhang et al. 2011)
PsHKR2 / histidinekinase rhodopsin-2 / Pleodorinastarri / JQ249906 / (Zhang et al. 2011)
MpHKRa / histidinekinaserhodopsin / MicromonaspusillaCCMP1545 / XM_003060208 / (Worden et al. 2009)
Msp.HKRa / histidinekinaserhodopsin / Micromonas sp. RCC299 / XM_002505317 / (Worden et al. 2009)
BpHKR1 / histidinekinaserhodopsin / Bathycoccusprasinos / FO082273 / (Moreau et al. 2012)
OtHKR / histidinekinaserhodopsin / Ostreococcustauri / XM_003083844 / (Derelle et al. 2006)
AaRh / rhodopsin / Acetabularia
acetabulum / 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 / Guillardiatheta / ABA08437 / (Sineshchekov et al. 2005)
Gt2Rh / rhodopsin 2 / Guillardiatheta / ABA08438 / (Sineshchekov et al. 2005)
GtR3 / rhodopsin 3 / Guillardia theta / JQ241365 / (Gradinaru et al. 2010)
CpOps1 / opsin-1 / Cyanophoraparadoxa / ACV05065 / (Frassanito et al. 2010)
CpOps2 / opsin-2 / Cyanophoraparadoxa / GU138075
ASR / sensory rhodopsin / Anabaena sp. / 1XIO_A / (Vogeley et al. 2004)
CrCop1 / chlamyopsin-1 / Chlamydomonasreinhardtii / Z48968 / (Deininger et al. 1995)
CrCop2 / chlamyopsin-2 / Chlamydomonasreinhardtii / AF295371 / (Fuhrmann et al. 2003)
Vop / volvoxopsin / Volvoxcarteri / Y11204 / (Ebnet et al. 1999)
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