Hierarchical alignments with the V. vinifera genome as reference

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Fabaceae genomes. We used P. vulgaris as a reference, and by comparing homologous gene locus maps and Ks values between P. vulgaris and other Fabaceae, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created two hierarchical lists of homologous genes using P. vulgaris as a reference.
  The relevant gene ids can be obtained from the Fabaceae blast and match under the Tools module. This link is Fabaceae blast and match.
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Select Download Tree Vvi Acco_1 Acco_2 Accr_1 Accr_2 Adu_1 Adu_2 Aed_1 Aed_2 Aev_1 Aev_2 Ahy_1 Ahy_2 Aip_1 Aip_2 Alju_1 Alju_2 Amo_1 Amo_2 Apr_1 Apr_2 Arst_1 Arst_2 Bach_1 Bach_2 Bisa_1 Bisa_2 Bva_1 Bva_2 Car_1 Car_2 Cca_1 Cca_2 Dere_1 Dere_2 Dod_1 Dod_2 Enph_1 Enph_2 Glsi_1 Glsi_2 Gma_1 Gma_2 Gma_3 Gma_4 Gso_1 Gso_2 Gso_3 Gso_4 Lal_1 Lal_2 Lal_3 Lal_4 Lal_5 Lal_6 Lan_1 Lan_2 Lan_3 Lan_4 Lan_5 Lan_6 Lapu_1 Lapu_2 Lasa_1 Lasa_2 Lele_1 Lele_2 Lele_3 Lele_4 Lele_5 Lele_6 Lele_7 Lele_8 Lja_1 Lja_2 Mal_1 Mal_2 Mepo_1 Mepo_2 Mesa_1 Mesa_2 Mibi_1 Mibi_2 Mtr_1 Mtr_2 Phac_1 Phac_2 Phco_1 Phco_2 Prci_1 Prci_2 Psa_1 Psa_2 Pste_1 Pste_2 Pte_1 Pte_2 Pte_3 Pte_4 Pumo_1 Pumo_2 Pvu_1 Pvu_2 Rops_1 Rops_2 Seca_1 Seca_2 Spst_1 Spst_2 Ssu_1 Ssu_2 Sto_1 Sto_2 Tpr_1 Tpr_2 Trre_1 Trre_2 Tsu_1 Tsu_2 Vian_1 Vian_2 Vifa_1 Vifa_2 Vimu_1 Vimu_2 Viun_1 Viun_2 Vivi_1 Vivi_2 Vra_1 Vra_2
Vvi3g0133 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g01596 Bva14g02295 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g0095 . . . . . . . . . . . . . . . . . .
Vvi3g0134 . . . . . Adu03g00746 . . Aev04g3555 Aev05g0422 Ahy13g0963 Ahy15g0411 Aip03g01041 Aip05g00403 . . Amo13g1107 . . . . Arst3g00955 . . . . . Bva14g02299 . . . . . . Dod03g3345 Dod02g0464 . . . . . . . Gma12g00231 . . . . Lal1g0110 Lal2g0063 Lal9g0086 . . . . . . . . . . Lapu11g00927 . Lasa7g02400 . . . . . . . . . . Mal7g2836 . . Mepo2g02578 . Mesa13g02428 . . Mtr4g2332 . . . . Phco9g00313 . . Psa7g4094 . . . . . . . . Pumo11g02039 . Pvu11g0271 . Rops3g00336 . Seca6g00538 . Spst2g02733 . . Sto2g0908 . Tpr3g2569 . . Trre7g02479 Tsu02g02724 . . Vian5g01656 . Vifa6g01420 . Vimu5g02573 . Viun11g02692 . Vivi5g03072 . .
