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
Vvi3g0633 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja3g0529 . Mal7g2518 . . . . . . . Mtr4g2071 . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g0685 . . . . . . . . . . . . . . . . . . .
Vvi3g0634 . . . . . . . . Aev04g3330 Aev05g0539 Ahy13g0676 Ahy15g0761 Aip03g00712 Aip05g00772 . . Amo13g0683 . Apr5g0285 . . Arst5g00972 . . . . Bva13g00220 Bva14g00289 . Car08g00574 Cca04g00457 . . . Dod03g3124 Dod02g0598 . . . . . . Gma11g01094 Gma12g00403 . . . . . . . . . . . . . . . . . Lapu2g00645 . Lasa2g03273 . . . . . . . . . Lja2g0429 . . . Mepo5g00858 . Mesa17g00897 . . . . . Phac2g02495 . Phco4g01011 . . . Psa2g3664 . Pste1g02647 . . . Pte12g00410 . Pumo8g01861 . Pvu2g0282 . Rops1g01680 . . . Spst2g00777 Ssu3g2819 . . Sto10g0192 . . . Trre9g01004 . . . Vian10g00671 . Vifa1g06911 . Vimu7g02917 . Viun2g01998 . Vivi2g03090 Vra2g0430 .
Vvi3g0635 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0636 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0637 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0638 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g00288 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal1g0459 . . . . . . . Mtr1g4120 . . . . . . Psa6g5052 . . . . . . . . . . . . . . . . . . . Sto2g0566 . . Tpr1g0386 . . . Tsu01g04790 . . . . . . . . . . . .
Vvi3g0639 . . . . . Adu05g01376 . Aed11g1962 . . . . . . . . . . Apr8g2473 . . Arst5g01762 . . . . . . Car04g01502 . . Cca06g02058 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g00008 . . . . . . . . . . . . . Mepo5g00014 . Mesa17g00008 . . . . . . . Phco4g00012 . . . . . Pste1g00512 . . . . . . . Pvu2g0558 . Rops1g02490 . Seca10g00019 . Spst2g00011 . Ssu2g3183 . . . . . Trre9g00011 . . . Vian10g00009 . Vifa1g04080 . Vimu7g02146 . Viun2g02977 . Vivi2g04337 . Vra11g0014
Vvi3g0640 . Acco12g2067 . . . . . Aed9g0125 Aev04g3331 Aev05g0532 Ahy13g0681 Ahy15g0771 Aip03g00716 Aip05g00779 . . Amo13g0692 . Apr5g0286 . . . . . . Bisa01g3922 Bva13g00218 Bva14g00287 Car06g03757 Car08g00578 Cca04g00456 Cca07g00160 . Dere13g0625 Dod03g3125 Dod02g0590 . Enph14g0536 . Glsi09g0549 Gma04g00128 . Gma11g01093 Gma12g00402 Gso4g0122 . Gso4g0122 Gso4g0122 Lal1g0237 Lal2g0150 . . . . Lan13g0246 Lan13g0246 . . . . . Lapu3g01637 . Lasa4g02383 . . . . . . . . Lja3g0528 Lja2g0439 Mal7g2521 . . Mepo1g02022 . . . Mibi10g0069 Mtr4g2074 . . . . . . Prci5g1010 Psa7g3223 Psa2g3657 . Pste7g01446 . . . Pte2g00311 . . . Pvu3g2599 . Rops2g03383 . . . Spst3g03906 Ssu3g2823 . Sto2g0690 Sto10g0191 Tpr3g2283 . . . Tsu02g02366 . . Vian1g01757 . Vifa4g02483 . Vimu7g02928 . . . . Vra2g0429 Vra5g1754
