Supplemental Data. Long et al. (2010). Plant Cell 10.1105/tpc.110.074096

A.

10 20 30 40 50 60 70 80 90 100 110 120 130 140 150

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POPTRDRAFT_646081 ------

POPTRDRAFT_667015 ------

RCOM_1514810 ------MGVTLSSIAILCIISSRCNLFFISFLS

ACJ84748 ------

LOC100265609 ------MQRGGGGRLGRGESVVTRKQLQTHVSDARVPFDAPPR

LOC100259339 MTYVGPFPLITRGTHLLMTRGAHSHPAKHHPNHPIRIQVMRPSYPDCLKEVQTTLINIDIXTDFTMYPNDQHRSPGYDVRVELLNQELVLVEIVRPSIGQLRGSPATRGLNNLVKRGGGGRLGRGESVVTRKQLQTHVSDARVPFDAPPR

PYE ------

Os03g0379300 ------

Os07g0628500 ------

AtbHLH011 ------

AtbHLH121 ------

AtbHLH115 ------MVSPENTNWLSDYPLIE------

IRL3 ------MVSPENANWICDLIDADY------

AtbHLH104 ------MYPSL-DDDFVSDLFCFDQSNGAELDDYTQFGVNLQT

AtbHLH034 ------MYPSIEDDDDLLAALCFDQSNGVE-DPYG---Y-MQT

AtbHLH020 ------MNSLVGDVPQSLSSLDDTTTCYNLDASCNK

AtbHLH025 ------MSILSTRWFSEQEIEENSIIQQFH--MNSIVGEVQEAQYIFPHSFTTNN-DPSYDD

AtbHLH019 ------MDEDFFLP------DFSLVDIDFDFNIYEENNLSP--DESLSN

AtbHLH018 ------MDDSSFMDLMIDTDEYLIDDWESDFPICGETNTNPG-SESGSG

AtbHLH092 ------MMHLILSCSYLISMDGYYNEASEEPSSSSSSGSLARSLFHEYRQSVIPLQNGHVPSMAFMNNLPYVEIRPQESQRLAFND

AtbHLH041 ------MDNFFLGLSCQE------EN

160 170 180 190 200 210 220 230 240 250 260 270 280 290 300

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POPTRDRAFT_646081 ------MSMGSEL------NETVEDV----TENRCFPAGENKGKVPKRI-HKSEREKLKREQL

POPTRDRAFT_667015 ------MSTGSEP------DVTVEEV----TGNRSFPAGKNKGKVPRRI-HKAEREKLKREQL

RCOM_1514810 SIMNYLIMIIAFVSIFITLVLTAF-----VGLICFWKFYLEIHVFDFGYLIGGVLVSRFEVDSFDISMASDISPS------ASDDVNVTVE----PTKRSCP-GKNKGKVPKRI-HKAEREKLKREQL

ACJ84748 ------MGSES------VAPMIEP----SNNRSDPGTMKQGKVPKRI-HKAEREKMKREHL

LOC100265609 SVLATLRLSILISRHASSLSKSAEGFQTSLGIMLALFFLSDLEFIHRLAKVGLGMRNFFCTQFIELRMDPEVPPS------LVDKVNVVAEN---PLTRSCPTKNNQRKVPKRV-HKAVREKLKREHL

LOC100259339 SVLATLRLSILISRHASSLSKSAEGFQTSLGIMLALFFLSDLEFIHRLAKVGLGMRNFFWTRFTELRMDPEVPPS------LVDKVNVVAEN---PLTRSCPTKNXQRKVPKRV-HKAVREKLKREHL

PYE ------MVSKT------PSTSSDE-----ANATADERCRKGKVPKRI-NKAVRERLKREHL

Os03g0379300 ------MVPSERGDV------ATAIRPAAADK---LVHGPISDKKCRKKVPRKV-HKSEREKLKRGHL

Os07g0628500 ------MVPRDRVNA------AAAGG-GGEGR---LVQSGIVNKKCDKKAPKRI-HKSEREKLKRDKQ

AtbHLH011 ------MDQPMKPKTCSESDFAD------DSSASSSSSSG---QNLRGAEMVVEVKKEAVCS-QKAEREKLRRDKL

AtbHLH121 ------MDVSARKS-QKAGREKLRREKL

AtbHLH115 ------GAFSDQNPTFPWQIDG------SATVSVEVDG------FLCDADVIKEP------SSRKRIKTESCTGSN-SKACREKQRRDRL

IRL3 ------GSFTIQGPGFSWPVQQP------IGVSSNSSAGVDG------SAGNSEASKEP------GSKKRGRCESSSATS-SKACREKQRRDRL

AtbHLH104 DQEDTFPDFVSYGVNLQQEPDE------VFS--IGASQLDLS-SYNGVLSLEPEQVG----QQD---CEVVQEEE------VEINSGSSGGAVKEEQEHLDDDCSRKRARTGSCSRGGGTKACRERLRREKL