Vvi3g0135 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0136 . Acco01g2125 . Accr1g01836 . Adu03g00743 . . Aev04g3554 . Ahy13g0958 . Aip03g01039 . . Alju02g1910 Amo13g1103 . . Apr5g1833 . Arst3g00951 . . . Bisa01g4087 Bva13g01594 . . . . . . Dere06g0119 Dod03g3344 . . Enph12g0626 . Glsi01g0111 . . . Gma12g00232 . . . . . Lal2g0064 Lal9g0089 . . . . . . . . . . Lapu11g00926 . Lasa7g02399 . . . . Lele45g1341 Lele46g1434 Lele47g0075 Lele48g0078 . . . . . Mepo2g02575 . Mesa13g02430 . Mibi01g1786 . . . . . Phco9g00314 . Prci14g0141 Psa7g3188 . . Pste1g01061 . . . . . Pumo11g02038 . Pvu11g0272 . Rops3g00337 . Seca6g00544 . Spst2g02732 . . Sto2g0910 Sto10g0094 . . . Trre7g02481 . . . . . Vifa6g01422 . Vimu5g02572 . Viun11g02690 . Vivi5g03070 . .
Vvi3g0137 . . . . . . . . Aev09g2631 . Ahy19g3163 . Aip09g03631 . . . Amo19g4040 . . . . . . . . . . . . . . . . . Dod06g0186 . . . . . . . . . . . . . Lal1g0111 . . . . . Lan13g0131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g3187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0138 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0139 . Acco01g2126 . Accr1g01837 . Adu03g00742 . . . . . . . . . Alju02g1907 . . . . . Arst3g00950 . . . Bisa01g4091 . Bva14g02300 . . . . . Dere06g0117 . . . Enph12g0627 . Glsi01g0110 . . . . . . . . . . . . . . . . . . . . . Lapu11g00925 . Lasa7g02398 . . . . Lele45g1342 Lele46g1435 Lele47g0074 Lele48g0077 . . . . . Mepo2g02573 . Mesa13g02435 . Mibi01g1785 . . . . . Phco9g00315 . Prci14g0137 . . . Pste1g01066 . . . . . Pumo11g02036 . Pvu11g0273 . Rops3g00338 . Seca6g00545 . Spst2g02731 . . . Sto10g0093 . . . Trre7g02485 . . . Vian5g01655 . Vifa6g01423 . Vimu5g02570 . Viun11g02689 . Vivi5g03069 . .
Vvi3g0140 . . . . . . . Aed9g0057 Aev04g3553 . Ahy13g0957 . Aip03g01038 . . . Amo13g1102 . . . . . . . . . Bva13g01593 . . . . Cca07g00065 . . Dod03g3343 . . . . . Gma04g00055 . . . Gso4g0049 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Vra5g1834
Vvi3g0141 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal2g0065 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0142 . Acco01g2129 . Accr1g01839 . Adu03g00741 . . . . . . . . . Alju02g1905 . . . . . Arst3g00948 . . . Bisa01g4092 . Bva14g02301 . . . . . Dere06g0116 . . . Enph12g0628 . Glsi01g0109 . . . . . . . . Lal1g0112 . . . . . Lan13g0134 . . . . . . Lapu11g00924 . Lasa7g02394 . . . . Lele45g1343 Lele46g1436 Lele47g0073 Lele48g0076 . . . . . Mepo2g02572 . Mesa13g02436 . Mibi01g1784 . . . . . . . Prci14g0133 Psa7g3183 . . . . . . . . . . Pvu11g0274 . . . . . Spst2g02730 . . . Sto10g0092 . . . Trre7g02487 . . . . . . . Vimu5g02569 . . . Vivi5g03064 . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Aev Aev09g2631 Chr09 27466147 27467637 -
