#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 July 30, 2025; 20:59 GMT

TreeBASE (cc) 1994-2008

Study reference:
Freixas-coutin J.A., Munholland S., Silva A., Subedi S., Lukens L., Crosby W.L.,
Pauls K.P., & Bozzo G.G. 2017. Proanthocyanidin accumulation and transcriptional
responses in the seed coat of cranberry beans (Phaseolus vulgaris L.) with different
susceptibility to postharvest darkening. BMC Plant Biology, .

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S20776]

[ The following blocks are input data for analysis step 20538 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep20538;
        DIMENSIONS NTAX=17;
        TAXLABELS
            Arabidopsis_thaliana_ANR
            Brassica_napus_A.BANa
            Brassica_napus_A.BANb
            Brassica_napus_C.BANa
            Brassica_napus_C.BANb
            Camellia_sinensis_ANR1
            Fragaria_x_ananassa_ANR
            Glycine_max_ANR1
            Glycine_max_ANR2
            Lotus_corniculatus_ANR
            Malus_domestica_ANR
            Medicago_truncatula_ANR
            Phaseolus_vulgaris_ANR1
            Phaseolus_vulgaris_ANR2
            Pisum_sativum_ANR
            Vitis_bellula_ANR
            Vitis_vinifera_ANR1
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M40736]