AtbHLH034 NEDNIFQDFGSCGVNLMQPQQEQFDSFNGNLEQVCSSFRGGNNGVVYSSSIGSAQLDLAASFSGVLQQETHQVCGFRGQNDDSAVPHLQQQQGQVFSGVVEINSSSSVGAVKEE---FEEECSGKRRRTGSCSKPG-TKACREKLRREKL

AtbHLH020 SLVEERPSKILKTTHISPNLHPFSSSNPPPPKHQPSS------RILSFEKTGLHVMNHN-SP------NLIFSPKDEEIGLPEHKKAELIIRGTKRAQSLTRSQSNAQDHILAERKRREKL

AtbHLH025 -LIEMKPPKILETTYISPSSHLPPNSKPHHIHRHSSS------RILSFEDYGSNDMEHEYSPTYL------NSIFSPKLEAQVQPHQKSDEFNRKGTKRAQPFSRNQSNAQDHIIAERKRREKL

AtbHLH019 SRRADQSSKFDHQMHFECLREKPKAAVKPMMKINNKQ------QLISF---DFSSNVISSPA------AEEIIMDKLVGRGTKRKTCSH--GTRSPVLAKEHVLAERKRREKL

AtbHLH018 TGFELLAERPTKQMKTNNNMNSTSSSPSSSSSSGSRTS------QVISFGSPDTKTNPVETSLN------FSNQVSMDQKVG--SKRKDCVNNGGRREPHLLKEHVLAERKRRQKL

AtbHLH092 TQRLFYQMKIEASLREWFPEDFNRKSSPANSDYLRPPHYPSSSSSSLSPNNISEYSSLLFPLIPKPSTTTEAVNVPVLPPLAPIN------MIHPQHQEPLFRNRQREEEAMTQAILAVLTGPSSPPSTSSSPQRKGRATA

AtbHLH041 NFWDLIVADISGDRSVSVPIRSAFR-----S------YMKDTELRMMSPKISS------SKVNVKKRMVNLLRKNWEEKKNTVAPEKERSRRHMLKERTRREKQ

310 320 330 340 350 360 370 380 390 400 410 420 430 440 450

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POPTRDRAFT 646081 NELFLELASALELSQ-PNNGKASMLCETTRLLKDL-HTQIESLKKEN-VALLSESH------YVTVEKNELREESSALEHQIG-KLHSELEMRAAS------QSKPDLNVPPP------EFLQP---PH

POPTRDRAFT_667015 NELFLDLASALELSE-PNTGKASILCETTRLLKDL-LTQIESLKKDN-VALLSESR------YVTVEKNELREENSVLENQIG-KLQGELESRVAA------QSTPVLNVPPP------EFQQP---PH

RCOM_1514810 NDLFLDLADALDLTQ-PNNGKASILCEAARLLKDL-FGQIECLKKEN-ESLLSESR------YVTVEKNELREENLALETQIE-SLQGELEAKAV------QSKPDLNMPPP------ELHHPELAPH

ACJ84748 NELFLDLANALDLSE-PNNGKASILIEASRLLKDL-LCQIQSLKKEN-VSLLSESH------YVTMEKNELKEENSSLETQIE-KLQGEIQARIA------QSKPDLNAPPQ------LELESPEQTT

LOC100265609 HDLFLELANALDLTH-QNTGKAFILCEAIRLVKDT-IAQIDCLKKEN-AALFSESH------YVNIEKNELRDENSVLEDQID-KLQTEIKERAA------LYKPDLNSAPS------EFQQTEVTQH

LOC100259339 XDLFLELANALDLTH-QNTGKAFILCEAIRLVKDT-IAQIDCLKKEN-AALFSESH------YVNIEKNELRDENSVLEDQID-KLQTEIKERAA------LYKPDLNSAPS------EFQQTEVTQH

PYE NELFIELADTLELNQ-QNSGKASILCEATRFLKDV-FGQIESLRKEH-ASLLSESS------YVTTEKNELKEETSVLETEIS-KLQNEIEARAN------QSKPDLNTSPAPEYHHH----HYQQQHPERVSQ

Os03g0379300 NDLFGELGNMLEADR-QSNGKACILTDTTRILRDL-LSQVKSLRQEN-STLQNESN------YVTMERNELQDENGALRSEIS-DLQNELRMRATGSPGW------GHGATGSPLPVPPSPG------TVFPSQQPMQP