Ahy Ahy19g3163 Chr19 154686856 154688768 +
Aip Aip09g03631 Chr09 143136500 143138512 +
Amo Amo19g4040 Chr19 156547231 156549417 +
Dod Dod06g0186 Chr06 2797477 2799630 -
Vvi Vvi3g0133 Chr3 1238289 1248488 -
Bva Bva13g01596 Chr13 9556705 9561079 +
Bva Bva14g02295 Chr14 19846866 19851557 -
Sto Sto10g0095 Chr10 722892 726258 +
Vvi Vvi3g0134 Chr3 1252448 1255340 -
Adu Adu03g00746 Chr03 6935909 6938835 +
Aev Aev04g3555 Chr04 33569093 33570479 +
Aev Aev05g0422 Chr05 2908703 2910234 +
Ahy Ahy13g0963 Chr13 10408745 10411700 +
Ahy Ahy15g0411 Chr15 4790407 4792536 +
Aip Aip03g01041 Chr03 10096542 10099484 +
Aip Aip05g00403 Chr05 4501103 4502606 +
Amo Amo13g1107 Chr13 14002475 14005526 +
Arst Arst3g00955 Chr3 6941511 6944441 +
Bva Bva14g02299 Chr14 19862534 19865547 -
Dod Dod03g3345 Chr03 66116912 66119738 +
Dod Dod02g0464 Chr02 6121458 6124007 +
Gma Gma12g00231 Chr12 1795228 1799508 -
Lal Lal1g0110 Chr1 735387 738811 -
Lal Lal2g0063 Chr2 353371 356756 -
Lal Lal9g0086 Chr9 553802 561462 -
Lapu Lapu11g00927 Chr11 11797471 11800051 +
Lasa Lasa7g02400 Chr7 521132982 521134583 +
Mal Mal7g2836 Chr7 90932541 90934408 +
Mepo Mepo2g02578 Chr2 35476516 35479099 +
Mesa Mesa13g02428 Chr13 28449111 28450400 -
Mtr Mtr4g2332 Chr4 36816685 36819285 +
Phco Phco9g00313 Chr9 2115357 2120061 -
Psa Psa7g4094 Chr7 335382884 335386110 +
Pumo Pumo11g02039 Chr11 52453184 52454748 +
Pvu Pvu11g0271 Chr11 2155218 2158126 -
Rops Rops3g00336 Chr3 4193554 4200529 -
Seca Seca6g00538 Chr6 16361401 16363279 -
Spst Spst2g02733 Chr2 27122498 27124069 +
Sto Sto2g0908 Chr2 7858602 7862406 -
Tpr Tpr3g2569 Chr3 24867467 24870896 -
Trre Trre7g02479 Chr7 20400840 20402580 -
Tsu Tsu02g02724 Chr02 28893813 28897569 +
Vian Vian5g01656 Chr5 39035684 39037126 +
Vifa Vifa6g01420 Chr6 517201225 517203148 -
Vimu Vimu5g02573 Chr5 36047197 36048706 +
Viun Viun11g02692 Chr11 39662746 39664996 +
Vivi Vivi5g03072 Chr5 119226901 119229925 +
Vvi Vvi3g0135 Chr3 1263103 1273954 +
Vvi Vvi3g0136 Chr3 1275051 1278857 +
Acco Acco01g2125 Chr01 37149351 37152758 +
Accr Accr1g01836 Chr1 48746690 48749936 +
Adu Adu03g00743 Chr03 6916923 6920351 -
Aev Aev04g3554 Chr04 33564551 33567328 -
Ahy Ahy13g0958 Chr13 10373986 10378109 -
Aip Aip03g01039 Chr03 10063337 10066790 -
Alju Alju02g1910 Chr02 18352755 18355991 -
Amo Amo13g1103 Chr13 13976439 13980693 -
Apr Apr5g1833 Chr5 21529422 21532386 +
Arst Arst3g00951 Chr3 6922041 6926039 -
Bisa Bisa01g4087 Chr01 98259945 98267401 +