	TITLE ANR_amino_acid_sequences_and_alignments;
	LINK TAXA = TaxaForAnalysisStep20538;
	DIMENSIONS NCHAR=347;
	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       ]
[                                     .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .       ]
Arabidopsis_thaliana_ANR     ---MDQTLTHTGSKKACVIGGTGNLASILIKHLLQSGYKVNTTVRDPENEKKIAHLRQLQELGDLKIFKADLTDEDSFESSFSGCEYIFHVATPINFKSEDPEKDMIKPAIQGVINVLKSCLKSKSVKRVIYTSSAAAVSINNLSGTGLVMNEENWTDIDFLTEEKPFNWGYPISKVLAEKKAWEFAEENKINLVTVIPALIAGNSLLSDPP-SSLSLSMSFITGKEMHVTG-LKEMQKLSGSISFVHVDDLARAHLFLAEKETASGRYICCAYNTSVPEIADFLIQRYPKYNVLSEFEEGLSIPKLTLSSQKLINEGFRFEYGINEMYDQMIEYFESKGLIKAKES
Brassica_napus_A.BANa        ---MTSTDQTTGTKKVCVIGGTGNLASILIDRLLQSGYEVNTTVRDPENEKKMAVLRVLQEQGDLNIFKADLTDEGSFNSPVSGCEYVFHVATPISFTSQDPEKDMINPAIQGVINVLKSCLNSNSVKRVIYTSSAAAVSINNLSGPGLVMTEENWSDIDFLRKEKPFNWAYPISKVLAEKAAYQFAQENKIDLVTVVPALIAGNTLIDDPPPSSLSLSMSLITRKEMHLNA-LKEMQKLSGSISFIHVDDLACAHLFLAEKETASGRYICCSYNTNIPELADFLRKRYPRYNVLSEFEECLSTAKLTLSSEKLINEGFQFEHDVEEMYDQMVEHFKTNRWA-----
Brassica_napus_A.BANb        MATVDQTAVTTGTKKACVIGGTGNLASILIKHLLQSGYKVNTTVRDPENEKKMAHLKVLQQLGDLKIFKADLTDEGSFTSPISGCEYVFHVATPISFTSQDPEKDMIKPAVQGVINVLKSCLKSNSIKRVIYTSSAAAVSINNLSEPGLVMTEENWSDVDFLTKEKPFNWGYPVSKTLAEKEAYKFAEENKIDLVTVVPALIAGNSLLSDPP-SSLSLSMSLITGKEMHLSG-LKEMQKLSGSISFIHVDDLARAHMFLAEKETASGRYICCYYNTNVPEIADFLRRRYTKYNVLSEFEECLSSAKLTLSSEKLIKEGFRFEYGISEMYDEMTEYFESKGLIKP---
Brassica_napus_C.BANa        ---MTSTDQTTGTKKVCVIGGTGNLASILIDRLLQSGYEVNTTVRDPENVKKMAVLRVLQEQGDLNIFKADLTDEGSFNSPVSGCEYVFHVATPISFTTQDPEKDMINPAIQGVINVLKSCLNSNSVKRVIYTSSAAAVSINNLSGPGLVMTEENWSDIDFLRKEKPFNWAYPISKVLAEKAAYQFAQENNIDLVTVVPALIAGNTLIDDPPPSSLSLSMSLITRKEMHLNA-LKEMQKLSGSISFIHVDDLACAHLFLAEKETASGRYICCSYNTNIPELADFLRKRYPRYNVLSEFEECLATAKLTLSSEKLINEGFEFEHDIDEMYDQMVEYFKTNRWA-----
Brassica_napus_C.BANb        MATVDQTAVTTGTKKACVIGGTGNLASILIKHLLQSGYKVNTTVRDPENEKKMAHLKVLQELGDLKIFKADLTDEGSFTSPISGCEYVFHVATPISFTSQDPEKDMIKPAVQGVINVLKSCLKSNSIKRVIYTSSAAAVSINSISEPGLVMTEENWSDVDFLTKEKPFNWGYPVSKTLAEKEAYKFAEENKIDLVTVVPALIAGNSLLSDPP-SSLSLSMSLITGKEMHLSG-LKEMQKLSGSISFIHVDDLARAHMFLAEKETASGRYICCYYNTNVPEIADFLRRRYPMYNVLSEFEEGLSSAKLTLSSEKLIKEGFRFEYGISEMYDEMTKYFESKGLIKP---
Camellia_sinensis_ANR1       -----MEAQPTAPKAACVVGGTGFVAATLIKLLLEKGYAVNTTVRDPGNQKKTSHLLALKGSGNLKIFRADLTDEQSFDTPVAGCDLVFHVATPVNFASEDPENDMIKPAIQGVVNVLKACAKAGTVKRVILTSSAAAVSINKLNGTGLVMDESHWTDTEFLNSAKPPTWGYPLSKTLAEKAAWKFAEENNINLITVIPTLMAGPSLTADVP-SSIGLAMSLITGNEFLING-LKGMQMLSGSISISHVEDVCRAHVFVAEKESASGRYICCAVNTSVPELAKFLNKRYPEYNVPTDFGDFPSKAKLILSSEKLTKEGFSFKYGIEEIYDQSVEYFKAKGILKN---
Fragaria_x_ananassa_ANR      ---MATTQPIISTKSACVIGGTGFVASQLIKLLLEKGYAVRTTVRDPDNLKKISHLTALQELGELTIFRGDLTDEGSFDAAIAGSDLVFHVATPVHFGSPDPENDMIKPGVQGVLNVMKSCVKAKTVKRVVLTSSAAAVTVNTLSGTGLIADENDWSDVEFLTTAKPPTWGYPVSKVLAEKTAWKFAEENNIDLITVIPSLMAGASLTPDIP-SSIGLATSLITGNEFLING-LKGMQMLSGSISITHVEDVCRAHIFLAEKESASGRYICCAENSSVPEVAKFLSKRYPEYKVPTEFGDFPSKAKTILSSEKLKKEGFTFKYGIEDIYDQTVEYLKLKGVLQN---
Glycine_max_ANR1             ---MATIKPTG--KKACVIGGSGFMASLLIKQLLEKGYAVNTTVRDPDNTKKIPHLLALQSLGELNIFGADLTGEKDFDVPIAGCELVFQLATPVNFAFEDPENDMIKPAITGVLNVLKACVRAKGVKRVILTFSAVAVTINQLKGTDLVMDESNWTDVEYLSTAKPPTGGYPASKALAEKAAWKFDEENHIDLITVIPTLTTGPSVTTDIP-SSVGMAASLITGNDFFINV-LKGMQLLSGSISITHVEDICRAQIFVAEKESASGRYICCAHNTSVPELAKFLSKRYPQYKIPTEFDDCPSKAKLIISSEKLVKEGFSFKYGIEEIYDQTLEYLKSKGALNN---
