#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; 1:01 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 15405 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep15405;
        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 CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M25152]

	TITLE Fagopyrum_ALS1;
	LINK TAXA = TaxaForAnalysisStep15405;
	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;

[ The following blocks are output data for analysis step 15405 ]
BEGIN TREES;
      TITLE Fagopyrum_ALS1;
      LINK TAXA = TaxaForAnalysisStep15405;
      TREE ALS1 = [&R] (((((('Zea mays NP_001151774 ',Oryza_sativa_Japonica_Group_ALS1),Hordeum_vulgare_AAG49002),('Nicotiana tabacum XP_004236062',Fagopyrum_tataricum_ALOL1)),(('Ricinus communis XP_002533538',Fagopyrum_tataricum_ALOL2),(Capsella_rubella_EOA17806_,Arabidopsis_thaliana_ALS1))),'Vitis vinifera XP_002277220'),('Saccharomyees cerevisiae NP_013289','Saccharomyees cerevisiae NP_015053'));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr79953]


END;