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
Vvi1g0101 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0102 . . . . . Adu04g01080 . . . . . . . . . . . . . . . Arst4g01508 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa1g01677 . . . . . . . . . . . . . Mepo6g01556 . . . . . . . Phac9g04028 . Phco7g02880 . . . . . Pste2g03257 . . . . . Pumo2g01463 . Pvu9g2513 . Rops11g01620 . Seca6g03924 . Spst9g03012 . . . . . . . Trre3g02039 . . . Vian4g00187 . Vifa1g09176 . Vimu10g00265 . Viun9g00237 . Vivi4g02580 . .
Vvi1g0103 . . . . Adu03g04375 . . . . Aev03g2345 . Ahy13g4320 . Aip03g04782 . . . . . Apr3g2144 Arst3g05784 . . . . . . . Car06g01231 . . Cca09g01638 . . . Dod04g1871 . . . . . . Gma08g00835 . . . . . . . . . . . . . . . . . Lapu3g02697 . . . . . . . . . . . . Lja4g4207 . . Mepo2g03687 . Mesa13g01483 . . . . . Phac2g02906 . Phco4g02181 . . . . . Pste3g02384 . . . . . Pumo6g01410 . Pvu2g1934 . Rops2g01535 . Seca12g05465 . . . . Ssu5g2145 . . . . Trre7g04298 . . . Vian1g02822 . Vifa6g01946 . Vimu11g01609 . Viun3g02031 . . . . Vra7g1016
Vvi1g0104 . . . . . Adu04g01082 . . . . . . . . . . . . . . . Arst4g01510 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa1g01678 . . . . . . . . . . . . . Mepo6g01557 . Mesa5g03045 . . . . . Phac9g04027 . Phco7g02879 . . . . . Pste2g03261 . . . . . . . Pvu9g2512 . Rops11g01621 . Seca6g03923 . Spst9g03010 . . Sto13g0101 . . . . Trre3g02041 . . . Vian4g00188 . Vifa1g09175 . Vimu10g00269 . Viun9g00238 . Vivi4g02579 . .
Vvi1g0105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0106 . . . . . . . . . Aev03g2344 . Ahy13g4319 . Aip03g04781 . . . Amo13g5367 . Apr3g2143 . . . . . . . . Car06g01233 . . Cca09g01637 . . . Dod04g1869 . . . . . . Gma08g00834 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g2000 . . . . . . . . . . . . . . . . . Ssu5g2143 Sto13g0102 . . . . . . . . . . . . . . . . . . Vra7g1017
Vvi1g0107 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g2946 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0110 Acco06g3110 . Accr5g00064 . Adu03g04372 . . . . Aev03g2342 . Ahy13g4316 . Aip03g04777 Alju03g0070 . . Amo13g5363 . Apr3g2141 Arst3g05781 . . . . . . . Car06g01235 . . Cca09g01635 Dere02g3126 . . Dod04g1867 Enph4g0059 . Glsi11g3374 . . . Gma08g00832 . . . . . . . . . . . . . . . . . Lapu3g02567 . Lasa7g03771 . Lele13g0052 Lele14g0049 Lele15g2391 Lele16g2348 . . . . . Lja4g4206 . . Mepo2g03682 . Mesa13g01485 . Mibi06g0074 . . . . . Phco4g02184 . Prci3g1337 . . Psa7g2017 . . . . . . Pumo6g01415 . Pvu2g1936 . Rops2g01537 . Seca12g05458 . Spst3g00020 . . Ssu5g2140 Sto13g0103 . . . Trre7g04294 . . . Vian1g02826 . Vifa6g01949 . . . Viun3g02026 . Vivi5g04728 . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi1g0101 Chr1 979517 981451 +