Glycine_max_ANR2             ---MANIKQIGK-KQACVIGGSGFIASLLIKQLLQKGYAVNTTVRDLGSINKIAHLLVLKNLGELKIFRADLTVEGDFEAPISGCELVFQFATPMNFGSEDPENDMIKPAISGVLNVLKTCAQTKEVKRVILTSSTDAVTINQLNGKGHVMDESNWTDVEYLTTAKPHGWGYPASKTLAEKAAWKFAEENHIDLITVIPSLTAGPSITADIP-FSVVLAASLMKGNDFYIKS-LREMQLLSGSISITHVEDICRAHIFVAEKESASGRYIVCAHNTSVPELAKFLSERYPRYEIPTEFHDIPSKAKLVISSEKLIKEGFSFKYGIEEIINQSVEYLRSEGALLN---
Lotus_corniculatus_ANR       ---MASIKPIYEKKKACVIGGTGFVASLLIKQLLEKGYAVNTTVRDPDNHKKISHLLALQSLGELNIFGGELTVENDFDTPIEGSELVFQLATPVNFASEDPENDMIKPAIKGVLNVLKSCARAK-VKRVILTSSAASVTISELKGTDLVMDESNWTDVEFLSNAKPPTWGYPASKTLAEKAAWKFAEENHIDLITVIPSLITGPSLTPDIP-SSVGLATSLITGNDFLINA-MKGMQLLSGSISITHVEDVCRAHIFVAEKQSASGRYICCAHNTSVPELAKFLNKRYPQYKVSTEFNDFPAKAKLIISPEKLIKEGFSFKYGVEEIFDQTLEYLKTKGALKN---
Malus_domestica_ANR          ----MATQQPISKKTACVVGGTGFVASLLVKLLLQKGYAVRTTVRDPDNHKKVSHLTALQELGELEILAGDLTDEGSFDAPIAGCDLVFHVATPVNFASEDPENDMIKPAIQGVLNVLKSCVKAKTVKRVVLTSSAATVSINTLEGTGLVMDEKDWSDLEFLTTVKPPTWGYPASKTLAEKTAWKFAEENNIDLITVIPSLMAGPSLTPDVP-SSIGLAMSLITGNDFLINMALKGMQMLSGSISISHVEDVCRAHIFLAEKESASGRYICCAANTSVPELARFLNKRYPQYKVPTEFGDFPSKAKLIISSEKLIQEGFDFKYGIEEIYDQTVEYFKAKGLLQN---
Medicago_truncatula_ANR      -MASIKQIEIEK-KKACVIGGTGFVASLLIKQLLEKGYAVNTTVRDLDSANKTSHLIALQSLGELNLFKAELTIEEDFDAPISGCELVFQLATPVNFASQDPENDMIKPAIKGVLNVLKACVRAKEVKRVILTSSAAAVTINELEGTGHVMDETNWSDVEFLNTAKPPTWGYPVSKVLAEKAAWKFAEENNIDLITVIPTLTIGPSLTQDIP-SSVAMGMSLLTGNDFLINA-LKGMQFLSGSISITHVEDICRAHIFVAEKESTSGRYICCAHNTSVPELAKFLSKRYPQYKVPTEFDDFPSKAKLIISSGKLIKEGFSFKHSIAETFDQTVEYLKTQGIK-----
Phaseolus_vulgaris_ANR1      ---MATVKKIG--KKACVIGGSGFMASCLVKQLLHKGYAVNTTVRDPDNAKKISHLLALQSLGDLNIFGADLTGERDFDAPIAGCELVFQLATPVNFASEDPENDMIKPAISGVLNVLKACARAKGVKRVILTSSAAAVTINPVKDTGLVMDESNWTDVEFLNTAKPPTWGYPVSKALAEKAAWKFAEENHIDLITVIPTLTTGPSLTPDIP-SSVGLATSLITGNDFLINA-LKGMQFLSGSISITHVEDICRAHIFVAENESASGRYIVSSHSTSVPELAKFLSKRYPQYKVPTEFDDCPSKAKLTISSEKLVKEGFSFKYGIEEIYDQSVEYLKSKGALKN---
Phaseolus_vulgaris_ANR2      ---MGSMKAMG--KKACVVGGSGFMASLLIKKLLKKGYAVNTTVTDPGNPNKISHLVELQSLGKLEIFGADLGVEEDFDAPISGCELVFQFATTANFASEDPENDMIKPAISGVLNVLKACARAKEVKRVILTSSTAAVTINQLNGTDLVMDESNWSDVEYLRTAKPHGWGYPASKALEEKAAWKFAEENHIDLITVLPSLTTGPSITLDIP-TSVALATSLITGNDFFMKA-FKGIQSLSGSISITHVEDICRAHMFLAEKESASGRYIVCAHNTSIPELAKFLSKRYPQHQIPTEFDDIPSKAKFVISSEKLVKEGFSFKHGIEEIFYHSLEYLDSKGALKN---
Pisum_sativum_ANR            ---MASIKEVGK-KKACVIGGTGFVASILIKQLLEKGYAVNTTVRDLDNPKKISHLVALKSLGELNLFKAELTVDGDFDAPIAGCELVFQLATPVNFASQDPENDMIKPAIKGVLNVLKACAKAKEVKRVILTSSAAAVTINELKGEDHVMDETNWSDVEFLNAAKPPTWGYPASKVLAEKAAWEFAEKNDIDLITVIPTLTMGPYLTQDMP-SSVGLAMSLITGNDFLVNA-LKGMQFLSGSISITHVEDICRAHIFVAEKESASGRYICCAQNTCVPELAKFFSKRYPQYKVPTKFEDCPSKAKLIIFFEKLIKEGFGFKYGIGETYAQTIEYLKIKGVLKK---
Vitis_bellula_ANR            ----MATQHPIGKKTACVVGGTGFVASLLVKLLLQKGYAVNTTVRDPDNQKKVSHLLELQKLGDLKIFRADLTDELSFEAPIAGCDFVFHVATPVHFASEDPENDMIKPAIQGVVNVMKACTRAKSVKRVILTSSAAAVTINQLDGTGLVVDEKNWTDIEFLTSAKPPTWGYPASKTLAEKAAWKFAEENNIDLITVIPTLMAGSSLTSDVP-SSIGLAMSLITGNEFLING-MKGMQMLSGSVSIAHVEDVCRAHIFVAEKESASGRYICCAANTSVPELAKFLSKRYPQYKVPTDFGDFPSKSKLIISSDKLVKEGFSFKYGIEEIYDESVEYFKAKGLLQN---
Vitis_vinifera_ANR1          ----MATQHPIGKKTACVVGGTGFVASLLVKLLLQKGYAVNTTVRDPDNQKKVSHLLELQELGDLKIFRADLTDELSFEAPIAGCDFVFHVATPVHFASEDPENDMIKPAIQGVVNVMKACTRAKSVKRVILTSSAAAVTINQLDGTGLVVDEKNWTDIEFLTSAKPPTWGYPASKTLAEKAAWKFAEENNIDLITVIPTLMAGSSLTSDVP-SSIGLAMSLITGNEFLING-MKGMQMLSGSVSIAHVEDVCRAHIFVAEKESASGRYICCAANTSVPELAKFLSKRYPQYKVPTDFGDFPPKSKLIISSEKLVKEGFSFKYGIEEIYDESVEYFKAKGLLQN---
;
END;

