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
Vvi3g0483 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g00286 Bva14g00360 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g0614 Sto10g0199 . . . . . . . . . . . . . . . . . .
Vvi3g0484 . . . . . Adu01g00951 . . . . . . . . . . . . . . . Arst1g01307 . . . Bisa01g1975 . . . . . . . Dere13g0529 . . . . . Glsi09g0468 . . . . . . . . . . . . . . . . . . . . . Lapu3g01552 . Lasa4g02494 . . . . . . . . . . . . . Mepo1g01903 . Mesa29g02023 . . . . . . . Phco8g00601 . . . . . Pste7g01181 . . Pte14g00966 Pte2g00354 . Pumo4g01982 . Pvu3g2514 . Rops2g04546 . Seca12g02463 . Spst3g04008 . . . . . . . Trre15g03861 . . . Vian1g01671 . Vifa4g02596 . Vimu11g00484 . Viun3g03812 . Vivi1g02893 . .
Vvi3g0485 . . . . . . . . . . . . . . . . . . Apr3g1669 . . . . . . . Bva13g00285 . Car06g01713 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02465 . . . . . . . . . . . . Mal7g3378 . . . . . . . Mtr4g2814 . . . . Phco8g00026 . . . . . . . . . . . . . Pvu3g3040 . . . . . . . . . Sto10g0200 Tpr4g1869 . . . Tsu02g03373 . . . . . . Vimu11g01086 . . . . . .
Vvi3g0486 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0487 . . . . . . . . . . . . . . . . . . Apr3g1670 . . . . . . . . Bva14g00359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02464 . . . . . . . . . . . . . . . . . . . . . . . . . Phco8g00027 . . . . . . . . Pte3g01835 . . . . Pvu3g3039 . . . . . . . . . . . . . . . . . . . . . Vimu11g01084 . . . . . .
Vvi3g0488 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g00358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g0202 . . . . . . . . . . . . . . . . . .
Vvi3g0489 . . . . . . . . . Aev05g1212 Ahy20g1679 Ahy15g1276 Aip10g01952 Aip05g01339 . . . Amo15g0168 . . . . . . . . . . . Car08g00056 . . . . . Dod02g1354 . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02458 . . . . . . . . . . . . . . . . . . . . . . . . . Phco8g00032 . . . . . . . . Pte3g01836 . . . . Pvu3g3035 . . . . . Spst3g02165 . . . . . . . . . . . . . . . Vimu11g01079 . . . . . .
Vvi3g0490 . . . . . . . . . Aev05g1211 . Ahy15g1275 . Aip05g01338 . . . . Apr3g1671 . . . . . . . . . . . . . . . . Dod02g1353 . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02460 . . . . . . . . . . . . Mal7g3382 . . . . . . . Mtr4g2817 . . . . Phco8g00031 . . . . . . . . . . . . . Pvu3g3036 . . . . . Spst3g02164 . . . . Tpr4g1866 . . . Tsu02g03389 . . . . . . Vimu11g01081 . . . . . .
Vvi3g0491 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02461 . . . . . . . . . . . . . . . . . . . . . . . . . Phco8g00030 . . . . . . . . . . . . . Pvu3g3037 . . . . . Spst3g02163 . . . . . . . . . . . . . . . Vimu11g01082 . . . . . .
Vvi3g0492 . . . . . . . . . Aev05g1210 . Ahy15g1274 . Aip05g01336 . . . Amo15g0166 Apr3g1672 . . . . . . . . . . Car08g00057 . . . . . Dod02g1351 . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02462 . . . . . . . . . . . . Mal7g3383 . . . . . . . Mtr4g2818 . . . . Phco8g00029 . . Psa7g2849 . . . . . . . . . . Pvu3g3038 . . . . . Spst3g02162 . . . . Tpr4g1864 . . . Tsu02g03390 . . . . . . Vimu11g01083 . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0483 Chr3 4176729 4178437 -