Vvi Vvi1g0102 Chr1 985039 986808 -
Adu Adu04g01080 Chr04 20184947 20187690 -
Arst Arst4g01508 Chr4 20297636 20300371 -
Lasa Lasa1g01677 Chr1 151213413 151215188 -
Mepo Mepo6g01556 Chr6 17097895 17100006 -
Phac Phac9g04028 Chr9 38581509 38584111 -
Phco Phco7g02880 Chr7 47813538 47815313 -
Pste Pste2g03257 Chr2 32479608 32480695 +
Pumo Pumo2g01463 Chr2 21878757 21879308 +
Pvu Pvu9g2513 Chr9 35657154 35658929 -
Rops Rops11g01620 Chr11 24733601 24735680 -
Seca Seca6g03924 Chr6 106924732 106933148 +
Spst Spst9g03012 Chr9 64202162 64205000 +
Trre Trre3g02039 Chr3 18084834 18085841 -
Vian Vian4g00187 Chr4 1697179 1698936 -
Vifa Vifa1g09176 Chr1 1451622586 1451624361 +
Vimu Vimu10g00265 Chr10 1634051 1635823 +
Viun Viun9g00237 Chr9 1495098 1497066 -
Vivi Vivi4g02580 Chr4 124938067 124941169 +
Vvi Vvi1g0103 Chr1 989416 993727 -
Adu Adu03g04375 Chr03 132718822 132721801 +
Aev Aev03g2345 Chr03 24946778 24951630 +
Ahy Ahy13g4320 Chr13 142808610 142812267 +
Aip Aip03g04782 Chr03 132099523 132102322 +
Apr Apr3g2144 Chr3 37335218 37340659 +
Arst Arst3g05784 Chr3 131481408 131486048 +
Car Car06g01231 Chr06 12183291 12186915 -
Cca Cca09g01638 Chr09 40243786 40247931 +
Dod Dod04g1871 Chr04 41559826 41563462 +
Gma Gma08g00835 Chr08 6858834 6863660 +
Lapu Lapu3g02697 Chr3 49608808 49612603 -
Lja Lja4g4207 Chr4 75520888 75525479 +
Mepo Mepo2g03687 Chr2 46202149 46207749 +
Mesa Mesa13g01483 Chr13 17728565 17735576 -
Phac Phac2g02906 Chr2 30853265 30858857 -
Phco Phco4g02181 Chr4 42513214 42517023 -
Pste Pste3g02384 Chr3 16902997 16908117 +
Pumo Pumo6g01410 Chr6 19213558 19219237 -
Pvu Pvu2g1934 Chr2 34334857 34340750 -
Rops Rops2g01535 Chr2 22832521 22836023 -
Seca Seca12g05465 Chr12 145293472 145298108 +
Ssu Ssu5g2145 Chr5 61728535 61732848 +
Trre Trre7g04298 Chr7 50909432 50913595 +
Vian Vian1g02822 Chr1 44186916 44190856 -
Vifa Vifa6g01946 Chr6 722494651 722498754 -
Vimu Vimu11g01609 Chr11 19858412 19862251 +
Viun Viun3g02031 Chr3 16212502 16220581 +
Vra Vra7g1016 Chr7 24603546 24607999 -
Vvi Vvi1g0104 Chr1 995790 997132 -
Adu Adu04g01082 Chr04 20284221 20287450 -
Arst Arst4g01510 Chr4 20396988 20400117 -
Lasa Lasa1g01678 Chr1 151217305 151218760 -
Mepo Mepo6g01557 Chr6 17102729 17106338 -
Mesa Mesa5g03045 Chr5 55322866 55324508 +
Phac Phac9g04027 Chr9 38575791 38579962 +
Phco Phco7g02879 Chr7 47809914 47811460 +
Pste Pste2g03261 Chr2 32500771 32504534 -
Pvu Pvu9g2512 Chr9 35650741 35654597 +
Rops Rops11g01621 Chr11 24740271 24747058 -
Seca Seca6g03923 Chr6 106918048 106921862 +
Spst Spst9g03010 Chr9 64195292 64196870 +
Sto Sto13g0101 Chr13 838795 840628 -
Trre Trre3g02041 Chr3 18092759 18094419 -
Vian Vian4g00188 Chr4 1706670 1708202 -
Vifa Vifa1g09175 Chr1 1451619274 1451621049 +