[ The following blocks are output data for analysis step 20538 ]
BEGIN TREES;
      TITLE Phylogenetic_comparison_of_P._vulgaris_ANR_amino_acid_sequences_with_known_ANRs_from_other_plant_species;
      LINK TAXA = TaxaForAnalysisStep20538;
      TREE Fig._S2 = [&R] ((((((Phaseolus_vulgaris_ANR1:0.06522946,Glycine_max_ANR1:0.06859889)0.3600:0.01333574,(Phaseolus_vulgaris_ANR2:0.11988507,Glycine_max_ANR2:0.13402555)0.9960:0.06683507)0.7300:0.02398319,Lotus_corniculatus_ANR:0.08276279)0.5920:0.01478304,(Medicago_truncatula_ANR:0.08982329,Pisum_sativum_ANR:0.08717346)0.9880:0.04794948)1.0000:0.10433537,((Malus_domestica_ANR:0.05304021,Fragaria_x_ananassa_ANR:0.1286951)0.6780:0.04186146,(Camellia_sinensis_ANR1:0.11094278,(Vitis_vinifera_ANR1:0.00294211,Vitis_bellula_ANR:0.0059312)1.0000:0.06577376)0.5780:0.02226376)0.4420:0.02536134)1.0000:0.08301588,(Arabidopsis_thaliana_ANR:0.07853926,((Brassica_napus_C.BANa:0.01607495,Brassica_napus_A.BANa:0.00750271)1.0000:0.12368723,(Brassica_napus_C.BANb:0.01491656,Brassica_napus_A.BANb:0.00592809)0.9940:0.05213912)0.7640:0.04213629)1.0000:0.24507962);
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr103365]


END;