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
Vvi3g0033 . . . . . . . Aed9g0082 . . . . . . . . . . . Apr5g1802 . . . . . . Bva13g01766 . . . . Cca07g00096 . . . . . . . . Gma04g00080 . . . . . . . . . . . . . . . . . . . Lapu9g02435 . Lasa5g04827 . . . . . . . . . Lja1g2332 . . . Mepo3g08006 . Mesa9g05664 . . . . . Phac9g02048 . Phco7g00115 . . . . . . . . . . . . . Pvu9g0038 . Rops10g02635 . Seca4g00149 . Spst9g00108 . . . Sto2g0800 . . . Trre5g05907 . . . . . . . Vimu10g03664 . Viun9g03896 . Vivi3g00985 . . Vra5g1800
Vvi3g0034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0037 . . . . . . . . Aev04g3404 . Ahy13g0762 . Aip03g00802 . . . Amo13g0797 . . . . . . . . . . . . . . . . . Dod03g3210 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0039 . . . . . Adu03g01566 Aed5g0351 . Aev04g3405 . Ahy13g0763 . Aip03g00803 . . . Amo13g0798 . . . . Arst3g01994 . . . . . Bva14g02265 . . Cca04g00377 . . . Dod03g3211 . . . . . . . Gma11g01020 . . . . . Lal1g0194 . Lal9g0137 . . . Lan13g0200 . Lan13g0200 . . . . Lapu11g01422 . Lasa7g02704 . . . . . . . . . . . . . . . . . . . . . . . Phco9g01525 . . . . . Pste1g03681 . . . . . . . Pvu11g1387 . . . . . Spst11g00830 Ssu3g2900 . Sto2g0806 . . . . . . . . . . . . Vimu5g01279 . . . . Vra2g0361 .
Vvi3g0040 . . . . . . . . . . . . . . . . . . . Apr5g1804 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g2340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0041 . . . . . . . Aed9g0081 . . . . . . . . . . . . . . . . . . Bva13g01768 . . . . Cca07g00095 . . . . . . . . Gma04g00079 Gma06g00074 . . Gso4g0076 Gso4g0076 . . . . . . . . . . . . . . Lapu9g02436 . Lasa5g04825 . . . . . . . . . . . . . Mepo3g08008 . Mesa9g05666 . . . . . . . Phco7g00114 . . . . . . . . . . . . . Pvu9g0037 . Rops10g02636 . Seca4g00147 . Spst9g00107 . . . . . . . Trre5g05911 . . . . . Vifa2g04756 . . . Viun9g03898 . Vivi3g00987 . . Vra5g1801
Vvi3g0042 . . . . . Adu03g01025 . Aed9g0078 Aev04g3407 . Ahy13g0765 . Aip03g00804 . . . Amo13g0807 . . Apr5g1805 Arst3g00894 . . . . . . Bva14g02275 . . . Cca07g00091 . . Dod03g3212 . . . . . Gma04g00076 Gma06g00069 Gma11g01019 . Gso4g0073 Gso4g0073 Gso4g0073 . . Lal2g0119 . . . . . . . . . . Lapu9g02440 . Lasa5g04822 . . . . . . . . . Lja1g2341 . . . Mepo3g08013 . Mesa9g05673 . . . . . Phac9g01814 Phac11g00073 Phco7g00109 . . . Psa7g3236 . . Pste1g00272 . Pte1g02727 . . . . Pvu9g0033 Pvu11g0055 Rops10g02641 . . . Spst9g00103 Spst2g02969 . . Sto2g0809 Sto10g0123 . . . . . . . . . . Vimu10g03673 Vimu5g02827 Viun9g03903 . . . . Vra5g1805
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0033 Chr3 462653 465274 -
Aed Aed9g0082 Chr9 585975 589597 +
Apr Apr5g1802 Chr5 21325175 21330031 -
Bva Bva13g01766 Chr13 14284207 14287563 -
Cca Cca07g00096 Chr07 1265750 1269058 +
Gma Gma04g00080 Chr04 693573 694536 +
