#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 May 06, 2024; 9:50 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]

[ The following blocks are input data for analysis step 15404 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep15404;
        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:M25151]

	TITLE Fagopyrum_FRD3;
	LINK TAXA = TaxaForAnalysisStep15404;
	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;

[ The following blocks are output data for analysis step 15404 ]
BEGIN TREES;
      TITLE Fagopyrum_FRD3;
      LINK TAXA = TaxaForAnalysisStep15404;
      TREE FRD3 = [&R] ((((((Fagopyrum_tataricum_FRDL2,Arabidopsis_thaliana_MATE),Oryza_sativa_Japonica_Group_10g0206800),(Fagopyrum_tataricum_FRDL1,Arabidopsis_thaliana_FRD3)),(Oryza_sativa_Japonica_Group_FRDL4,Oryza_sativa_Japonica_Group_FRDL1)),((Oryza_sativa_Japonica_Group_12g0106600,Arabidopsis_thaliana_2g38330),(Arabidopsis_thaliana_4g38380,Oryza_sativa_Japonica_Group_09g0548300))),(Oryza_sativa_Japonica_Group_02g0122200,(Arabidopsis_thaliana_2g21340,Arabidopsis_thaliana_4g39030)));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr79952]


END;