Vvi3g0641 . . . . . . . Aed9g0124 . . . . . . . . . . . . . . . . . . Bva13g00215 Bva14g00286 . . . Cca07g00159 . . . . . . . . Gma04g00127 Gma06g00120 . . Gso4g0121 Gso4g0121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g0190 . . . . . . . . . . . . . . . . . Vra5g1755
Vvi3g0642 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Sto Sto2g0566 Chr2 4805838 4810024 +
Vvi Vvi3g0633 Chr3 5443023 5443295 -
Lja Lja3g0529 Chr3 5297998 5300742 +
Mal Mal7g2518 Chr7 86262234 86267199 -
Mtr Mtr4g2071 Chr4 34224162 34225925 -
Sto Sto2g0685 Chr2 5806644 5808852 -
Vvi Vvi3g0634 Chr3 5446009 5454012 -
Aev Aev04g3330 Chr04 32188490 32190583 -
Aev Aev05g0539 Chr05 3720544 3722950 +
Ahy Ahy13g0676 Chr13 6966578 6969403 -
Ahy Ahy15g0761 Chr15 10400050 10403285 -
Aip Aip03g00712 Chr03 6837496 6840263 -
Aip Aip05g00772 Chr05 10019940 10022684 -
Amo Amo13g0683 Chr13 8334901 8337705 -
Apr Apr5g0285 Chr5 2481055 2484168 -
Arst Arst5g00972 Chr5 9360425 9363489 -
Bva Bva13g00220 Chr13 1071411 1074474 +
Bva Bva14g00289 Chr14 1491923 1495421 +
Car Car08g00574 Chr08 4884263 4888462 -
Cca Cca04g00457 Chr04 4541614 4544210 +
Dod Dod03g3124 Chr03 63799313 63801591 -
Dod Dod02g0598 Chr02 7725723 7728984 +
Gma Gma11g01094 Chr11 9255373 9258286 +
Gma Gma12g00403 Chr12 3311795 3314667 +
Lapu Lapu2g00645 Chr2 5664722 5669250 -
Lasa Lasa2g03273 Chr2 529206124 529209064 -
Lja Lja2g0429 Chr2 3933119 3936453 -
Mepo Mepo5g00858 Chr5 8352779 8356950 -
Mesa Mesa17g00897 Chr17 11441945 11445220 -
Phac Phac2g02495 Chr2 26366418 26370794 -
Phco Phco4g01011 Chr4 8003789 8007751 +
Psa Psa2g3664 Chr2 393659156 393661882 +
Pste Pste1g02647 Chr1 10291121 10294807 -
Pte Pte12g00410 Chr12 3398915 3402938 -
Pumo Pumo8g01861 Chr8 54912579 54916391 +
Pvu Pvu2g0282 Chr2 2903818 2908009 -
Rops Rops1g01680 Chr1 35420076 35425111 +
Spst Spst2g00777 Chr2 6581435 6586121 -
Ssu Ssu3g2819 Chr3 82532988 82535533 -
Sto Sto10g0192 Chr10 1593757 1596782 +
Trre Trre9g01004 Chr9 7893349 7896756 -
Vian Vian10g00671 Chr10 6478474 6482356 -
Vifa Vifa1g06911 Chr1 1065115206 1065117205 +
Vimu Vimu7g02917 Chr7 24572261 24574913 -
Viun Viun2g01998 Chr2 28461855 28466127 +
Vivi Vivi2g03090 Chr2 130849470 130852462 +
Vra Vra2g0430 Chr2 3358238 3361119 +
Vvi Vvi3g0635 Chr3 5454209 5455278 -
Vvi Vvi3g0636 Chr3 5457823 5458095 -
Vvi Vvi3g0637 Chr3 5459440 5459856 -
Vvi Vvi3g0638 Chr3 5462377 5464132 -
Bva Bva14g00288 Chr14 1489341 1491377 +
Mal Mal1g0459 Chr1 5288245 5291450 -
Mtr Mtr1g4120 Chr1 52734166 52734852 +
Psa Psa6g5052 Chr6 437280906 437283695 +
Sto Sto2g0566 Chr2 4805838 4810024 +
Tpr Tpr1g0386 Chr1 3327004 3327723 -
Tsu Tsu01g04790 Chr01 54972352 54973056 +
Vvi Vvi3g0639 Chr3 5469647 5470680 -
Adu Adu05g01376 Chr05 20921857 20926084 -
Aed Aed11g1962 Chr11 22300317 22301654 +
Apr Apr8g2473 Chr8 34742832 34744260 -
Arst Arst5g01762 Chr5 20970056 20974206 -