Vimu Vimu10g00269 Chr10 1646566 1648087 -
Viun Viun9g00238 Chr9 1500573 1504376 -
Vivi Vivi4g02579 Chr4 124935349 124937844 +
Vvi Vvi1g0105 Chr1 997178 1000698 -
Vvi Vvi1g0106 Chr1 1002569 1009495 -
Aev Aev03g2344 Chr03 24940487 24945539 +
Ahy Ahy13g4319 Chr13 142802755 142807919 +
Aip Aip03g04781 Chr03 132093321 132098362 +
Amo Amo13g5367 Chr13 153903757 153913257 +
Apr Apr3g2143 Chr3 37327272 37333853 +
Car Car06g01233 Chr06 12188843 12195074 -
Cca Cca09g01637 Chr09 40235722 40243743 +
Dod Dod04g1869 Chr04 41549735 41553354 +
Gma Gma08g00834 Chr08 6850819 6856948 +
Psa Psa7g2000 Chr7 145734069 145739868 +
Ssu Ssu5g2143 Chr5 61700520 61705472 +
Sto Sto13g0102 Chr13 846378 853360 -
Vra Vra7g1017 Chr7 24623760 24630227 -
Vvi Vvi1g0107 Chr1 1017874 1019921 +
Vvi Vvi1g0108 Chr1 1030308 1032146 +
Psa Psa7g2946 Chr7 211025582 211026788 +
Vvi Vvi1g0109 Chr1 1049293 1049673 -
Vvi Vvi1g0110 Chr1 1060701 1062011 +
Acco Acco06g3110 Chr06 41376114 41377463 +
Accr Accr5g00064 Chr5 1565794 1567152 -
Adu Adu03g04372 Chr03 132673186 132674572 -
Aev Aev03g2342 Chr03 24932012 24933376 -
Ahy Ahy13g4316 Chr13 142758503 142760215 -
Aip Aip03g04777 Chr03 132052707 132054093 -
Alju Alju03g0070 Chr03 1427208 1428560 -
Amo Amo13g5363 Chr13 153856040 153857426 -
Apr Apr3g2141 Chr3 37313410 37316495 +
Arst Arst3g05781 Chr3 131436865 131438251 -
Car Car06g01235 Chr06 12210240 12211600 +
Cca Cca09g01635 Chr09 40218903 40220219 -
Dere Dere02g3126 Chr02 37545506 37546867 -
Dod Dod04g1867 Chr04 41537086 41538402 -
Enph Enph4g0059 Chr4 1620581 1621885 +
Glsi Glsi11g3374 Chr11 54430925 54432217 -
Gma Gma08g00832 Chr08 6840973 6842289 -
Lapu Lapu3g02567 Chr3 47938581 47941767 -
Lasa Lasa7g03771 Chr7 613724687 613726012 -
Lele Lele13g0052 Chr13 583261 584607 -
Lele Lele14g0049 Chr14 724679 726040 -
Lele Lele15g2391 Chr15 28174732 28176090 +
Lele Lele16g2348 Chr16 23872156 23873514 +
Lja Lja4g4206 Chr4 75514076 75515425 -
Mepo Mepo2g03682 Chr2 46164896 46166215 -
Mesa Mesa13g01485 Chr13 17781618 17782901 +
Mibi Mibi06g0074 Chr06 1078180 1079538 -
Phco Phco4g02184 Chr4 42540895 42542634 +
Prci Prci3g1337 Chr3 21659128 21660456 +
Psa Psa7g2017 Chr7 147884447 147886356 -
Pumo Pumo6g01415 Chr6 19385356 19386654 +
Pvu Pvu2g1936 Chr2 34357705 34359009 +
Rops Rops2g01537 Chr2 22885613 22886887 +
Seca Seca12g05458 Chr12 145247461 145248783 -
Spst Spst3g00020 Chr3 653660 654973 -
Ssu Ssu5g2140 Chr5 61682583 61683896 -
Sto Sto13g0103 Chr13 861961 863347 +
Trre Trre7g04294 Chr7 50872490 50873836 -
Vian Vian1g02826 Chr1 44290563 44291861 +
Vifa Vifa6g01949 Chr6 724088510 724089841 +
Viun Viun3g02026 Chr3 16169842 16171933 -
Vivi Vivi5g04728 Chr5 146078871 146080393 +
Lapu Lapu3g02567 Chr3 47938581 47941767 -