Bva Bva13g00286 Chr13 1346964 1349799 +
Bva Bva14g00360 Chr14 1789225 1791077 +
Sto Sto2g0614 Chr2 5200513 5203173 -
Sto Sto10g0199 Chr10 1648649 1653000 -
Vvi Vvi3g0484 Chr3 4180639 4181979 -
Adu Adu01g00951 Chr01 13038822 13042386 +
Arst Arst1g01307 Chr1 13124951 13128249 +
Bisa Bisa01g1975 Chr01 34813274 34816921 +
Dere Dere13g0529 Chr13 6587926 6591116 -
Glsi Glsi09g0468 Chr09 3242333 3245627 -
Lapu Lapu3g01552 Chr3 18745758 18749793 -
Lasa Lasa4g02494 Chr4 484050598 484053072 +
Mepo Mepo1g01903 Chr1 19118027 19120412 -
Mesa Mesa29g02023 Chr29 27208178 27210965 -
Phco Phco8g00601 Chr8 6044659 6048555 +
Pste Pste7g01181 Chr7 10839077 10839895 -
Pte Pte14g00966 Chr14 31288791 31291550 +
Pte Pte2g00354 Chr2 2685857 2688457 +
Pumo Pumo4g01982 Chr4 27072972 27077380 -
Pvu Pvu3g2514 Chr3 46941000 46945458 -
Rops Rops2g04546 Chr2 83072229 83076831 -
Seca Seca12g02463 Chr12 37355955 37360488 -
Spst Spst3g04008 Chr3 90762653 90766608 +
Trre Trre15g03861 Chr15 48382366 48386040 -
Vian Vian1g01671 Chr1 19178211 19182054 -
Vifa Vifa4g02596 Chr4 793741760 793744243 +
Vimu Vimu11g00484 Chr11 5190757 5194662 -
Viun Viun3g03812 Chr3 45336207 45339901 +
Vivi Vivi1g02893 Chr1 62963831 62966549 -
Vvi Vvi3g0485 Chr3 4192892 4198388 -
Apr Apr3g1669 Chr3 32252795 32256925 -
Bva Bva13g00285 Chr13 1342955 1346466 +
Car Car06g01713 Chr06 16900648 16905463 +
Lapu Lapu3g02465 Chr3 46565820 46570438 +
Mal Mal7g3378 Chr7 98607346 98610530 -
Mtr Mtr4g2814 Chr4 41830978 41835392 -
Phco Phco8g00026 Chr8 284259 287509 -
Pvu Pvu3g3040 Chr3 52061346 52065409 +
Sto Sto10g0200 Chr10 1655883 1657684 -
Tpr Tpr4g1869 Chr4 19562408 19566804 +
Tsu Tsu02g03373 Chr02 37800316 37804805 -
Vimu Vimu11g01086 Chr11 11556019 11556396 +
Vvi Vvi3g0486 Chr3 4201263 4202164 +
Vvi Vvi3g0487 Chr3 4207763 4209088 -
Apr Apr3g1670 Chr3 32269293 32270915 -
Bva Bva14g00359 Chr14 1784327 1786017 +
Lapu Lapu3g02464 Chr3 46548581 46550269 +
Phco Phco8g00027 Chr8 294788 296621 -
Pte Pte3g01835 Chr3 29190096 29192157 -
Pvu Pvu3g3039 Chr3 52055649 52056835 +
Vimu Vimu11g01084 Chr11 11536767 11538549 -
Vvi Vvi3g0488 Chr3 4216614 4236062 -
Bva Bva14g00358 Chr14 1773765 1780925 +
Sto Sto10g0202 Chr10 1676150 1684850 -
Vvi Vvi3g0489 Chr3 4250969 4251940 +
Aev Aev05g1212 Chr05 8477791 8478546 +
Ahy Ahy20g1679 Chr20 73641265 73642559 +
Ahy Ahy15g1276 Chr15 20445048 20446284 +
Aip Aip10g01952 Chr10 69520731 69522001 +
Aip Aip05g01339 Chr05 19732141 19733403 +
Amo Amo15g0168 Chr15 6501033 6502290 -
Car Car08g00056 Chr08 512914 514199 -
Dod Dod02g1354 Chr02 16264081 16265669 +
Lapu Lapu3g02458 Chr3 46495256 46496917 +
Phco Phco8g00032 Chr8 321771 322694 -
Pte Pte3g01836 Chr3 29197989 29199337 -
Pvu Pvu3g3035 Chr3 52031897 52035256 +
Spst Spst3g02165 Chr3 60356600 60357556 +
Vimu Vimu11g01079 Chr11 11473499 11475603 +
Vvi Vvi3g0490 Chr3 4254017 4254466 +
Aev Aev05g1211 Chr05 8471569 8472687 -
Ahy Ahy15g1275 Chr15 20360046 20361422 +
Aip Aip05g01338 Chr05 19651519 19652493 +
Apr Apr3g1671 Chr3 32286258 32288301 -
Dod Dod02g1353 Chr02 16258706 16259826 +
Lapu Lapu3g02460 Chr3 46513729 46514679 +
Mal Mal7g3382 Chr7 98646664 98647734 +
Mtr Mtr4g2817 Chr4 41855304 41856633 -