Os07g0628500 NDLFNELGNLLEPDR-QNNGKACVLGETTRILKDL-LSQVESLRKEN-SSLKNESH------YVALERNELHDDNSMLRTEIL-ELQNELRTRMEGNPVW------SHVNTRPALRVPYPTT------GVFPVQH-LPH

AtbHLH011 KEQFLELGNALDPNR-PKSDKASVLTDTIQMLKDV-MNQVDRLKAEY-ETLSQESR------ELIQEKSELREEKATLKSDIE-ILNAQYQHRIKTMVPW------VPHYSYHIPFVAITQGQSS------FIPYSASVNP

AtbHLH121 NEHFVELGNVLDPER-PKNDKATILTDTVQLLKEL-TSEVNKLKSEY-TALTDESR------ELTQEKNDLREEKTSLKSDIE-NLNLQYQQRLRSMSPWGAAMDHTVMMAPPPSFPYPMP-IAMPPGSIP------MHPSMPSYTY

AtbHLH115 NDKFTELSSVLEPGRTPKTDKVAIINDAIRMVNQA-RDEAQKLKDLN-SSLQEKIK------ELKDEKNELRDEKQKLKVEKE-RIDQQLKAIKT------QP--QPQPCFLPN------PQTLSQAQ

IRL3 NDKFMELGAILEPGNPPKTDKAAILVDAVRMVTQL-RGEAQKLKDSN-SSLQDKIK------ELKTEKNELRDEKQRLKTEKE-KLEQQLKAMNAP------QPSFFPAPPMMPT------AFASAQGQ

AtbHLH104 NERFMDLSSVLEPGRTPKTDKPAILDDAIRILNQL-RDEALKLEETN-QKLLEEIK------SLKAEKNELREEKLVLKADKE-KTEQQLKSMTA------PSSGFIP------HIPAAFNH

AtbHLH034 NDKFMDLSSVLEPGRTPKTDKSAILDDAIRVVNQL-RGEAHELQETN-QKLLEEIK------SLKADKNELREEKLVLKAEKE-KMEQQLKSMVV------PSPGFMPS------QHPAAFHS

AtbHLH020 TQRFVALSALIPGLK--KMDKASVLGDAIKHIKYL-QESVKEYEEQK-KEKTMES------VVLVKKSSLVLDENHQPS------SSSSSDGNRN------SSSSNLPEIEVRVS------GKDVLIKIL

AtbHLH025 TQRFVALSALVPGLK--KMDKASVLGDALKHIKYL-QERVGELEEQK-KERRLES------MVLVKKSKLILDDNNQSF------SSSCEDG------FSDLDLPEIEVRFS------DEDVLIKIL

AtbHLH019 SEKFIALSALLPGLK--KADKVTILDDAISRMKQL-QEQLRTLKEEKEATRQMES------MILVKKSKVFFDEEPN------LSCSPSVHI------EFDQALPEIEAKIS------QNDILIRIL

AtbHLH018 NERLIALSALLPGLK--KTDKATVLEDAIKHLKQL-QERVKKLEEERVVTKKMDQS------IILVKRSQVYLDDDSSSYSSTCSAASPLSSSSDEVS------IFKQTMPMIEARVS------DRDLLIRVH

AtbHLH092 FKRYYSMISDRGRAPLPSVRKQSMMTRAMSFYNRLNINQRERFTRENATTHGEGSGGSGGGGRYTSGPSATQLQHMISERKRREKLNESFQALRSLLPPG------TKKDKASVLSIAREQLSSLQGEISKLLERNREVEAK

AtbHLH041 KQSYLALHSLLPFAT--KNDKNSIVEKAVDEIAKLQRLKKELVRRIK------VIEEKSAKDGHDEMSETKVRVNLKEPLSGLDS------MLEALHYLKS------MGTKLKTV

460 470 480 490 500 510 520 530 540 550 560 570 580

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POPTRDRAFT_646081 FPVD-SFRLPAVD-----AVALQQTSTVFVVPISPDH------VQGFPMATSN------VSKPHPRYPTAADSWPSQLLR------EQQIGRKEV------

POPTRDRAFT_667015 FPGD-SFRLPAVDAA---AAALQQTPAVFVVPIRPDH------VQGLPMATSN------VRKPHARYPTAADSWPSQLLG------EQQIARKEVQFSGKDSAICNPGERCHP------

RCOM_1514810 FTGE-SLGLPVADG------IPQQAPAVFVVPLHPS------LQAYPRTTTN------VSKPHARYATPADSWPSQLLE------EQLTIRKEVQ------

ACJ84748 FSGQ-SFQLPTVDP------TLQQGPTVLVVPFRPDL------QAAYPAPTEITPNPPLVISKPHARYPTPADSWPSQLLG------EQPTSS------

LOC100265609 CPGS-SLRFPSADQA---LQQSSVVGPVLVVPFASG------LRAYPGAGAPR--SISIVSKPHARYPTPGDSWPSQVLG------DQPTARQKFELSGSINNSSSCGIGEEGSGKV--

