#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on April 25, 2024; 17:00 GMT TreeBASE (cc) 1994-2008 Study reference: Feng Z.H., Hua W., Fang Z.Y., Wen Z.J., Jie Z.F., & Feng H.C. 2015. Genome-wide transcriptomic and phylogenetic analyses reveal distinct aluminum-tolerance mechanisms in the aluminum-accumulating species buckwheat (Fagopyrum tataricum). BioMed Central, . TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S16751] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=7; TAXLABELS Arabidopsis_thaliana_ALS3 Fagopyrum_tataricum_STAR2 Oryza_sativa_Japonica_Group_STAR2 'Sorghum bicolor XP_002440497' 'Theobroma cacao XP_007027163' 'Vitis vinifera XP_002274040' 'Zea mays NP_001146856' ; END; BEGIN TAXA; TITLE Taxa2; DIMENSIONS NTAX=12; TAXLABELS Arabidopsis_thaliana_ALS1 Capsella_rubella_EOA17806_ Fagopyrum_tataricum_ALOL1 Fagopyrum_tataricum_ALOL2 Hordeum_vulgare_AAG49002 'Nicotiana tabacum XP_004236062' Oryza_sativa_Japonica_Group_ALS1 'Ricinus communis XP_002533538' 'Saccharomyees cerevisiae NP_013289' 'Saccharomyees cerevisiae NP_015053' 'Vitis vinifera XP_002277220' 'Zea mays NP_001151774 ' ; END; BEGIN TAXA; TITLE Taxa3; DIMENSIONS NTAX=12; TAXLABELS Aegilops_tauschii_EMT26835 Arabidopsis_thaliana_STOP1 'Brachypodium distachyon XP_003564719' Fagopyrum_tataricum_ARL1 Fagopyrum_tataricum_ARL2 Lotus_japonicus_BAN67817 Nicotiana_tabacum_BAN67816 Oryza_sativa_Japonica_GroupART1 'Ricinus communis XP_002526844' 'Solanum lycopersicum XP_004250372' Triticum_aestivum_AGS15193 Zea_mays_ACN25425 ; END; BEGIN TAXA; TITLE Taxa4; DIMENSIONS NTAX=10; TAXLABELS Aegilops_tauschii_EMT05468 Arabidopsis_thaliana_STAR1 Fagopyrum_tataricum_STOL1 Fagopyrum_tataricum_STOL2 Oryza_sativa_Japonica_Group_STAR1 'Populus trichocarpa XP_002325227' 'Setaria italica XP_004966143' 'Solanum tuberosum XP_006366268' Triticum_uraatu_EMS52544 Vitis_vinifera_CAN70271 ; END; BEGIN TAXA; TITLE Taxa5; DIMENSIONS NTAX=14; TAXLABELS Arabidopsis_thaliana_2g21340 Arabidopsis_thaliana_2g38330 Arabidopsis_thaliana_4g38380 Arabidopsis_thaliana_4g39030 Arabidopsis_thaliana_FRD3 Arabidopsis_thaliana_MATE Fagopyrum_tataricum_FRDL1 Fagopyrum_tataricum_FRDL2 Oryza_sativa_Japonica_Group_02g0122200 Oryza_sativa_Japonica_Group_09g0548300 Oryza_sativa_Japonica_Group_10g0206800 Oryza_sativa_Japonica_Group_12g0106600 Oryza_sativa_Japonica_Group_FRDL1 Oryza_sativa_Japonica_Group_FRDL4 ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M25149] TITLE Fagopyrum_STAR2; LINK TAXA = Taxa1; DIMENSIONS NCHAR=286; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Arabidopsis_thaliana_ALS3 ------------MDLKWDDFFNDYEWLIVFLKGMVKPAAALVVVLLAVILSYSQNLSLEGEMIYSVSRSFLQLSVIGFVLQFIFNQENSGWIILAYLFMVSVAGYTAGQRARHVPRGKYVAGLSILAGTSITMFLLVLLNVFPFTPRYMIPIAGMLVGNAMTVTGVTMKQLRDDIKMQLNLVETALALGATPRQATLQQVKRALVISLSPVLDSCKTVGLISLPGAMTGMIMGGASPLEAIQLQIVVMNMMVGAATVSSITSTYLCWPSFFTKAYQLQTHVFSSD- Fagopyrum_tataricum_STAR2 -------------ISQVRLIKMDWGWLSEFMKGMLKPVAALTVVLMAVALSYLQRLDLQGEMIYSIFRAFLQLSIIGFVLQFIFNQQNIAWILLAYLFMVSVAGYTAGKRAKHVPKGMYVAGASILAGTSVTMFLLVVLNVFPFTPRYIIPVAGMMVGNAMTVTGVTMKRLRDDIKSQTNLVETALALGATPRQAVLQNMKRALVIALSPVLDNAKTVGLISLPGAMTGLIMGGASPLEAIQLQIIVMNMLIGASTFSSIMSTYLCWPNFFTKTYQLESKVFSSD- Oryza_sativa_Japonica_Group_STAR2 MMASMAALLQRLLVVVNQVDPGAPGFWREFLVGMLKPVAATAVVAMAVALSFTQRLGLEGEMLYAMARAFLQLSVIGFVLQFIFTQKSAAWILLAYLFMVTVAGYTAGQRARHVPRGKHIAAVSILAGTSVTMALLVALRVFPFTPRYIIPVAGMMVGNAMTVTGVTMKKLREDVGMQRGVVETALALGATPRQATARQVRRSLVIALSPVIDNAKTVGLIALPGAMTGLIMGGASPLEAIQLQIVVMNMLMGASTVSSILSTYLCWPAFFTGAFQLNDAVFAAD- 'Sorghum bicolor XP_002440497' ----MAAFLD--QLVAGQVDPGAPGFWRDFLIGMLKPVAATAVVAMAVALSFSQRLGLEGEMLYAIARAFLQLSVIGFVLQFIFTQKNVLWILLAYLFMVTVAGYTAGQRAKQVPRGKYIACVSILVGTAITMFLLVVLNVFPFTPRYIIPVAGMMVGNAMTVTGVTMKKLREDVKIQRNLVETALALGATPRQATLQQVKRSLVIALSPVIDSAKTVGLIALPGAMTGLIMGGASPLEAIQLQIVVMNMLMGAATVSSILSTYLCWPAFFTKAFQLEDKVFA--- 'Theobroma cacao XP_007027163' ---------------------MDWDWLFEFLKGMVKPVAALSVVLMAVLLSFMQKLGLEKEMIYSILRAFLQLSVIGFVLQFIFNQENSGWIVLAYLFMVSVAGYTAGQRAKHVPRGKYVAGISILAGTAVTMFLLVILNVFPFTPRYVIPVAGMMVGNAMTVTGVTMKRLRDDIKIQMNLVETALALGATPRQATLEQVKRALVIALSPVLDNAKTVGLISLPGAMTGLIMGGASPIEAIHLQIVVMNMLIGASTVSSIMSTYLCWPAFFTKAYQLETKVFSSD- 'Vitis vinifera XP_002274040' ---------------------MDFDWVMEFLRGMVKPVAALAVVLMAVALSYFQKLGLEGEMVYSILRAFLQLSVIGFVLQFIFTQANSGWILLVYFFMVSVAGYTAGQRAKHVPRGKYVAGASILAGTAVTLFLLVVLNVFPFTPRYIIPVAGMMVGNAMTVTGVTMKRLRDDIKIQLNLVETALALGATPRQATLQQMKRALVIALSPVLDNAKTVGLISLPGAMTGLIMGGASPLEAIQVQIVVMNMLVGASTVSSIMSTYLCWPAFFTKAYQLETHVFRSD- 'Zea mays NP_001146856' ------------------------GFWRDFLVGMLKPAAATAVVAMAVGLSFSQRLGLEGEMLYAIARAFLQLSAIGFVLQFIFAQKNALWILLAYLFMVTVAGYTAGQRARQVPRGKRIACVSILVGTAVTMLLLVLLDVFPFTPRYIIPVAGMMVGNAMTVTGVTMKKLREDVKIQRNLVETALALGATPRQATLQQVKRSLVIALSPVIDSAKTVGLIALPGAMTGLIMGGASPLEAIQLQIVVMNMLMGASTVSSILSTYLCWPAFFTKAFQLDDRVFAD-- ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M25151] TITLE Fagopyrum_FRD3; LINK TAXA = Taxa5; DIMENSIONS NCHAR=676; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Arabidopsis_thaliana_2g21340 ----------------MQIQCKTLTFT-VSSIPCNPKLPFPSSLTLRSWNPSFPSFRSSAVSGPKSSLKLNRFLRNCASTNQELVVDGETGNGSISELQGDAA-----------------------NGSISPVEVEAEVEEVKVDDLATQSIWGQMKEIVMFTGPAAGLWLCGPLMSLIDTAVIGQGSSLELAALGPATVICDYLCYTFMFLSVATSNLVATSLARQDK---------------------------------------------------------------------------DEVQHQISILLFIGLACGVTMMVLTRLFGSWALTAFTGVKNADIVPAANKYVQIRGLAWPAVLIGWVAQSASLGMKDSWGPLKALAVASAINGVGDVVLCTFLGYGIAGAAWATMVSQVVAAYMMMDALNKKGYSAFSFCVPSPSELLTIFGLAAPVFITMMSKVLFYTLLVYFATSMGTNIIAAHQVMLQIYTMSTVWGEPLSQTAQSFMPELLFGINRNLPKARVLLKSLVIIGATLGIVVGTIGTAVPWLFPGIFTRDKVVTSEMHKVIIPYFLALSITPSTHSLEGTLLAGRDLRYISLSMTGCLAVAGLLLMLLSNGGFGLRGCWYALVGFQWARFSLSLFRLLSRDGVLYSEDTSRY-AEKVKAA- Arabidopsis_thaliana_2g38330 --------------MAAVATSFCFSPHRSP------------SRFG-------NPNSS---------IRRTIVCKSSPRDESPAVSTSSQRPEKQ------------------------------------QNPLTSQNKPDHDHK-PDPGIGKIGMEIMSIALPAALALAADPITSLVDTAFVGHIGSAELAAVGVSVSVFNLVSKLFNVPLLN----VTTSFVAEEQAIAAK-----------------------DDNDSIETS--------------------------------------KKVLPSVSTSLVLAAGVGIAEAIALSLGSDFLMDVMAIPFDSPMRIPAEQFLRLRAYGAPPIVVALAAQGAFRGFKDTTTPLYAVVAGNVLNAVLDPILIFVLGFGISGAAAATVISEYLIAFILLWKLNEN--VVLLSPQIKVGRANQYLKSGGLLIGRTVALLVPFTLATSLAAQNGPTQMAGHQIVLEIWLAVSLLTDALAIAAQSLLATTYS--QGEYKQAREVLFGVLQVGLATGTGLAAVLFITFEPFSSLFTTDSEVLKIALSGTLFVAGSQPVNALAFVLDGLYYGVSDFGFAAYSMVIVGFISSLFMLVAAPT-FGLAGIWTGLFLFMALRLVAGAWRLGTRTGPWKMLWSAPEKPE------ Arabidopsis_thaliana_4g38380 MESSRVVVGGGLPLANRRNSSFAKPKIQQG-------TFLPLSRINNVSAPQKCSLHTNPNPMFP--FVTRRKSQTNPDCG-VVKLGEEDDS---------------------------------------CSSLDKLPEVNGVHT-GVARPVDIKRELVMLSLPAIAGQAIDPLTLLMETAYIGRLGSVELGSAGVSMAIFNTISKLFNIPLLS----VATSFVAEDIAKIAA-----------------------QDLASEDSQ------SDIPSQGLP----------------------ERKQLSSVSTALVLAIGIGIFEALALSLASGPFLRLMGIQSMSEMFIPARQFLVLRALGAPAYVVSLALQGIFRGFKDTKTPVYCLGIGNFLAVFLFPLFIYKFRMGVAGAAISSVISQYTVAILMLILLNKR--VILLPPKIGSLKFGDYLKSGGFVLGRTLSVLVTMTVATSMAARQGVFAMAAHQICMQVWLAVSLLTDALASSGQALIASSAS--KRDFEGVKEVTTFVLKIGVVTGIALAIVLGMSFSSIAGLFSKDPEVLRIVRKGVLFVAATQPITALAFIFDGLHYGMSDFPYAACSMMVVGGISSAFMLYAPAG-LGLSGVWVGLSMFMGLRMVAGFSRLMWRKGPWWFMHTSDKRLA------ Arabidopsis_thaliana_4g39030 ----------------MLIKSQRLTLF-SPLLSKTRRIPVNSHQTLVAES-VITRRTLGAITATPS------FHKNPVVIRRRIKLERVTRNCVRIDRE---------------------------------IDEEEEEEEKERGDLVKQSIWEQMKEIVKFTGPAMGMWICGPLMSLIDTVVIGQGSSIELAALGPGTVLCDHMSYVFMFLSVATSNMVATSLAKQDK---------------------------------------------------------------------------KEAQHQISVLLFIGLVCGLMMLLLTRLFGPWAVTAFTRGKNIEIVPAANKYIQIRGLAWPFILVGLVAQSASLGMKNSWGPLKALAAATIINGLGDTILCLFLGQGIAGAAWATTASQIVSAYMMMDSLNKEGYNAYSFAIPSPQELWKISALAAPVFISIFSKIAFYSFIIYCATSMGTHVLAAHQVMAQTYRMCNVWGEPLSQTAQSFMPEMLYGANRNLPKARTLLKSLMIIGATLGLVLGVIGTAVPGLFPGVYTHDKVIISEMHRLLIPFFMALSALPMTVSLEGTLLAGRDLKFVSSVMSSSFIIGCLTLMFVTRSGYGLLGCWFVLVGFQWGRFGLYLRRLLSPGGILNSDGPSPYTVEKIKSI- Arabidopsis_thaliana_FRD3 -------------------------------------------------------------------------------------MTETGD------------------------------------DLATVK-KPIPFLVIFKDLRHVFSRDTTGREILGIAFPAALALAADPIASLIDTAFVGRLGAVQLAAVGVSIAIFNQASRITIFPLVS----LTTSFVAEEDTMEK------MKEEANKANLVHAETILVQDSLEKGISSPTSNDTNQPQQPPAPDTKSNSGNKSN--------KKEKRTIRTASTAMILGLILGLVQAIFLIFSSKLLLGVMGVKPNSPMLSPAHKYLSIRALGAPALLLSLAMQGIFRGFKDTKTPLFATVVADVINIVLDPIFIFVLRLGIIGAAIAHVISQYFMTLILFVFLAKK--VNLIPPNFGDLQFGRFLKNGLLLLARTIAVTFCQTLAAAMAARLGTTPMAAFQICLQVWLTSSLLNDGLAVAGQAILACSFA--EKDYNKVTAVASRVLQMGFVLGLGLSVFVGLGLYFGAGVFSKDPAVIHLMAIGIPFIAATQPINSLAFVLDGVNFGASDFAYTAYSMVGVAAISIAAVIYMAKT-NGFIGIWIALTIYMALRAITGIARMATGTGPWRFLRGRSSSSSS----- Arabidopsis_thaliana_MATE -------------------------------------------------------------------------------------MMSEDG------------------------------------YNTDFPR--NPLYIFFSDFRSVLKFDELGLEIARIALPAALALTADPIASLVDTAFIGQIGPVELAAVGVSIALFNQVSRIAIFPLVS----ITTSFVAEEDACSS------QQD--TVRDHKECIEIGINNPTEETIELIPEKHKDSLSDEFKTSSSIFSISKP---------PAKKRNIPSASSALIIGGVLGLFQAVFLISAAKPLLSFMGVKHDSPMMRPSQRYLSLRSLGAPAVLLSLAAQGVFRGFKDTTTPLFATVIGDVTNIILDPIFIFVFRLGVTGAATAHVISQYLMCGILLWKLMGQ--VDIFNMSTKHLQFCRFMKNGFLLLMRVIAVTFCVTLSASLAAREGSTSMAAFQVCLQVWLATSLLADGYAVAGQAILASAFA--KKDYKRAAATASRVLQLGLVLGFVLAVILGAGLHFGARVFTKDDKVLHLISIGLPFVAGTQPINALAFVFDGVNFGASDFGYAAASLVMVAIVSILCLLFLSST-HGFIGLWFGLTIYMSLRAAVGFWRIGTGTGPWSFLRS------------ Fagopyrum_tataricum_FRDL1 -------------------------------------------------------------------------------------MAEKVG------------------------------------FIVAQKRKKNPLFVLFKDARMVFQFDELGKEIAQIALPAALALAADPIASLVDTAFIGHIGPIELAAVGVSIALFNQVSRIAIFPLVS----ITTSFVAEEDAKAM------AKANLQVKHESEDLEMASVCLNDETEELIPRADSEEIDQESKTET--FDIDRP---------EHHKRHIPSASSALIIGTVLGIFQAIFLIFLAKPLLNYMGIKSDSPMLHPAQQYLKLRSLGAPAVLLSLAMQGVFRGFKDTKTPLYATIAGDGTNIILDPIFIFVFRMGVSGAAIAHVISQYLISAILFWKLTQQ--VDLLPPRFKDLQFERFLKNGFLLLMRVVAATFCVTLAASMAAHEGPTPMAAFQVCLQVWLTTSLLADGLAVAGQAILASAFA--NSDYEKAKATASRVLQLGFILGLVLAIMLGFGLQFGAKLFTKDDNVLRLISIGIPFVALTQPINALAFVFDGINFGASDFLYSGYSMVTVSLFSILCLLVLSLR-HGFVGIWFALTIFMSLRAFAGFLRIGTGSGPWKFLS------------- Fagopyrum_tataricum_FRDL2 -------------------------------------------------------------------------------------MEDHQG------------------------------------GLQESHSKMIPCSVVFKDIRDVFKMDELGSEIIQIALPAALALAADPIASLIDTAFIGHLGPVELAAVGVSIAIFNQASKITIFPLVS----ITTSFVAEEDTFDK------MTVEDD------------EDKRVQGMEN------------------------------------QRRHIPSASTSIIIGVFLGLFQAFFLVIGAKPLLSVMGVKSDSPMFKPAHKYLTLRSLGSPAVLLSLAMQGVFRGFKDTKTPLYATVVGDLSNIILDPILIYVCHMGVSGAAIAHVISQYLMCCILLWRLMKK--VDLVPPTIKALQFKRFLKNGFLLLARVIAVTLCVTLAASMAARLGSTPMASFQICLQVWMTSSLLADGLAVAAQALLATAFA--EKNHDKAIAAACRVIQMGFVLGLGLALLVGLGLHFGSTIFTKDVHVLHLITIGIPFVAATQPINSIAFVMDGVNFGASDFAYTAYSMVGVAIVSIASLVVLSKS-NGFVGIWIALAIYMALRAIAGVWRIGSTTGPWSFLRINR---------- Oryza_sativa_Japonica_Group_02g0122200 ----------------MSAHLRLLSAAPLPALLPTRRLPAVPTPALAARAARLVLSRPLTEPQPPR------LPRGAAARCRGVAVAGADG------------------------------------------------DEPAAAAAGTAGLWEQVRDIVVFAGPALGLWICGPLMSLIDTMVIGQTSSLQLAALGPGTVFCDYLCYIFMFLSIATSNMVATSLAKKDE---------------------------------------------------------------------------ELAQHQVSMLLFVALTCGLGMFLFTKLFGTQVLTVFTGSGNYDIISAANTYAQIRGFAWPAVLVGLVAQSASLGMKDSWGPLKALAAASVINGVGDLLLCSVCGYGIAGAAWATMVSQIVAAFMMMQNLNKRGFRAFSFTIPSSSELLQIFEIAAPVFITMTSKVAFYALLTYSATSMGAITLAAHQVMVNVLCMCTVWGEPLSQTAQSFMPELIYGAKCNLMKARMLLKSLVMIGAITGTTVGAVGTLVPWLFPSLFTNDFMVVQQMHKVLIPYFCALLVTPSVHSLEGTLLAGRDLRFLSQSMGACFGIGTFLLMV------------------------------------------------------ Oryza_sativa_Japonica_Group_09g0548300 ME----LAGGGTGVVRQRAEPLGAGLLLRGGGRSVGGGGIGCARRATLRGLALSPLARRAVSAAGGHFLPRRAVRAAAAAGDGGFYGEEDAASDQP-------------------------------FPARASPSDDANDSTAVRSLGGDHPGEIKKELLNLALPAIVGQAIDPVAQLLETAYIGRLGPVELASAAVGVSVFNIISKLFNIPLLS----ITTSFVAEDVARHDS-----------------------DQFTSEGNM------SSESGG--------------------------RKRLPSISSAILLAAAIGVIEASALILGSEILLSIMGVSHASTMHSPAKLFLSLRALGAPAVVVSLAIQGIFRGLKDTKTPLLYSGLGNISAVLLLPFLVYSLNLGLNGAALATIASQYLGMFLLLWSLSKR--AVLLPPKIEDLDFVGYIKSGGMLLGRTLSVLITMTLGTAMAARQGTIAMAAHQICLQVWLAVSLLSDALAVSAQALIASSFA--KLDYEKVKEVTYYVLKIGLLVGAALALLLFASFGRIAELFSKDPMVLQIVGSGVLFVSASQPINALAFIFDGLHFGVSDFSYSASSMITVGAISSLFLLYAPKV-FGLPGVWAGLALFMGLRMTAGFLRLGSRAGPWWFLHQKEPTYKLHSSTC Oryza_sativa_Japonica_Group_10g0206800 -------------------------------------------------------------------------MNGESLLDRSSSADAAMN------------------------------------DAVPGHRHHHPLSVFLRDARLAFRWDELGREIMGIAVPGALALMADPVASLVDTAFIGHIGPVELAAVGVSIAVFNQVSRIAIFPLVS----VTTSFVAEEDATSS------DREKYEINGENE-----FNVSDSEMEELVSHEEASAAPSKSSFETD-SSDVKI---------EHKRKNIPSVSTALLLGGVLGLLQALLLVICAKPLLGYMGVKQGSAMLMPALKYLVVRSLGAPAVLLSLAMQGVFRGLKDTKTPLYATVAGDATNIVLDPIFMFVFQYGVSGAAIAHVISQYFIASILLWRLRLH--VDLLPPSFKHMQFSRFLKNGFLLLARVIAATCCVTLSASMAARLGSVPMAAFQICLQIWLASSLLADGLAFAGQAILASAFA--RQDHSKAAATASRILQLGLVLGLLLSIFLGIGLRLGSRLFTDDQDVLHHIYLGIPFVSLTQPINALAFVFDGINYGASDFGYAAYSMILVAIVSIIFIVTLASY-NGFVGIWIALTVYMSLRMLAGFLRIGTARGPWTFYAAQRMHSHEVVGLC Oryza_sativa_Japonica_Group_12g0106600 ------MTATSPPMRSVAAAALVLTPTPTL------------NRLS-------FPFAHRHCPSTAAPRWRPARCRGKPAVEDVVHDDEEETWRRE------------------------------------ANPERKDGGEEMLGR-GWFMVDEIGMEILTIALPAVLALAADPITALIDTAFVGHVGSTELAAVGVSISIFNLVSKLLNVPLLN----VTTSFVAEQQAVDA------------------------DYNSSVENSHIGEEISISQEKAGE----------------------QRKFLPAVSTSLALAAGIGLMETVALILGSGTLLDIVGVPVDSPMRIPAEQFLTLRAYGAPPVIVALAAQGAFRGFMDTKTPLFAVVAGNLVNALLDAIFIFPLGLGVSGAALATVTSEYLTAFILLWKLNSK--IVLFSWNIVSGDIIRYLKSGALLIARTIAVVLTFTVSTSLAAREGSVPMAGYEICLQVWLTISLLNDALALAGQALLASEYA--KGNYKKARIVLYRVLQIGGVTGAALSTTLLLGFGYLSMLFTDDAAVLDVAQTGVWFVTVSQPINAVAFVMDGLYYGVSDFAFVAYSTLFAGAISSAVLLVAAPK-FGLGGVWAGLTLFMSLRAIAGFWRLGSKGGPWKIIWSETE--------- Oryza_sativa_Japonica_Group_FRDL1 -----------------------------------------------MAGLKKMEEVTAAAAAVAASSTAEKRAAAVVVPDAALTMNGAAGAEEKTAAAAAAP-----------------EDLP-APAALSGWPRRVGLYLFVMNIRSVFKLDELGSEVLRIAVPASLALAADPLASLVDTAFIGRLGSVEIAAVGVSIAIFNQVSKVCIYPLVS----VTTSFVAEEDAIISKCIE--ENSSQDLEKAS------PVDSETNNLPVSGPDKVECVNSCIPTECTNPSDQG-----------CKRKYIPSVTSAVIVGSFLGLLQAVFLVFSAKFVLNIMGVKNDSPMLRPAVRYLTIRSLGAPAVLLSLAMQGVFRGFKDTKTPLYATVVGDAANIILDPILMFVCHMGVTGAAVAHVISQYLITMILLCRLIRQ--VDVIPPSLKSLKFGRFLGCGFLLLARVVAVTFCVTLASSLAARHGPTIMAAFQICCQLWLATSLLADGLAVAGQAVLASAFA--KNDKGKVVVATSRVLQLSIVLGMGLTVVLGVGMKFGAGIFTKDIDVIDVIHKGIPFVAGTQTINSLAFVFDGINFGASDYTYSAYSMVGVAAISIPCLVYLSAH-NGFIGIWIALTIYMSLRTIASTWRMGAARGPWVFLRK------------ Oryza_sativa_Japonica_Group_FRDL4 -----------------------------------------------MQIDELSNTCMARSSSAPESMEADHQLTATVTAAASGDMPVTEQQQQKQMVAVAAPPATENADAAGGGGGDNGDHLPPTATSLLGGARRTGLHLFVLNARSALRLDELGAEVLRIAVPASLALTADPLASLIDTAFIGRIGSVEIAAVGVAIAVFNQVMKVCIYPLVS----VTTSFVAEEDAILSKGAAGADDDNDDGHDAKGHGASAAAVADPEKQQVVGVDSAETNGAEVSTAAVRTTDDKKAAAAGVGVGKCRRRFVPSVTSALIVGAFLGLLQAVFLVAAGKPLLRIMGVKPGSPMMIPALRYLVVRSLGAPAVLLSLAMQGVFRGFKDTKTPLYATVTGDLANIALDPILIFTCRFGVVGAAIAHVISQYLITLIMLCKLVRK--VDVIPSSLKSLKFRRFLGCGFLLLARVVAVTFCVTLAASLAARHGATAMAAFQICAQVWLASSLLADGLAVAGQALLASAFA--KKDHYKVAVTTARVLQLAVVLGVGLTAFLAAGMWFGAGVFTSDAAVISTIHRGVPFVAGTQTINTLAFVFDGVNFGASDYAFAAYSMVGVAAVTIPCLVLLSSH-GGFVGIWIALAIYMSVRAFASTWRMGAARGPWKFLRK------------ ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M25150] TITLE Fagopyrum_STAR1; LINK TAXA = Taxa4; DIMENSIONS NCHAR=294; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Aegilops_tauschii_EMT05468 ------------------------------------------------------------------------------------------------------------------------------MDVLALRRKVGMLFQLPAMFDGSVGDNVRYGPQLRGKKLSEAEVKSLLSLSDLDPALSSRPASELSVGQAQRVALARPLANDPEVLLLDEPTSALDPISTQNIEEAIVRLKTARGLTTVIVSHSVKQIQRIADLVCLVVDGEVVEVLAPSALSEAKHPMARRFLELSS Arabidopsis_thaliana_STAR1 ----------------------------MPSLWSNESDGSLREHLVDVVVSGSEPKIRVHDLTRVADD-GSRILKGVTIDIPKGMIVGVIGPSGSGKSTFLRSLN--RLWEPPESTVFLDGEDITNVDVIALRRRVGMLFQLPVLFQGTVADNVRYGPNLRGEKLSDEEVYKLLSLADLDASFAKKTGAELSVGQAQRVALARTLANEPEVLLLDEPTSALDPISTENIEDVIVKLKKQRGITTVIVSHSIKQIQKVADIVCLVVDGEIVEVLKPSELSHATHPMAQRFLQLSS Fagopyrum_tataricum_STOL1 CALYCFHIKLSSLPLTASYFYELTAMSARENLQDDEEATELSILVQGDDRDTSEVKIRVRGLRKESDA-GTTILSGVDVDIPAGKIVGIVGPSGSGKSTFLRALN--RLWEPPPGTVYLDGCDICNLDVINLRRRVGMLFQLPALFQGTVADNVRYGPKLKGKRLGDDEVYKLLSFADLDSSFYHKNHNELSVGQAQRVALARTLANEPEVLLLDEPTSALDPISTQNIEDALLKLKKN-GMTIVIVSHSIKQVQRVANLVYLFDNGTVVELLEPDKLHQAKHPIALRFLQIAG Fagopyrum_tataricum_STOL2 ------PQKIQQP------------MAPSLSFQEESREHLLSVDEEAGDGDHRGVKFEVRDLVKESLT-GSTILDKVNVDIPRASIVGIIGPSGSGKSTFLRSLN--RLWEPPVGSVFLDGQDICQMDVLTLRRRVGMLFQLPALFEGTVADNVRYGPKLRGKKLSDQEVYKFLSLADLDASFYNKNHNELSIGQAQRVALARTLANEPEVLLLDEPTSALDPISTQNIESVLLKLKNSVGMTIVMVSHSIKQIQRIADVVCLLVNGSVVEVLKPEQLSEAKHPMALTFLQLSS Oryza_sativa_Japonica_Group_STAR1 MRIARIPTSIPPHLRLPLDLSAVSPMGSASEHDVREHLLDVDGVGEEGAAAAAGPKIRVRGLTRRSEARGEEILRGVDLDVPRGVVVGVIGPSGSGKSTLLRALNRLRLWEPAPGAVLLDGVDICGIDVLALRRKVGMLFQLPAMFDGTVADNVRYGPQLQGKKLTDAEVQSLLSLADLDPALCSKPASELSVGQAQRVALARTLANDPEVLL-DEPTSALDPISTQNIEEAIVRLKKTRGLTTVMVSHSVKQIQRIADLVCLLVAGEVVEVLPPSELSEAKHPMAR-FLELS- 'Populus trichocarpa XP_002325227' -------------------------------------------------KDGAEAKFRIRNLTKVSDA-GVPILNGINMDIPKGMIVGIIGPSGSGKSTVLRALN--RLWEPPSGTVFLDGHDVKDLDVLGHRRKVGMLFQLPALFDGTVADNIRYGPQLKGKKLTDDEVYKLLSLADLDSSFYKKTSNELSVGQAQRVALARTLANEPEVLLLDEPTSALDPISTQNIEDVLVKLKKQRGLTVVIVSHSIKQIQRIADVVCLLVNGEIVEVLKPDDLSEAKHPMAQRFLQLG- 'Setaria italica XP_004966143' -------------------------------------------------------KIRVR-ELRRQAAGGQEILRGVDLDVPRGVVMGVIGPSGSGKSTLLRALN--RLWEPAPGAVLLDGADICGLDVRTLRRRVGMLFQQPAMFEGTVAYNVRYGPKLRGKELTEAEVQNLLNLADLDPAMSSKPATELSVGQAQRVALARTLANEPEVLLLDEPTSALDPISTQNIEDTIVRLNKTRGLTAVIVSHSVKQIQRIADLVCLLVAGEIVEVLPPSELSSAKHPMARRFLELS- 'Solanum tuberosum XP_006366268' --------------------------------------------DIKGAAET---KIEIRGLNKVSDK-GDSILKSVRVDIPRGVIMGIIGPSGSGKSTILRALN--RLWEPPKNTVFLDGTDICDLDVLCLRRKVGMLFQLPVLFEGTVADNIRYGPKLKGKKLSDNEVYKLLTLADLDSSFFYKSGGELSVGQAQRVALARTLANEPEVLLLDEPTSALDPISTQNIEDVLVKLRKDQMMTIVIVSHSIKQIQRIADIVCLLVDGEIVEIIKPDQLSEAKHPMALRFLQLS- Triticum_uraatu_EMS52544 ---------------------------------------------------------------------------------------------------------------------------------------------------GTVADNVRYGPRLRGETLTDAQVEELLGLSDLDPALASRPASELSVGQAQRVALARTLANDPEVLLLDEPTSALDPISTQNIEEAIVRLKKARGITTVIVSHSVRQIQRIADLVCLVVDGVVVEVLPPSDLSQAKHLMARRFLELS- Vitis_vinifera_CAN70271 -----------------------------------------------------KPKFRVRNLIKVSES-GEAILRGIDVDVPKGAIVGVIGPSGSGKSTLLRVLN--RLWEPPSGTVYLDGTDIRELDVLGLRRKVGMLFQLPVLFEGTVADNIRYGPQLRGKKLTDNEVLKLLTLADLDSSFMKKTGGELSVGQAQRVALARTLANEPEVLLLDEPTSALDPISTQNIEDVIVKLKKSRGMTIVMVSHSIKQIQRIADRVCLLVDGEITEVLEPDKLSEARHPMALRFLQLSS ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M25152] TITLE Fagopyrum_ALS1; LINK TAXA = Taxa2; DIMENSIONS NCHAR=782; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 640 650 660 670 680 690 700 710 720 730 740 750 760 770 780 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Arabidopsis_thaliana_ALS1 -----------------MGNKKLLTGGSSKT--HGSGSSYRDPLLQNQEDKPKAN--GSENGLNDLEHG-VVEAANVG--------------------------FGRVFALAKPDAGKLVIGTIALLIGSTTNLLVPKFGGMIIDIVSR----DVKTPEQQTESLIAVRNAVVIILLIVVIGSICTALRAWLFNSASERVVARLRKDLFRHLMHQEIAFYDVTKTGELLSRLSEDTQIIKNAATTNLSEALRNVTTALIGVGFMFTSSWKLTLLALVVVPVISVAVKQFGRYLRELSHTTQAAAAVAASIAEESFGAVRTVRSFAKESYMVSQYSKKVDETLKLGLKQAVLVGLFFGGLNAAFTLSVITVVSYGAYLTIYGSMTVGALTSFILYSLT-----VGSSVSSLSSLYTTAMKAAGASRRVFQILDRVSSMSSSGDKCPVGNPDGDVELNDVWFAYPSRPSHMILKGISLRLTPGSKVALVGPSGGGKTTIANLIERFYDPLKGKILLNGVSLMEISHQYLHKQISIVSQEPILFNCSVEENIAYGFDG--EASFTDIENAAKMANAHEFIEAFPDKYNTVVGERGLRLSGGQKQRIAIARALLTNPSVLLLDEATSALDAESEYLVQDAMDSLMAG--RTVLVIAHRLSTVKTADCVAVIS-DGEVAEKGTHDELLSL-NGIYTNLVKR--------------------------QLQSSSSVTTL------------------------------------------------- Capsella_rubella_EOA17806_ -----------------MGNKKLLTGGSSKG--YGSGSSYRDPLLQNQ-DKTKAN--GSENGQNDLEHG-VVEAANVG--------------------------FGRVFALAKPDAGKLVIGTIALLIGSTTNLLVPKFGGMIIDIVSR----DVKTPEQQTESLIAVRNSVVIILLIVVIGSLCTALRSWLFNSASERVVARLRKDLFKHLMHQEIAFYDVTKTGELLSRLSEDTQIIKNAATTNLSEALRNVTTALIGVGFMFTSSWKLTLLALVVVPVISVAVKQFGRYLRELSHTTQAAAAVAASIAEESFGAIRTVRSFAKESYMVSQYSEKVDETLKLGLKQAVLVGLFFGGLNAAFTLSVITVVSYGAYLTIYGSMTVGALTSFILYSLTDSVLAVGSSVSSLSSLYTTAMKAAGASRRVFQILDRVSSMADSGDKCPVGNPDGDVEIDDVWFAYPSRPSHMILKGISLRLTPGSKVALVGPSGGGKTTIANLIERFYDPLKGKILLNGVSLMEISHQYLHKQISIVSQEPILFNCSVEENIAYGFDG--EASLSDVENAAKMANAHEFIEAFPDKYKTVVGERGLRLSGGQKQRIAIARALLTNPSVLLLDEATSALDAESEYLVQDAMDSLMAG--RTVLVIAHRLSTVKTADCVAVIS-DGEVAEKGTHDELLSL-NGIYTNLVKR--------------------------QLQSSSSVTNL------------------------------------------------- Fagopyrum_tataricum_ALOL1 -----------------MNFGGGGGGGGGGGGMHGFGGGERIPLLRR--EGRKRDDTLLNPSVTDLELGDAVPAANVG--------------------------FGRVISLAKPDAGKLIIATIALLIASTSSILIPKFGGKIIDIAAR----DMTKPEQKTEALNAVKSTILYIFLIVIVGSVCTALRAWLFYSSSERVVARLRKRLYSHLINQEIAFFDVTRTGELLSRLSEDTQIIKNAATTNLSEALRNLSTALIGLGFMFTTSWKLTLLALAVVPAISVAVRSFGRYLRELSHKTQAAAAAASSIAEESFGAIRTVRSFAQEEYEVEHYAEQVHETLDLGLKQAKLVGLFSGSLNAASTLSVIIVVIYGATLTINGAMTTGDLTSFILYSLT-----VGSSVSGLSGLYTVAMKAAGASRRVFQLLDRESSMQKAGDKCPLSAQDAEVQLDDVWFAYPSRPSHTVLKGITLKLETGSKVALVGPSGGGKTTIANLIERFYDPIKGRILINGVPLVEISHEHLHKKISIVSQEPTLFNCTIEQNIAYGLSG--KASITDIENAAKMANAHDFISKFPDKYQTHVGERGVRLSGGQKQRVAIARALLMDPKILLLDEATSALDAESEYLVQDAMDSLMKG--RTVLVIAHRLSTVKSANTVAVVS-DGQVVETGTHDELLKK-DGIYTALVRR--------------------------QLQQATKTEVI------------------------------------------------- Fagopyrum_tataricum_ALOL2 -----------------MGKNQHLD-WTAKS--IMSTGSERVPLLNKEVKRKKNSEQSADNNGTDVALGDVLPDTKVG--------------------------VCRVFSLAKPEGRKLAIGTVALLIASTTNLLVPKFGGIIIDIVSR----DIRTPEQQAEALQAVWNTILNIVLIVVIGSTCTAIRGWLFASASERVVARLRKELFSHLIQQEISFFDVTRTGELLSRLSEDTQIIKNAATTNFSEALRNLSTALIGLMFMFSSSWKLSLLALVVVPVILVSVRKFGRYLRELSHETQAAAAVSASIAEECFGAIRTVRSFARESYAISTYSEKVDDALTLGIRQARVVGLFFGGLNAASTLSVIIVVVYGAYLTITGSMTSGALTSFILYSLT-----VGSSISSLSGLYTTAMKAAGASRRVFQLLDRVSTMPTSGNKCPEGDVDGGVEWEWNWMMS------------------GLHILLGQPTWSSRASH--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Hordeum_vulgare_AAG49002 -----------------MVRELRINTAPR---------GNRVPLLNNGETSR---------ILSDLEEGSNVQAANVG--------------------------FCRVIKLAKHDAGKLVFATIALLVASLSNLLVPKYGGKIIDIVSR----DVQRPEDKAQALADVNGTILYIVLIVVTGSVCTALRAWLFNSASERVVARLRQDLFSHLINQEIAFFDVTRTGELLSRLSEDTQIIKNAATTNLSEALRNLTTTAIGLGFMFSTSWKLTLLALVIVPVISVAVRKFGRFLRELSHQTQAAAAVASSIAEESFGAIRTVRAFAQEPHEISRYGGKVNETLKLGLKQAKVVGLFSGGLNAASTLSVVVVVIYGANLTINGYMTTGSLTSFILYSLT-----VGSSVSALSGLYTTVMKASGASRRVFQLLDRVSSMTNTGDKCPKNENEGEVELDDVWFAYPSRPSHMILKGITLKLAPGSKVALVGPSGGGKTTIANLIERFYDPLKGRILLNGVPLVEISHQYLHQKVSIVSQEPTLFNCSIEENIAYGLEG--KASSADVENAAKMANAHDFICSFPDQYKTVVGERGIRLSGGQKQRVAIARALLMNPRVLLLDEATSALDAESEYLVQDAMDSLMKG--RTVLVIAHRLSTVKSADTVAVIS-EGQIVESGTHDELLER-DGIYTALVKR--------------------------QLQLPKFEGTANG----TAEVEPSSNGQ-------------------------------- 'Nicotiana tabacum XP_004236062' -----------------MDCQLGVQG-------HGFG-NARTPLLDRPALGRKRND-AGDGQLGDLEHGDSVPAPNVG--------------------------FGRVISLAKPEAGSLVLATIALLFAATSSILIPKFGGKIIDIVSG----DIQTPEQKSEALNAVKNTILEIFLIVIVGSVCTALRAWLFSSASERVVARLRKNLLSHLVHQEIAFFDVTRTGELLSRLSEDTQIIKNAATTNLSEALRNLATAFIGLGFMFQTSWKLTLLSLAVVPVISVAVRRFGRYMRELSHKTQAAAAVASSIAEETFGAIRTVRSFAQEDYEISRYSEKVDETLNLGLGQAKVVGLFSGSLSAASTLSVIVVVIYGATLTIQGAMTPGALTSFILYSLT-----VGSSVSGLSGLYTVAMKAAGASRRVFQILDRTSSMPKSGDLCPMGDQAAEVELDDVWFAYPSRPSHMVLKGITMKLQSGSKVALVGPSGGGKTTIANLIERFYDPVKGKILLNGVSLVEISHKHLHHKVSIVSQEPVLFNCSIEENIAYGLGG--KASSEDIEKAAKMANAHEFVSKFPEKYQTHVGERGLRLSGGQKQRIAIARALLMNPTILLLDEATSALDAESEYLVQDAMDSLMQG--RTVLVIAHRLSTVKSANTVAVIS-DGQIVESGTHDDLLNK-NGIYTALVRR--------------------------QLQGYKSDS--------------------------------------------------- Oryza_sativa_Japonica_Group_ALS1 -----------------MGKNLRIKTG------------NRAPLLAQGETSR---------ALSDLEEGSNVQPENVG--------------------------FCRVIKLARHDAGKLVIATMALLVASLSNILVPKYGGKIIDIVSR----DVRRPEDKAQALDDVTGTILYIVIIVVTGSVCTALRAWLFNSASERVVARLRKDLFSHLVNQEIAFFDVTRTGELLSRLSEDTQIIKNAATTNLSEALRNITTTSIGLGFMFATSWKLTLLALVIVPVISIAVRKFGRFLRELSHQTQAAAAVASSIAEESFGAIRTVRSFAQESHEVLRYGEKVDETLKLGLKQAKVVGMFSGGLNAASTLSVVIVVIYGANLTINGYMTTGSLTSFILYSLT-----VGSSVSALSGLYTTVMKASGASRRVFQLLDRVSSMANSGDRCPTNENDGEVELDDVWFAYPSRPSHMILKGITLKLTPGSKVALVGPSGGGKTTIANLIERFYDPLKGRILLNGVPLPEISHQFLHRKVSIVSQEPVLFNCSIEENIAYGLEG--KASSADVENAAKMANAHNFICSFPDQYKTVVGERGIRLSGGQKQRVAIARALLMNPRVLLLDEATSALDAESEYLVQDAMDSLMKG--RTVLVIAHRLSTVKSADTVAVIS-DGQIVESGTHDELLSR-DGIYTALVKR--------------------------QLQGPRFEGTSNA----TAEIEPISNGQ-------------------------------- 