Phco Phco8g00031 Chr8 315846 316859 -
Pvu Pvu3g3036 Chr3 52036637 52037678 +
Spst Spst3g02164 Chr3 60348734 60349684 +
Tpr Tpr4g1866 Chr4 19529596 19530996 +
Tsu Tsu02g03389 Chr02 37958302 37959800 +
Vimu Vimu11g01081 Chr11 11498235 11498651 +
Vvi Vvi3g0491 Chr3 4259150 4260121 +
Lapu Lapu3g02461 Chr3 46522935 46524232 +
Phco Phco8g00030 Chr8 310689 311639 -
Pvu Pvu3g3037 Chr3 52045794 52047139 +
Spst Spst3g02163 Chr3 60310484 60311434 +
Vimu Vimu11g01082 Chr11 11498856 11499299 +
Vvi Vvi3g0492 Chr3 4261888 4262850 +
Aev Aev05g1210 Chr05 8465068 8466072 -
Ahy Ahy15g1274 Chr15 20271915 20273147 -
Aip Aip05g01336 Chr05 19573988 19575275 -
Amo Amo15g0166 Chr15 6459791 6461156 +
Apr Apr3g1672 Chr3 32294661 32295783 -
Car Car08g00057 Chr08 521584 522579 +
Dod Dod02g1351 Chr02 16180682 16182178 +
Lapu Lapu3g02462 Chr3 46529128 46530416 +
Mal Mal7g3383 Chr7 98655365 98656330 +
Mtr Mtr4g2818 Chr4 41860531 41861936 +
Phco Phco8g00029 Chr8 303325 304766 -
Psa Psa7g2849 Chr7 204122675 204124400 -
Pvu Pvu3g3038 Chr3 52047623 52048921 +
Spst Spst3g02162 Chr3 60233839 60234759 +
Tpr Tpr4g1864 Chr4 19514046 19515519 -
Tsu Tsu02g03390 Chr02 37961695 37962660 +
Vimu Vimu11g01083 Chr11 11512721 11517369 +
Lapu Lapu3g02462 Chr3 46529128 46530416 +
Phco Phco8g00029 Chr8 303325 304766 -
Pvu Pvu3g3038 Chr3 52047623 52048921 +
Spst Spst3g02162 Chr3 60233839 60234759 +
Vimu Vimu11g01083 Chr11 11512721 11517369 +
Lapu Lapu3g02461 Chr3 46522935 46524232 +
Phco Phco8g00030 Chr8 310689 311639 -
Pvu Pvu3g3037 Chr3 52045794 52047139 +
Spst Spst3g02163 Chr3 60310484 60311434 +
Vimu Vimu11g01082 Chr11 11498856 11499299 +
Lapu Lapu3g02460 Chr3 46513729 46514679 +
Phco Phco8g00031 Chr8 315846 316859 -
Pvu Pvu3g3036 Chr3 52036637 52037678 +
Spst Spst3g02164 Chr3 60348734 60349684 +
Vimu Vimu11g01081 Chr11 11498235 11498651 +
Ahy Ahy20g1679 Chr20 73641265 73642559 +
Aip Aip10g01952 Chr10 69520731 69522001 +
Lapu Lapu3g02458 Chr3 46495256 46496917 +
Phco Phco8g00032 Chr8 321771 322694 -
Pte Pte3g01836 Chr3 29197989 29199337 -
Pvu Pvu3g3035 Chr3 52031897 52035256 +
Spst Spst3g02165 Chr3 60356600 60357556 +
Vimu Vimu11g01079 Chr11 11473499 11475603 +
Adu Adu01g00951 Chr01 13038822 13042386 +
Arst Arst1g01307 Chr1 13124951 13128249 +
Bisa Bisa01g1975 Chr01 34813274 34816921 +
Dere Dere13g0529 Chr13 6587926 6591116 -
Glsi Glsi09g0468 Chr09 3242333 3245627 -
Lapu Lapu3g01552 Chr3 18745758 18749793 -
Lasa Lasa4g02494 Chr4 484050598 484053072 +
Mepo Mepo1g01903 Chr1 19118027 19120412 -
Mesa Mesa29g02023 Chr29 27208178 27210965 -
Phco Phco8g00601 Chr8 6044659 6048555 +
Pste Pste7g01181 Chr7 10839077 10839895 -
Pte Pte14g00966 Chr14 31288791 31291550 +
Pte Pte2g00354 Chr2 2685857 2688457 +
Pumo Pumo4g01982 Chr4 27072972 27077380 -
Pvu Pvu3g2514 Chr3 46941000 46945458 -
Rops Rops2g04546 Chr2 83072229 83076831 -
Seca Seca12g02463 Chr12 37355955 37360488 -
Spst Spst3g04008 Chr3 90762653 90766608 +
Trre Trre15g03861 Chr15 48382366 48386040 -
Vian Vian1g01671 Chr1 19178211 19182054 -
Vifa Vifa4g02596 Chr4 793741760 793744243 +
Vimu Vimu11g00484 Chr11 5190757 5194662 -
Viun Viun3g03812 Chr3 45336207 45339901 +
Vivi Vivi1g02893 Chr1 62963831 62966549 -
Pte Pte3g01836 Chr3 29197989 29199337 -