Lapu Lapu9g02435 Chr9 38790442 38794773 -
Lasa Lasa5g04827 Chr5 698824161 698827606 +
Lja Lja1g2332 Chr1 27011205 27014957 -
Mepo Mepo3g08006 Chr3 92925009 92928853 -
Mesa Mesa9g05664 Chr9 92390594 92393777 -
Phac Phac9g02048 Chr9 19133479 19134499 -
Phco Phco7g00115 Chr7 755934 760461 +
Pvu Pvu9g0038 Chr9 704193 710384 +
Rops Rops10g02635 Chr10 45669792 45674116 -
Seca Seca4g00149 Chr4 2197203 2202395 +
Spst Spst9g00108 Chr9 799884 803939 +
Sto Sto2g0800 Chr2 6900064 6901013 -
Trre Trre5g05907 Chr5 58656334 58660249 -
Vimu Vimu10g03664 Chr10 45779947 45784699 -
Viun Viun9g03896 Chr9 43196539 43199925 -
Vivi Vivi3g00985 Chr3 16387217 16391739 -
Vra Vra5g1800 Chr5 24033801 24038810 -
Vvi Vvi3g0034 Chr3 480460 480767 -
Vvi Vvi3g0035 Chr3 484539 485384 +
Vvi Vvi3g0036 Chr3 503106 504318 +
Vvi Vvi3g0037 Chr3 510038 511819 +
Aev Aev04g3404 Chr04 32695297 32697491 +
Ahy Ahy13g0762 Chr13 8009052 8012259 +
Aip Aip03g00802 Chr03 7787642 7790619 +
Amo Amo13g0797 Chr13 9929015 9932001 +
Dod Dod03g3210 Chr03 64716957 64719939 +
Vvi Vvi3g0038 Chr3 512368 513361 -
Vvi Vvi3g0039 Chr3 524877 530285 -
Adu Adu03g01566 Chr03 24756985 24759691 -
Aed Aed5g0351 Chr5 2455947 2459761 -
Aev Aev04g3405 Chr04 32698482 32701472 +
Ahy Ahy13g0763 Chr13 8013045 8016128 +
Aip Aip03g00803 Chr03 7791607 7794706 +
Amo Amo13g0798 Chr13 9933095 9934382 +
Arst Arst3g01994 Chr3 24038217 24039538 -
Bva Bva14g02265 Chr14 19401876 19405546 +
Cca Cca04g00377 Chr04 3808678 3813252 -
Dod Dod03g3211 Chr03 64726087 64730210 +
Gma Gma11g01020 Chr11 8642565 8646198 -
Lal Lal1g0194 Chr1 1161938 1164728 -
Lal Lal9g0137 Chr9 882814 886434 -
Lan Lan13g0200 Chr13 1253403 1257069 -
Lan Lan13g0200 Chr13 1253403 1257069 -
Lapu Lapu11g01422 Chr11 16959822 16961976 -
Lasa Lasa7g02704 Chr7 542260677 542261807 +
Phco Phco9g01525 Chr9 35652196 35653305 -
Pste Pste1g03681 Chr1 17785271 17796526 -
Pvu Pvu11g1387 Chr11 30600012 30601121 -
Spst Spst11g00830 Chr11 32453903 32455443 +
Ssu Ssu3g2900 Chr3 83860047 83865160 +
Sto Sto2g0806 Chr2 6965365 6968791 +
Vimu Vimu5g01279 Chr5 22751998 22753111 -
Vra Vra2g0361 Chr2 2769432 2772921 -
Vvi Vvi3g0040 Chr3 532527 544775 -
Apr Apr5g1804 Chr5 21342082 21353156 +
Lja Lja1g2340 Chr1 27099784 27112143 +
Vvi Vvi3g0041 Chr3 547679 557859 -
Aed Aed9g0081 Chr9 580711 585674 -
Bva Bva13g01768 Chr13 14296390 14298637 +
Cca Cca07g00095 Chr07 1249387 1255527 -
Gma Gma04g00079 Chr04 685723 690214 -
Gma Gma06g00074 Chr06 663611 668834 -
Gso Gso4g0076 Chr4 676712 681016 -
Gso Gso4g0076 Chr4 676712 681016 -
Lapu Lapu9g02436 Chr9 38798213 38803096 +
Lasa Lasa5g04825 Chr5 698298586 698300556 -
Mepo Mepo3g08008 Chr3 92939337 92943415 +
Mesa Mesa9g05666 Chr9 92405315 92407632 +
Phco Phco7g00114 Chr7 746408 748341 -
Pvu Pvu9g0037 Chr9 627527 632096 -
Rops Rops10g02636 Chr10 45675938 45685705 +