Car Car04g01502 Chr04 15228895 15233053 -
Cca Cca06g02058 Chr06 35808448 35809976 +
Lasa Lasa2g00008 Chr2 338786 341733 +
Mepo Mepo5g00014 Chr5 220097 223616 +
Mesa Mesa17g00008 Chr17 114545 118040 +
Phco Phco4g00012 Chr4 122853 125936 +
Pste Pste1g00512 Chr1 1643166 1649132 -
Pvu Pvu2g0558 Chr2 4934895 4937922 -
Rops Rops1g02490 Chr1 48039599 48044651 -
Seca Seca10g00019 Chr10 233126 238206 +
Spst Spst2g00011 Chr2 190404 193992 +
Ssu Ssu2g3183 Chr2 94158809 94160113 +
Trre Trre9g00011 Chr9 249245 252745 +
Vian Vian10g00009 Chr10 122271 126107 +
Vifa Vifa1g04080 Chr1 628108436 628112666 -
Vimu Vimu7g02146 Chr7 19069823 19073406 +
Viun Viun2g02977 Chr2 33763899 33767862 -
Vivi Vivi2g04337 Chr2 157264566 157268137 -
Vra Vra11g0014 Chr11 165480 167135 -
Vvi Vvi3g0640 Chr3 5487912 5489687 +
Acco Acco12g2067 Chr12 32304269 32306182 +
Aed Aed9g0125 Chr9 886741 888447 -
Aev Aev04g3331 Chr04 32202008 32204086 +
Aev Aev05g0532 Chr05 3671680 3675171 -
Ahy Ahy13g0681 Chr13 7030075 7032619 -
Ahy Ahy15g0771 Chr15 10519045 10521486 +
Aip Aip03g00716 Chr03 6893709 6896203 -
Aip Aip05g00779 Chr05 10141749 10144359 +
Amo Amo13g0692 Chr13 8457073 8464148 -
Apr Apr5g0286 Chr5 2498810 2502351 +
Bisa Bisa01g3922 Chr01 94594913 94599578 +
Bva Bva13g00218 Chr13 1052994 1064109 -
Bva Bva14g00287 Chr14 1479261 1482546 -
Car Car06g03757 Chr06 69173539 69175960 +
Car Car08g00578 Chr08 4928747 4932418 +
Cca Cca04g00456 Chr04 4508308 4510540 -
Cca Cca07g00160 Chr07 2031090 2033998 -
Dere Dere13g0625 Chr13 7842220 7844306 +
Dod Dod03g3125 Chr03 63846630 63850280 +
Dod Dod02g0590 Chr02 7625048 7628544 -
Enph Enph14g0536 Chr14 7337806 7339100 +
Glsi Glsi09g0549 Chr09 3825464 3827039 +
Gma Gma04g00128 Chr04 1088912 1091451 -
Gma Gma11g01093 Chr11 9212054 9215049 -
Gma Gma12g00402 Chr12 3293985 3297079 -
Gso Gso4g0122 Chr4 1070752 1073281 -
Gso Gso4g0122 Chr4 1070752 1073281 -
Gso Gso4g0122 Chr4 1070752 1073281 -
Lal Lal1g0237 Chr1 1412161 1414707 -
Lal Lal2g0150 Chr2 904791 906490 -
Lan Lan13g0246 Chr13 1534067 1537103 -
Lan Lan13g0246 Chr13 1534067 1537103 -
Lapu Lapu3g01637 Chr3 21231652 21233911 +
Lasa Lasa4g02383 Chr4 466651159 466652894 -
Lja Lja3g0528 Chr3 5283921 5287086 -
Lja Lja2g0439 Chr2 4035309 4037911 +
Mal Mal7g2521 Chr7 86399694 86401978 +
Mepo Mepo1g02022 Chr1 20828451 20833283 +
Mibi Mibi10g0069 Chr10 1067817 1069848 -
Mtr Mtr4g2074 Chr4 34284284 34287161 +
Prci Prci5g1010 Chr5 28188933 28190790 -
Psa Psa7g3223 Chr7 240619431 240636286 -
Psa Psa2g3657 Chr2 393271209 393275283 +
Pste Pste7g01446 Chr7 13258021 13260815 +
Pte Pte2g00311 Chr2 2406389 2408773 +
Pvu Pvu3g2599 Chr3 48054449 48056759 +
Rops Rops2g03383 Chr2 62204533 62206797 -
Spst Spst3g03906 Chr3 89124074 89126522 -
Ssu Ssu3g2823 Chr3 82634492 82638353 +