'Ricinus communis XP_002533538' -----------------MGKKQNLD-WTSRS--ISSSGSERVSLLSKEARRKANEDQSPDGSPNDLELGDGVEAANVG--------------------------FGRVFSLAKPDAGKLAVGTIALLIASTSSLLIPKYGGMIIDIVSR----DIKSPEEQSEALDAVKNTILDIVLIVVIGSVCTALRAWLFASASERVVARLRKNLFSHLINQEIAFFDVTRTGELLSRLSEDTQVIKNAATTNLSEALRNVTTALIGVAFMFTSSWKLTLLALAVVPLISIAVRKFGRYVRDLSHATQAAAAVAASIAEESFGAIRTVRSFAQESYTISRYSEKVDETLKLGLRQARVVGLFFGGLNAASTLSVIIVVVYGAYLTIIGSMTAGSLTSFILYSLT-----VGSSVSSLSGLYTTAMKAAGASRRVFQLLDRISSMPKSGDKCPIIDPDGDVELDDVWFAYPSRPSHMVLKGITLKLNPGSKVALVGPSGGGKTTIANLIERFYDPLKGKILLNGVPLVEISHEYLHSKVSIVSQEPVLFNCSIEENIAYGFNG--KASSSDVEAVAKMANAHEFIDKFPEKYQTVVGERGLRLSGGQKQRVAIARALLMNPKLLLLDEATSALDAESEYLVQDAMDSLMKG--RTVLVIAHRLSTVKSADIVAVIS-DGQITESGTHEELLRK-DGIYTALVRR--------------------------QLQEPNSAL--------------------------------------------------- 'Saccharomyees cerevisiae NP_013289' MIVR---MIRLCKGPKLLRSQFASASALYSTKSLFKPPMYQKAEINLIIPHR----KHFLLRSIRLQSDIAQGKKSTKPTLKLSN---------ANSKSSGFKDIKRLFVLSKPESKYIGLALLLILISSSVSMAVPSVIGKLLDLASESDGEDEEGSKSNKLYGFTKKQFFTALGAVFIIGAVANASRIIILKVTGERLVARLRTRTMKAALDQDATFLDTNRVGDLISRLSSDASIVAKSVTQNVSDGTRAIIQGFVGFGMMSFLSWKLTCVMMILAPPLGAMALIYGRKIRNLSRQLQTSVGGLTKVAEEQLNATRTIQAYGGEKNEVRRYAKEVRNVFHIGLKEAVTSGLFFGSTGLVGNTAMLSLLLVGTSMIQSGSMTVGELSSFMMYAVY-----TGSSLFGLSSFYSELMKGAGAAARVFELNDRKPLIRPTIGKDPVSLAQKPIVFKNVSFTYPTRPKHQIFKDLNITIKPGEHVCAVGPSGSGKSTIASLLLRYYDVNSGSIEFGDEDIRNFNLRKYRRLIGYVQQEPLLFNGTILDNILYCIPPEIAEQDDRIRRAIGKANCTKFLANFPDGLQTMVGARGAQLSGGQKQRIALARAFLLDPAVLILDEATSALDSQSEEIVAKNLQRRVER-GFTTISIAHRLSTIKHSTRVIVLGKHGSVVETGSFRDLIAIPNSELNALLAE--------------------------QQDEEGKGGVIDLDN------------------------------SVAREV--------- 'Saccharomyees cerevisiae NP_015053' MLNGRLPLLRLGICRNMLSRPRLAKLPSIRFRSLVTPSSSQLIPLSRLCLRSPAVGKSLILQSFRCNSSKTVPETSLPSASPISKGSARSAHAKEQSKTDDYKDIIRLFMLAKRDWKLLLTAILLLTISCSIGMSIPKVIGIVLDTLKTSSGSDFFDLKIP-IFSLPLYEFLSFFTVALLIGCAANFGRFILLRILSERVVARLRANVIKKTLHQDAEFFDNHKVGDLISRLGSDAYVVSRSMTQKVSDGVKALICGVVGVGMMCSLSPQLSILLLFFTPPVLFSASVFGKQIRNTSKDLQEATGQLTRVAEEQLSGIKTVQSFVAEGNELSRYNVAIRDIFQVGKTAAFTNAKFFTTTSLLGDLSFLTVLAYGSYLVLQSQLSIGDLTAFMLYTEY-----TGNAVFGLSTFYSEIMQGAGAASRLFELTDRKPSISPTVG-HKYKPDRGVIEFKDVSFSYPTRPSVQIFKNLNFKIAPGSSVCIVGPSGRGKSTIALLLLRYYNPTTGTITIDNQDISKLNCKSLRRHIGIVQQEPVLMSGTIRDNITYGLT--YTPTKEEIRSVAKQCFCHNFITKFPNTYDTVIGPHGTLLSGGQKQRIAIARALIKKPTILILDEATSALDVESEGAINYTFGQLMKSKSMTIVSIAHRLSTIRRSENVIVLGHDGSVVEMGKFKELYANPTSALSQLLNEKAAPGPSDQQLQIEKVIEKEDLNESKEHDDQKKDDNDDNDNNHDNDSNNQSPETKDNNSDDIEKSVEHLLKDAAKEANPIKITPQP 'Vitis vinifera XP_002277220' -----------------MASG-----------------NETAPPLNEVERQN---------ANDDLEHGLAYQAAKVG--------------------------FFRVFSLAKPEAGKLIVATIALLVASTSIVMLPKYGGMVIDIVSR----DIRTPEQQSEALTAVKNAALAVVLMVVLGSLCVAVREWLFASVSERIVAHLRKDLFSHLINQDIAFFDVTPTGELLSRLSEDSQIIKNVATSNLSSALTSITIVFIGLGFMFSSSWKLTLLVLALVPVVSVAAHVFGRYLRELSHKTQAAAAVACSMAEESFGAIQTVRSFAQEGYAISSYSEKVHETLKLALRQSKLVALFYGGINAVFTLSIVIVVVYGASLTIARSMTAGSLASFILYSLT-----VGISMLSLFGLYTTAMKAAGASRRVFQLLDRVSPMPISGHKCPLGNPDGDVELDDIWFAYPSRPSHMILKGISLKLRPGSKVALVGPSGGGKTTIASLIERFYDPLKGKILLNGVPLVEISHKYLHKKISIVSQEPVLFNCSVEENIAYGFDG--KASSSEIENAAKMANAHDFIANFPEKYRTVVGERGLRLSGGQKQRIAIARALLMDPRVLLLDEATSALDAESEYLVQDAMESLMRG--RTVLVIAHRLSTVKTADIVAVIC-DGRIAQSGSHEELLSK-NGIYTGLVKR--------------------------QLQGPSTPH--------------------------------------------------- 'Zea mays NP_001151774 ' -----------------MGKNMRIKTAPK---------ANRVPLLGDGETSR---------ALSDLEEGSDVQPANVG--------------------------FCRVIKLAKHDAGKLVLATAALLVASLSNLLVPKYGGKIIDIVSR----DVRRPEDKAQALEDVKGTILYIVTIVLVGSVCTALRAWLFNSASERVVARLRKDLFSHLINQEIAFFDVTRTGELLSRLSEDTQIIKNAATTNLSEALRNVTTTAIGLGFMFSTSWKLTLLALVIVPVISVAVRRFGRFLRELSHQTQAAAAVASSIAEESFGAIRTVRSFAQEYHEISRYGEKVEETLKLGLKQAKVVGLFSGGLNAASTMSVVIVVIYGANLTINGYMTTGSLTSFILYSLT-----VGSSVSALSGLYTTVMKASGASRRVFQLLDRVSSMTNSGDKCPINEKDGEVELDDVWFAYPSRPSHMILKGITLKLAPGSKVALVGPSGGGKTTIANLIERFYDPLKGRILLNGVPLAEISHQYLHSKVSIVSQEPTLFNCTIEENIAYGLEG--TTNFADVESAAEMANAHNFICGFPDQYKTVVGERGIRLSGGQKQRIAIARALLMNPRVLLLDEATSALDAESEYLVQDAMDSLMKG--RTVLVIAHRLSTVKSADTVAVIS-DGLIVESGTHDELLDR-DGIYTALVKR--------------------------QLQGPKFEATSSISEASEIEAEPSSNGQ-------------------------------- ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M25148] TITLE Fagopyrum_ART1; LINK TAXA = Taxa3; DIMENSIONS NCHAR=563; FORMAT DATATYPE=Protein SYMBOLS= "A C D E F G H I K L M N P Q R S T V W Y" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Aegilops_tauschii_EMT26835 ----------------------MASDASGNTE-PGQQGVRFSSMDQSCFARPGQSIPGYPPFFGPQSSNFYLPDDSV-------------AKACDLFEPNPPQNNPVADWDPQAMLSNLTFLEQKIKQVKDIVQSMGNRGSQDAGGSCELAAK-QQLVTADLTSIIIQLISTAGSMLPSMKTP-LLSSNPAVRQLN-TPGSPMGFGSIVNQRPSTIREEVVNDISKTSDYEELMNTLNTAHDEKDDLIKCPNPCVGEGPEPVPMEDHDVKESDDGGEAEHLPPGS----YVVLQLEKEEILAPHTHFCVICGKGFKRDANLRMHMRGHGDEYKTPAALAKPMRD---SGSDPTPVTRYSCPYVGCKRNKEHRKFQPLKTILCVKNHYKRSHCDKRYTCSRCNTKKFSVIADLKTHEKHCGRDKWLCSCGTTFSRKDKLFGHVALFQGHTPALPMDDIKASGALEQPQGSEA----MDDMVASTGYNFPGSTSDGIPNLDMKVADDTRGYFSPLNFDPC-FGALDDFARPGFDISENPFSFLPSGPGSCSFGQLSGDS------ Arabidopsis_thaliana_STOP1 -METEDDLCNTNWGSSS-----SKSREPGSSD-CGNSTFAGFT---SQQKWEDASILDYEMGVEPGLQESIQANVDF------------------------LQGVRAQAWDPRTMLSNLSFMEQKIHQLQDLVHLLVGRGGQLQGRQDELAAQQQQLITTDLTSIIIQLISTAGSLLPSVKHN-MS--TAPGPFTGQPGSAVFPYVREANNVASQSQNN--NNCGAREFDLPKPVLVDEREG-------------------HVVEEHEMKDEDDVEEGENLPPGS----YEILQLEKEEILAPHTHFCTICGKGFKRDANLRMHMRGHGDEYKTAAALAKPNKESV-PGSEPMLIKRYSCPFLGCKRNKEHKKFQPLKTILCVKNHYKRTHCDKSFTCSRCHTKKFSVIADLKTHEKHCGKNKWLCSCGTTFSRKDKLFGHIALFQGHTPAIPLEETKPSASTSTQRGSSEGGNNNQGMVGFNLGSASNANQETTQPGMTDGRICFEESFSPMNFDTCNFGGFHEFPRLMFDDSESSFQMLIANACGFSPRNVGESVSDTSL- 'Brachypodium distachyon XP_003564719' MESGMRRSSETSVKALS----SMASEASRNTD-PGQQGLRFNSTDQSYFARAGQSIPVFPPFFGPQSSSFCLPDGSG-------------AKVGGQFEPNPSLNNPISDWDPQAMLSNLSFLEQKIKQVKDVVQSMSNRGSQVVGGSGELAAK-QQLVTADLTCIIIQLISTAGSMLPSMKSP-LLSSNPAVRQLSNTLGSPMGFGSIANQRPSINKEQTIPDITKTSDYEELMNTINTTHDGKDDLIKCPNPCVGEGSDPIPFEDHDVKESDDGGEGENLPPGS----YVVLQLEKEEILAPHTHFCVICGKGFKRDANLRMHMRGHGDEYKTPAALAKPMKD---SSSDHTPVTRYSCPFVGCKRNKEHRKFQPLKTILCVKNHYKRSHCDKSYTCSRCNTKKFSVIADLKTHEKHCGRDKWLCSCGTTFSRKDKLFGHVALFQGHTPALPMDDIKGTCVSDQPEGSEV----MDDMVGSTGYNFPGSASDGIPNLDMKVADDVRGYFSPLSFDPC-FGALDDFTRPGFDISENPFSFLPSGPGSCSFGQPSGDS------ Fagopyrum_tataricum_ARL1 -MEQKEGSSEDSWTKPM-----SFMASTQSLL-FNDQSFGVANSQQREQNWENSPMLDYGALMESLLSKFDQTSRTP----------------------PFLEEKIHQDWDPTAMLSNLSFLEEKIHQLQELVHIFVARRGQVSTCTDELATR-QQLITADVTTIFVQLISMAGNLLPSPK-----------------IDLVADEVEENG-GLNKSLNQ--TNCGAMENDS------------------------------CMIDDHELKDDDEPNDEEHLPPGS----YEILQLEKEEILAPHTHFCTICGKGFKRDANLRMHMRGHGDEYKTPAALAKPLKDS--NSSEPVLPKRYSCPYMGCKRNKDHKKFQPLKTILCVKNHYKRTHCDKTYTCSRCNTKKFSVIADLKTHEKHCGREKWLCSCGTTFSRKDKLFGHIALFQGHTPAIPIEFNKGSAATSSNPVENN-------EPSINKDGMDFSFISDNSYGNATRNIMDDSYFSLSSFDGCNIL--QEFSQSSFDDPGTSFPFLLSGCKNGLQSGTDDIDS----- Fagopyrum_tataricum_ARL2 -MEPEKG---ESWAKAM-----PFMGLTQNLS-FSNQSFNVANLQQCEQNWENN--------MFSQFNDQNKIPHAD----------------------DGLNNNNNQDWDPKATLSNLSFLEQKIHQLQELVHIIVGHRSQVTVGVNELATQ-QQLITANLTSIIMQLTSTAASLLPSVNN-------------GQLNDVFFPPAQKNMSDVNTHVQN--CQVGPTENRGET-----EKSY-------------------NCMDGHELKEED---DEEHLPPGS----YEILQLEKEEILAPHAHFCTICGKGFKRNANLRMHMRGHGDEYKTLAALAKPQKES--EELEPVILKRYSCPSRGCKRNKEHKRFQPLKTLLCVKNHYKRTHCDKTYICSRCNTKKFSIISDLKTHEKHCGKDKWLCSCGTSFSRKDKLFGHIALFQGHTPALPYEENKVLVGSSSDPAENG-------EASNNK--LESMTFSDDSNG----------FGVFMGFDGCNMVGLQEYAQSAYDDSETSFPFLQ--------------------- Lotus_japonicus_BAN67817 -MDSKGSLRATTWAKSSSLTTSAENGLQTNISSADSFSLPGFGSLHNQHKWPDPSISDYGVREEAPLQGFSQPSQAQTLLPCDTNNKIKIPDQENCPLSESSQTNRLQNWDPSVMLYNLSFLENKIHELQDLVHLIVSQK----DQPNEIVTQEQQLITTDLTSIIVQLISTAGSLLPSVRQT-LINGNPLVGQLGQLCGIAVPSGSGPSSSCIQPQNNNGNKLSDQSMQNDLPSNREMEQN-------------------Y-MEEHEYKDE-DADDGDNLPPGS----YEILQLEKEEILAPHAHFCTICGKGFKRDANLRMHMRGHGDEYKTPAALAKPHKE---SGSQPKLIKRYSCPYHGCKRNKDHKKFLPLKTILCVKNHYKRTHCDKSYTCSRCNTKKFSVLADLKTHEKHCGKDKWLCSCGTTFSRKDKLFGHIALFQGHTPAIPLDESKENNKVG-------------GMNSCLVSNPSTENGVQNIMDARANIDDPISYLSSLNFEAN-FGAFNEFTRPPPEESESSFSFFMPGSFKPGGESSRDNIL----- Nicotiana_tabacum_BAN67816 -MDPDDSLSEDPWTKPS----SSGNELLKIVP-SDNHSFTNFN--LHAQKWEGSSYLDQQTRIEQQFSGFTQPKHTY------------QMDQHGNQMNENHDSTSTKDWDPSNLLNNLSFLEQKIHQLQELVHLIVGRRGQTGLQGNDLIVQQQQLITADLTSIIVQLVSTAGSLLPTMKHS-LSSVSHAASQLVQFGGVTVPSATCTNGGGLPCNDGGVTKVEDQSNHVDQLRDCGIEQS-------------------HAVDGHESKDEDEAEEEENLPPGS----YEILQLEKEEILAPHTHFCTICGKGFKRDANLRMHMRGHGDEYKTPAALAKPHKE---PSSEPTLIKRYSCPNVGCKRNKEHKKFQPLKTILCVKNHYKRTHCEKAYTCSRCNIKKFSVIADLKTHEKHCGKDKWLCSCGTTFSRKDKLFGHIALFQGHTPAVPLDETKGSAGTSDRGQTSE--VTMKARQEDFKVNASHGNEFQDPRDIKSAADDPGSYFSPLNFDTSNLNGFQEFPRPPFDESDSSFSFLLSGSCEYPPHKAAKYMSFTELE Oryza_sativa_Japonica_GroupART1 -MD--------------------RDQMTNTMR-DQAANLTSMNPLFYPFMADDALLG-----MAPPPPQQLLPSVSI----------------------------QHMDWSPDTMLDNLTFIEEKIRQVKDVIRSMAGRR----ASSSSAATPEQQLVNADLTCLIVQLISTAGSLLPSLKNSSFLSRTTPPPAAAAGAAQAVSLAAGESSSSARNNETNREDEEEQMGSPDYDELFKVWTNG------------------GAMDECVGAAGDEQDARENPAAAAEEEKYEVLQLEEDEILAPHTHFCGICGKGFKRDANLRMHMRGHGDEYKSAAALAKPPPPPEGEEQPPQPERRYSCPHAGCKRNRMHASFQPLKTILCVKNHYKRSHCEKRHVCGRCGAKRFSVMADLKTHEKHCGRDRWLCSCGTSFSRKDKLFAHVALFQGHAPALPPPPPPPTSGRRRHKQEEP-------EFTWGGGGGNEFLDVKGIAGVGSGSGGGDEFFSAGSFGAMDFG---------FGQLDASLAMLLPSEQFAGDHQEENGDK----- 'Ricinus communis