Seca Seca4g00147 Chr4 2185443 2188328 -
Spst Spst9g00107 Chr9 782914 786947 -
Trre Trre5g05911 Chr5 58669893 58671544 +
Vifa Vifa2g04756 Chr2 1402683916 1402686510 +
Viun Viun9g03898 Chr9 43207238 43212127 +
Vivi Vivi3g00987 Chr3 16401295 16405455 -
Vra Vra5g1801 Chr5 24042487 24047313 +
Vvi Vvi3g0042 Chr3 565597 568081 +
Adu Adu03g01025 Chr03 10656146 10658713 +
Aed Aed9g0078 Chr9 545061 549007 -
Aev Aev04g3407 Chr04 32704905 32709698 +
Ahy Ahy13g0765 Chr13 8023329 8027397 +
Aip Aip03g00804 Chr03 7802137 7805835 +
Amo Amo13g0807 Chr13 10060494 10064361 +
Apr Apr5g1805 Chr5 21356971 21360447 +
Arst Arst3g00894 Chr3 6575443 6580063 -
Bva Bva14g02275 Chr14 19558196 19562411 +
Cca Cca07g00091 Chr07 1213096 1215292 -
Dod Dod03g3212 Chr03 64731956 64736629 +
Gma Gma04g00076 Chr04 655098 658788 -
Gma Gma06g00069 Chr06 635366 639086 -
Gma Gma11g01019 Chr11 8634132 8640987 -
Gso Gso4g0073 Chr4 645683 649887 -
Gso Gso4g0073 Chr4 645683 649887 -
Gso Gso4g0073 Chr4 645683 649887 -
Lal Lal2g0119 Chr2 719062 727430 -
Lapu Lapu9g02440 Chr9 38835734 38839772 +
Lasa Lasa5g04822 Chr5 697955319 697958112 -
Lja Lja1g2341 Chr1 27121178 27124682 +
Mepo Mepo3g08013 Chr3 92990306 92994340 +
Mesa Mesa9g05673 Chr9 92460145 92463957 +
Phac Phac9g01814 Chr9 14838179 14845319 +
Phac Phac11g00073 Chr11 510605 519286 -
Phco Phco7g00109 Chr7 706276 709999 -
Psa Psa7g3236 Chr7 242735267 242736187 -
Pste Pste1g00272 Chr1 943982 945976 -
Pte Pte1g02727 Chr1 47266885 47271402 +
Pvu Pvu9g0033 Chr9 584396 588292 -
Pvu Pvu11g0055 Chr11 396295 398045 -
Rops Rops10g02641 Chr10 45726669 45730397 +
Spst Spst9g00103 Chr9 754096 758145 -
Spst Spst2g02969 Chr2 29459586 29462750 +
Sto Sto2g0809 Chr2 6998503 7003741 +
Sto Sto10g0123 Chr10 943136 945995 -
Vimu Vimu10g03673 Chr10 45820841 45824270 +
Vimu Vimu5g02827 Chr5 37587151 37588426 +
Viun Viun9g03903 Chr9 43234725 43238616 +
Vra Vra5g1805 Chr5 24076990 24080853 +
Adu Adu03g01566 Chr03 24756985 24759691 -
Arst Arst3g01994 Chr3 24038217 24039538 -
Lapu Lapu11g01422 Chr11 16959822 16961976 -
Lasa Lasa7g02704 Chr7 542260677 542261807 +
Phco Phco9g01525 Chr9 35652196 35653305 -
Pste Pste1g03681 Chr1 17785271 17796526 -
Pvu Pvu11g1387 Chr11 30600012 30601121 -
Spst Spst11g00830 Chr11 32453903 32455443 +
Vimu Vimu5g01279 Chr5 22751998 22753111 -
Lapu Lapu11g01422 Chr11 16959822 16961976 -
Adu Adu03g01025 Chr03 10656146 10658713 +
Phac Phac11g00073 Chr11 510605 519286 -
Pste Pste1g00272 Chr1 943982 945976 -
Pvu Pvu11g0055 Chr11 396295 398045 -
Spst Spst2g02969 Chr2 29459586 29462750 +
Vimu Vimu5g02827 Chr5 37587151 37588426 +
Aed Aed9g0081 Chr9 580711 585674 -
Cca Cca07g00095 Chr07 1249387 1255527 -
Gma Gma04g00079 Chr04 685723 690214 -
Gma Gma06g00074 Chr06 663611 668834 -
Gso Gso4g0076 Chr4 676712 681016 -
Gso Gso4g0076 Chr4 676712 681016 -
Vra Vra5g1801 Chr5 24042487 24047313 +