Sto Sto2g0690 Chr2 5847721 5851993 +
Sto Sto10g0191 Chr10 1570377 1573150 -
Tpr Tpr3g2283 Chr3 21461300 21464088 +
Tsu Tsu02g02366 Chr02 24097714 24100612 +
Vian Vian1g01757 Chr1 20582600 20589714 +
Vifa Vifa4g02483 Chr4 747919269 747920935 -
Vimu Vimu7g02928 Chr7 24658794 24660134 +
Vra Vra2g0429 Chr2 3332325 3334762 -
Vra Vra5g1754 Chr5 23683948 23686430 +
Vvi Vvi3g0641 Chr3 5494395 5528939 -
Aed Aed9g0124 Chr9 868965 886018 +
Bva Bva13g00215 Chr13 1034144 1048722 +
Bva Bva14g00286 Chr14 1462550 1478313 +
Cca Cca07g00159 Chr07 2009972 2028316 +
Gma Gma04g00127 Chr04 1069721 1087794 +
Gma Gma06g00120 Chr06 1034486 1056552 +
Gso Gso4g0121 Chr4 1051546 1070007 +
Gso Gso4g0121 Chr4 1051546 1070007 +
Sto Sto10g0190 Chr10 1549565 1567930 +
Vra Vra5g1755 Chr5 23687087 23706632 -
Vvi Vvi3g0642 Chr3 5538206 5538415 +
Aev Aev05g0539 Chr05 3720544 3722950 +
Ahy Ahy15g0761 Chr15 10400050 10403285 -
Aip Aip05g00772 Chr05 10019940 10022684 -
Arst Arst5g00972 Chr5 9360425 9363489 -
Dod Dod02g0598 Chr02 7725723 7728984 +
Lapu Lapu2g00645 Chr2 5664722 5669250 -
Lasa Lasa2g03273 Chr2 529206124 529209064 -
Lja Lja2g0429 Chr2 3933119 3936453 -
Mepo Mepo5g00858 Chr5 8352779 8356950 -
Mesa Mesa17g00897 Chr17 11441945 11445220 -
Phac Phac2g02495 Chr2 26366418 26370794 -
Phco Phco4g01011 Chr4 8003789 8007751 +
Psa Psa2g3664 Chr2 393659156 393661882 +
Pste Pste1g02647 Chr1 10291121 10294807 -
Pte Pte12g00410 Chr12 3398915 3402938 -
Pumo Pumo8g01861 Chr8 54912579 54916391 +
Pvu Pvu2g0282 Chr2 2903818 2908009 -
Rops Rops1g01680 Chr1 35420076 35425111 +
Spst Spst2g00777 Chr2 6581435 6586121 -
Trre Trre9g01004 Chr9 7893349 7896756 -
Vian Vian10g00671 Chr10 6478474 6482356 -
Vifa Vifa1g06911 Chr1 1065115206 1065117205 +
Vimu Vimu7g02917 Chr7 24572261 24574913 -
Viun Viun2g01998 Chr2 28461855 28466127 +
Vivi Vivi2g03090 Chr2 130849470 130852462 +
Acco Acco12g2067 Chr12 32304269 32306182 +
Bisa Bisa01g3922 Chr01 94594913 94599578 +
Dere Dere13g0625 Chr13 7842220 7844306 +
Enph Enph14g0536 Chr14 7337806 7339100 +
Glsi Glsi09g0549 Chr09 3825464 3827039 +
Lapu Lapu3g01637 Chr3 21231652 21233911 +
Lasa Lasa4g02383 Chr4 466651159 466652894 -
Mepo Mepo1g02022 Chr1 20828451 20833283 +
Mibi Mibi10g0069 Chr10 1067817 1069848 -
Prci Prci5g1010 Chr5 28188933 28190790 -
Pste Pste7g01446 Chr7 13258021 13260815 +
Pte Pte2g00311 Chr2 2406389 2408773 +
Pvu Pvu3g2599 Chr3 48054449 48056759 +
Rops Rops2g03383 Chr2 62204533 62206797 -
Spst Spst3g03906 Chr3 89124074 89126522 -
Vian Vian1g01757 Chr1 20582600 20589714 +
Vifa Vifa4g02483 Chr4 747919269 747920935 -
Vimu Vimu7g02928 Chr7 24658794 24660134 +
Mal Mal7g2521 Chr7 86399694 86401978 +
Mtr Mtr4g2074 Chr4 34284284 34287161 +
Tpr Tpr3g2283 Chr3 21461300 21464088 +
Tsu Tsu02g02366 Chr02 24097714 24100612 +