LOC100259339 CPGS-SLRFPSADQA---LQQSSVVGPVLVVPFASG------LRAYPGAGAPR--SISIVSKPHARYPTPGDSWPSQVLG------DQPTARQKFELSGSINNSSSCGIGEEGSGXV--

PYE FPGLPIFQGPGFQQS---ATTLHPPATVLVLPIQPDPQTQD------ISEMTQAQQPLMFNSSNVSKPCPRYASAADSWSSRLLG------ERLKASE------

Os03g0379300 SPMTTSTVFPLQQPLPQPTVIEPSARQPLELKLFLEA------PPAEDPEPSEDQEAPNNVARPQPRYPTEASSWPISLG------LPRMEDEQM------

Os07g0628500 LPVTTTAAFPQQLPV---IIEQHYAATPRELQLFPES------ATSEDSEPSQEHGISDHVTRPQPRYPTPTATLPVNLFP------VFPGRQDQQCSSGTSGTNEEDRIGRS------

AtbHLH011 LTEQQASVQQHSSSSADASMKQDSKIKPLDLDLMMNSNHSG------QGNDQKDDVRLKLELKIHASSLAQQDVSGKEK------KVSLTTTASSSNSYSLSQAVQDSSPGTVNDMLKP----

AtbHLH121 FGNQNPSMIPAPCPTYMPYMPPNTVVEQQSVHIPQNPGNRSREPRAKVSRESRSEKAEDSNEVATQLELKTPGSTSDKDTLQRPEKTKRCKRNNNNNSIEESSHSSKCSSSPSVRDHSSSSSVAGGQKPDDAK

AtbHLH115 APGSKLVPFTTYP-----GFAMWQFMPPAAVDTSQDH------VLRPPVA------

IRL3 APGNKMVPIISYP-----GVAMWQFMPPASVDTSQDH------VLRPPVA------

AtbHLH104 NKMAVYPSYGY------MPMWHYMPQSVRDTSRDQ------ELRPPAA------

AtbHLH034 HKMAVAYPYGYYPP----NMPMWSPLPPADRDTSRDL------KNLPPVA------

AtbHLH020 CEKQKGNVIKIMG-----EIEKLGLSITNSNVLPFG------PTFDISIIAQKNNNFDM------KIEDVVKNLSFGLSKLT------

AtbHLH025 CEKQKGHLAKIMA-----EIEKLHILITNSSVLNFG------PTLDITIIAKKESDFDM------TLMDVVKSLRSALSNFI------

AtbHLH019 CEKSKGCMINILN-----TIENFQLRIENSIVLPFGD------STLDITVLAQMDKDFSMS------ILKDLVRNLRLAMV------

AtbHLH018 CEKNKGCMIKILS-----SLEKFRLEVVNSFTLPFGN------STLVITILTKMDNKFSR------PVEEVVKNIRVALAE------

AtbHLH092 LAGEREIENDLRPEE-RFNVRIRHIPESTSRERTLDLRVVLRG-DIIRVDDLMIRLLEFLKQINNVSLVSIEARTLARAEGDTSIVLVISLR------LKIEGEWDESAFQEAVRRVVADLAH------

AtbHLH041 HANFSPQEFSAT------MTIETQIRGEEVEKRVER------R-----LQETEWKLLFLPEASFYKDY------

Supplemental Dataset 4. Alignment of PYE and putative PYE homologs

A. Protein alignment of PYE, and putative PYE homologs from Arabidopsis, Ricinus communis, Medicago truncatula, Populus trichocarpa, Vitis vinifera and Oryza sativa. Genes and associated AGI identifiers and accession numbers (indicated in parenthesis) are as follows: PYE (At3g47640), AtbHLH011 (At4g36060)AtbHLH121 (At3g19860), AtbHLH115 (At1g51070), AtbHLH104 (At4g14410), IRL3 (At5g54680), AtbHLH034 (At3g23210) , RCOM_1514810 (XP_002511561.1) , ACJ84748 (ACJ84748.1), POPTRDRAFT_646081 (XP_002303343.1), POPTRDRAFT_667015 (XP_002321908.1), LOC100265609 (XP_002268400.1), LOC100259339 (XP_002283284.1), Os03g0379300 (NP_001050234.1), Os07g0628500 (NP_001060350.1), AtbHLH020 (At2g22770), AtbHLH019 (At2g22760), AtbHLH018 (At2g22750), AtbHLH025 (At4g37850), AtbHLH041 (At5g56980), AtbHLH092 (At5g43850).

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