#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; 1:39 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 15401 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep15401;
        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 CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M25148]

	TITLE Fagopyrum_ART1;
	LINK TAXA = TaxaForAnalysisStep15401;
	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;

[ The following blocks are output data for analysis step 15401 ]
BEGIN TREES;
      TITLE Fagopyrum_ART1;
      LINK TAXA = TaxaForAnalysisStep15401;
      TREE ART1 = [&R] (((Fagopyrum_tataricum_ARL1,(Fagopyrum_tataricum_ARL2,Oryza_sativa_Japonica_GroupART1)),(Arabidopsis_thaliana_STOP1,(Nicotiana_tabacum_BAN67816,'Solanum lycopersicum XP_004250372'))),((Lotus_japonicus_BAN67817,('Ricinus communis XP_002526844',Aegilops_tauschii_EMT26835)),('Brachypodium distachyon XP_003564719',(Zea_mays_ACN25425,Triticum_aestivum_AGS15193))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr79949]


END;