Bva Bva13g01594 Chr13 9543767 9551281 -
Dere Dere06g0119 Chr06 1340733 1344682 -
Dod Dod03g3344 Chr03 66105528 66109917 -
Enph Enph12g0626 Chr12 12706205 12710456 +
Glsi Glsi01g0111 Chr01 940940 944753 -
Gma Gma12g00232 Chr12 1800222 1803904 +
Lal Lal2g0064 Chr2 355592 365169 +
Lal Lal9g0089 Chr9 564275 567889 +
Lapu Lapu11g00926 Chr11 11790353 11794267 -
Lasa Lasa7g02399 Chr7 521090013 521092706 -
Lele Lele45g1341 Chr45 23084482 23087496 +
Lele Lele46g1434 Chr46 21147043 21149949 +
Lele Lele47g0075 Chr47 509754 512968 -
Lele Lele48g0078 Chr48 1232403 1236301 -
Mepo Mepo2g02575 Chr2 35428717 35432605 -
Mesa Mesa13g02430 Chr13 28483152 28486459 +
Mibi Mibi01g1786 Chr01 26147899 26151129 -
Phco Phco9g00314 Chr9 2121094 2126297 +
Prci Prci14g0141 Chr14 1170998 1174805 -
Psa Psa7g3188 Chr7 238358970 238361849 -
Pste Pste1g01061 Chr1 3427396 3430932 +
Pumo Pumo11g02038 Chr11 52448972 52449914 -
Pvu Pvu11g0272 Chr11 2160535 2164311 +
Rops Rops3g00337 Chr3 4202312 4206947 +
Seca Seca6g00544 Chr6 16436485 16439279 +
Spst Spst2g02732 Chr2 27116478 27119503 -
Sto Sto2g0910 Chr2 7871253 7874892 +
Sto Sto10g0094 Chr10 715820 719215 -
Trre Trre7g02481 Chr7 20431523 20434469 +
Vifa Vifa6g01422 Chr6 517770668 517779168 +
Vimu Vimu5g02572 Chr5 36040661 36042889 -
Viun Viun11g02690 Chr11 39653621 39656840 -
Vivi Vivi5g03070 Chr5 119189782 119192764 -
Vvi Vvi3g0137 Chr3 1283329 1285442 +
Aev Aev09g2631 Chr09 27466147 27467637 -
Ahy Ahy19g3163 Chr19 154686856 154688768 +
Aip Aip09g03631 Chr09 143136500 143138512 +
Amo Amo19g4040 Chr19 156547231 156549417 +
Dod Dod06g0186 Chr06 2797477 2799630 -
Lal Lal1g0111 Chr1 739680 747468 +
Lan Lan13g0131 Chr13 767098 770823 +
Psa Psa7g3187 Chr7 237937226 237938581 -
Vvi Vvi3g0138 Chr3 1286455 1287825 +
Vvi Vvi3g0139 Chr3 1291536 1293360 +
Acco Acco01g2126 Chr01 37161139 37163190 +
Accr Accr1g01837 Chr1 48759073 48761325 +
Adu Adu03g00742 Chr03 6910351 6912454 -
Alju Alju02g1907 Chr02 18342874 18344994 -
Arst Arst3g00950 Chr3 6915969 6918008 -
Bisa Bisa01g4091 Chr01 98408351 98411664 +
Bva Bva14g02300 Chr14 19871518 19873815 +
Dere Dere06g0117 Chr06 1329253 1331165 -
Enph Enph12g0627 Chr12 12713800 12715836 +
Glsi Glsi01g0110 Chr01 935803 939637 -
Lapu Lapu11g00925 Chr11 11784852 11787146 -
Lasa Lasa7g02398 Chr7 520970967 520973013 -
Lele Lele45g1342 Chr45 23090981 23092615 +
Lele Lele46g1435 Chr46 21153447 21155479 +
Lele Lele47g0074 Chr47 504654 506310 -
Lele Lele48g0077 Chr48 1227395 1229286 -
Mepo Mepo2g02573 Chr2 35398101 35400758 -
Mesa Mesa13g02435 Chr13 28508811 28510841 +