XP_002526844' -MDRKERLCTETWANSS----SSGSGLPEHLS-TEKPSFANFSSQQDQQKWEDTAI--YGIRTDPPFQEFNLPSETQTLLPSNPDDQIKIMDEEDSHINEALQINKIPDWDPKAMLSNLSFLEQKIHQLQDLVHLIVGRRGQILERPDDLVAQQQQLITADLTSIIVQLISTAGSLLPSVKHT-LFAATP-GGQLGHLGEILFPSGMG-MNSIVQPQHSSGNKLSHHSNQMDISGNCGTEQN-------------------YSVDEHELKDEEDVEEGENLPPGS----YEILQLEKEEILAPHTHFCTICGKGFKRDANLRMHMRGHGDEYKTPAALAKPNKE---SSSEP-VLKRYSCPFAGCKRNKDHKNYN-----LGIG-----------YLSPPLNNLKINKMAI-------------------------------------------------------------------------------------------------------------------------------------------------------- 'Solanum lycopersicum XP_004250372' -MDPDDSLSEDPWIKSS----SSGNELLKIMP-SDNHSFTNLN--LHEQKWEGSSYLDQEIRIEQQFTGFAKPKHTS------------EMDQQG---NQNHDTTRIHDWDPRALLNNLSFLEQKIHQLQELVHLIVGRRGQDEVQGNDLIVQQQQLITADLTSIIVQLISTAGSLLPTMKYT-LSSAIPAASQLGQVGGVTVPSTAGTSAGGLTCNDG-VAKLEDQSNHIDQLRDCGIEHN-------------------HAADEHELKDEDEAEEEENLPPGS----YEILQLEKEEILAPHTHFCTICGKGFKRDANLRMHMRGHGDEYKTPAALAKPHKE---PSSEPTLIKRYSCPYVGCKRNKEHKKFQPLKTILCVKNHYKRTHCEKAYTCSRCNIKKFSVIADLKTHEKHCGKDKWLCSCGTTFSRKDKLFGHISLFQGHTPAVSPDETKGSAGTSDRGQTGE--VTMKARQENYKVNASLGNEFQNPGVVKECPYNPSSYFSPLNFDTSNLNGFQEFPRPPFDESDSSFSFLLSGSCEYPPHKAAKFMSSSEME Triticum_aestivum_AGS15193 ------------MKASS----SMASDASGNTD-PGQQGARFSSMDQSCFARPGQSIPGYPPFFGPQSSNFYLPDDSV-------------AKACDPFEPNPPQNNPVADWDPQAMLSNLTFLEQKIKQVKDIVQSMGNRGSQDVGGSCELAAK-QQLVTADLTSIIIQLISTAGSMLPSMKTP-LLSSNPAVRQLN-TPGSPMGFGSIVNQRPSTVREEMVPDITKTPDYEDLMNTLNPAHDEKDDLIKCPNPCVGEGPEPVPMEDHDVKESDDGGEAEHLPPGS----YVVLQLEKEEILAPHTHFCVICGKGFKRDANLRMHMRGHGDEYKTPAALAKPMRD---SVSDPTPVTRYSCPYVGCKRNKEHRKFQPLKTILCVKNHYKRSHCDKRYTCSRCNTKKFSVIADLKTHEKHCGRDKWLCSCGTTFSRKDKLFGHVALFQGHTPALPMDDIKATGASE--QRSEA----MDDMVGSTGYNFPGSTSDGIPNLDMKVADDTRGYFSPLNFDPC-FGALDDFARPGFDISENPFSFLPSGPGSCSFGQLSGDS------ Zea_mays_ACN25425 -MEGRMTSLEATMKVSS----SMASSISRNAD-PDQQTLRPNSVEQFYFPRPGQSLPGIPPFFGPPSSSLYLPNDNE-------------AKFGNQFESNPSQN---TDWDPQAIVSNLTFLEQKIKQVKDIVQSMSNRENQLAGGSSELAAK-QHLVTADLTSIIIQLISTAGSLLPSMKNP-LLSSNPAVRQLGNTLGSPMGLGMNANQRPSVDSKTDIPDTGKTSDYDELMNSLNPAQDERDEMIKCPNPCGGEGSEPTPMEDHDVKESDDGGEGENLPPGS----YVVLQLEKEEILAPHTHFCLICGKGFKRDANLRMHMRGHGDEYKTPAALAKPTKD---SGADHAPVTRYSCPFVGCKRNKEHKKFQPLKTILCVKNHYKRSHCDKSYTCSRCNTKKFSVIADLKTHEKHCGRDKWLCSCGTTFSRKDKLFGHVALFQGHTPALPMEDVKVSEASEQPQDSEP----MNEMARSNMYSFPCSSSDGISNLDMKMADDVRGYFSPLNFDPC-FGALDDFTRPGFDISENPFSFLPSG--SCSYGQQNGDS------ ; END; BEGIN TREES; TITLE Fagopyrum_FRD3; LINK TAXA = Taxa5; TRANSLATE 1 Fagopyrum_tataricum_FRDL1, 2 Fagopyrum_tataricum_FRDL2, 3 Oryza_sativa_Japonica_Group_FRDL1, 4 Oryza_sativa_Japonica_Group_FRDL4, 5 Oryza_sativa_Japonica_Group_12g0106600, 6 Oryza_sativa_Japonica_Group_09g0548300, 7 Oryza_sativa_Japonica_Group_10g0206800, 8 Oryza_sativa_Japonica_Group_02g0122200, 9 Arabidopsis_thaliana_MATE, 10 Arabidopsis_thaliana_FRD3, 11 Arabidopsis_thaliana_2g38330, 12 Arabidopsis_thaliana_4g38380, 13 Arabidopsis_thaliana_2g21340, 14 Arabidopsis_thaliana_4g39030; TREE FRD3 = [&R] ((((((2,9),7),(1,10)),(4,3)),((5,11),(12,6))),(8,(13,14))); END; BEGIN TREES; TITLE Fagopyrum_ART1; LINK TAXA = Taxa3; TRANSLATE 1 Fagopyrum_tataricum_ARL1, 2 Fagopyrum_tataricum_ARL2, 3 Oryza_sativa_Japonica_GroupART1, 4 Arabidopsis_thaliana_STOP1, 5 Nicotiana_tabacum_BAN67816, 6 'Solanum lycopersicum XP_004250372', 7 Lotus_japonicus_BAN67817, 8 'Ricinus communis XP_002526844', 9 Aegilops_tauschii_EMT26835, 10 'Brachypodium distachyon XP_003564719', 11 Zea_mays_ACN25425, 12 Triticum_aestivum_AGS15193; TREE ART1 = [&R] (((1,(2,3)),(4,(5,6))),((7,(8,9)),(10,(11,12)))); END; BEGIN TREES; TITLE Fagopyrum_STAR1; LINK TAXA = Taxa4; TRANSLATE 1 Fagopyrum_tataricum_STOL1, 2 Fagopyrum_tataricum_STOL2, 3 Vitis_vinifera_CAN70271, 4 'Populus trichocarpa XP_002325227', 5 'Solanum tuberosum XP_006366268', 6 Arabidopsis_thaliana_STAR1, 7 Aegilops_tauschii_EMT05468, 8 'Setaria italica XP_004966143', 9 Triticum_uraatu_EMS52544, 10 Oryza_sativa_Japonica_Group_STAR1; TREE STAR1 = [&R] (((((1,2),4),(3,5)),6),(8,((7,9),10))); END; BEGIN TREES; TITLE Fagopyrum_ALS1; LINK TAXA = Taxa2; TRANSLATE 1 'Nicotiana tabacum XP_004236062', 2 Hordeum_vulgare_AAG49002, 3 Oryza_sativa_Japonica_Group_ALS1, 4 'Zea mays NP_001151774 ', 5 'Ricinus communis XP_002533538', 6 Arabidopsis_thaliana_ALS1, 7 Capsella_rubella_EOA17806_, 8 'Vitis vinifera XP_002277220', 9 Fagopyrum_tataricum_ALOL1, 10 Fagopyrum_tataricum_ALOL2, 11 'Saccharomyees cerevisiae NP_013289', 12 'Saccharomyees cerevisiae NP_015053'; TREE ALS1 = [&R] ((((((4,3),2),(1,9)),((5,10),(7,6))),8),(11,12)); END; BEGIN TREES; TITLE Fagopyrum_STAR2; LINK TAXA = Taxa1; TRANSLATE 1 Fagopyrum_tataricum_STAR2, 2 Arabidopsis_thaliana_ALS3, 3 Oryza_sativa_Japonica_Group_STAR2, 4 'Theobroma cacao XP_007027163', 5 'Vitis vinifera XP_002274040', 6 'Zea mays NP_001146856', 7 'Sorghum bicolor XP_002440497'; TREE STAR2 = [&R] (((1,(4,5)),2),(3,(6,7))); END;