Mibi Mibi01g1785 Chr01 26140542 26142354 -
Phco Phco9g00315 Chr9 2129337 2130769 +
Prci Prci14g0137 Chr14 1164338 1167133 -
Pste Pste1g01066 Chr1 3453276 3455310 +
Pumo Pumo11g02036 Chr11 52439182 52441746 -
Pvu Pvu11g0273 Chr11 2167596 2169586 +
Rops Rops3g00338 Chr3 4211278 4213310 +
Seca Seca6g00545 Chr6 16453375 16455920 +
Spst Spst2g02731 Chr2 27108861 27116438 -
Sto Sto10g0093 Chr10 704103 712091 -
Trre Trre7g02485 Chr7 20451623 20454188 +
Vian Vian5g01655 Chr5 38995968 39030142 -
Vifa Vifa6g01423 Chr6 518063237 518065533 +
Vimu Vimu5g02570 Chr5 36034827 36036574 -
Viun Viun11g02689 Chr11 39647856 39649661 -
Vivi Vivi5g03069 Chr5 119144640 119147082 -
Vvi Vvi3g0140 Chr3 1298261 1299515 +
Aed Aed9g0057 Chr9 397126 399060 -
Aev Aev04g3553 Chr04 33557477 33559778 -
Ahy Ahy13g0957 Chr13 10367657 10369800 -
Aip Aip03g01038 Chr03 10056572 10058915 -
Amo Amo13g1102 Chr13 13970218 13972401 -
Bva Bva13g01593 Chr13 9539372 9541928 -
Cca Cca07g00065 Chr07 886332 887762 -
Dod Dod03g3343 Chr03 66098001 66100693 -
Gma Gma04g00055 Chr04 456526 457571 -
Gso Gso4g0049 Chr4 449710 451192 -
Vra Vra5g1834 Chr5 24272305 24273594 +
Vvi Vvi3g0141 Chr3 1301501 1302755 +
Lal Lal2g0065 Chr2 366954 368944 +
Vvi Vvi3g0142 Chr3 1303982 1304387 +
Acco Acco01g2129 Chr01 37172250 37203132 +
Accr Accr1g01839 Chr1 48767877 48791923 +
Adu Adu03g00741 Chr03 6891278 6909220 -
Alju Alju02g1905 Chr02 18314213 18335770 -
Arst Arst3g00948 Chr3 6900031 6914855 -
Bisa Bisa01g4092 Chr01 98431149 98450213 +
Bva Bva14g02301 Chr14 19882365 19900020 +
Dere Dere06g0116 Chr06 1295638 1322987 -
Enph Enph12g0628 Chr12 12717384 12739693 +
Glsi Glsi01g0109 Chr01 904486 932645 -
Lal Lal1g0112 Chr1 749060 767742 +
Lan Lan13g0134 Chr13 776375 794075 +
Lapu Lapu11g00924 Chr11 11756376 11781103 -
Lasa Lasa7g02394 Chr7 520261871 520294716 -
Lele Lele45g1343 Chr45 23092728 23098448 +
Lele Lele46g1436 Chr46 21155814 21176717 +
Lele Lele47g0073 Chr47 497234 501682 -
Lele Lele48g0076 Chr48 1202220 1222893 -
Mepo Mepo2g02572 Chr2 35375616 35395160 -
Mesa Mesa13g02436 Chr13 28512947 28530903 +
Mibi Mibi01g1784 Chr01 26108788 26130737 -
Prci Prci14g0133 Chr14 1123479 1144891 -
Psa Psa7g3183 Chr7 237799595 237826563 -
Pvu Pvu11g0274 Chr11 2171771 2183673 +
Spst Spst2g02730 Chr2 27105443 27108745 -
Sto Sto10g0092 Chr10 694057 701486 -
Trre Trre7g02487 Chr7 20466197 20489063 +
Vimu Vimu5g02569 Chr5 36010301 36032707 -
Vivi Vivi5g03064 Chr5 119044214 119076458 -
Aev Aev05g0422 Chr05 2908703 2910234 +
Ahy Ahy15g0411 Chr15 4790407 4792536 +
Aip Aip05g00403 Chr05 4501103 4502606 +
Dod Dod02g0464 Chr02 6121458 6124007 +