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
Vvi3g0523 . . . . . Adu10g01296 . . Aev03g0210 . Ahy20g1543 . Aip10g01800 . . . . . Apr3g1685 . . . . . . . Bva13g00270 Bva14g00346 Car06g01697 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02450 . . . . . . . . . . . . Mal7g3402 . . . . . . . Mtr4g2834 . . . . Phco8g00049 . . . . . . . . Pte3g01841 . . . . Pvu3g3024 . . . . . . . . Sto2g0633 Sto10g0209 . . . . Tsu02g03414 . . . . . . Vimu11g01076 . . . . . .
Vvi3g0524 . . . . . . . . Aev03g0209 Aev05g0613 Ahy20g1540 Ahy15g0678 Aip10g01793 Aip05g00691 . . . . Apr3g1686 . . . . . . . Bva13g00269 Bva14g00345 Car06g01696 Car08g00521 . . . . . Dod02g0671 . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02449 . . . . . . . . . . . Lja2g0367 Mal7g3403 . . . . . . . Mtr4g2835 . . . . . . . . Psa2g3747 . . . . . . . . . Pvu3g3023 . . . . . . . . Sto2g0634 Sto10g0211 . . . . Tsu02g03415 . . . . . . . . . . . . .
Vvi3g0525 . Acco11g2162 . Accr9g00310 . Adu05g00705 . . . Aev05g0612 . Ahy15g0679 . Aip05g00693 . Alju09g2166 . . . . . Arst5g00890 . Bach4g00549 . Bisa11g1555 . . . Car08g00522 . . . Dere09g0783 . Dod02g0670 . Enph13g1009 . Glsi05g1564 . . . . . . . . . . . . . . . . . . . . . Lapu2g00591 . Lasa2g03195 . . . . Lele49g0247 Lele50g0259 Lele51g0257 Lele52g0265 . Lja2g0368 . . . Mepo5g00795 . Mesa17g00799 . Mibi12g1873 . . . Phac2g02402 . Phco4g01076 . Prci10g0418 . Psa2g3743 . Pste1g02477 . . . . . Pumo8g01923 . Pvu2g0219 . Rops1g01748 . Seca10g00784 . Spst2g00714 . . . . . . . Trre9g00903 . . . Vian10g00615 . Vifa1g07073 . Vimu7g02847 . Viun2g02074 . Vivi2g03221 . .
Vvi3g0526 . . . . . . . . Aev03g0207 Aev05g0611 Ahy20g1534 Ahy15g0681 Aip10g01778 Aip05g00695 . . Amo20g1722 . Apr3g1687 . . . . . . . Bva13g00266 Bva14g00343 Car06g01694 Car08g00523 . . . . . Dod02g0669 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g3376 Mal7g3404 . . . . . . . Mtr4g2836 . . . . . . . Psa6g2202 Psa2g3742 . . . . . . . . . . . . . . . . . . Sto2g0636 Sto10g0212 . . . . Tsu02g03416 . . . . . . . . . . . . .
Vvi3g0527 . . . . . Adu10g03043 . . . . . . . . . . . . . . . . . . . . . Bva14g00342 . . . . . . . . . . . . . . . . . . . . Lal1g0270 . . . . . Lan13g0270 . . . . . . Lapu2g01754 . . . . . . . . . . . Lja2g3377 . . . Mepo4g01247 . Mesa1g01373 . . . . . . . Phco8g03295 . . Psa6g2203 . . Pste1g03634 . . . . . Pumo8g00200 . Pvu3g0124 . Rops1g00237 . Seca10g05326 . Spst2g02138 . . Sto2g0638 . . . . Trre1g01322 . . . Vian10g01807 . Vifa3g03851 . Vimu7g00356 . Viun2g00244 . Vivi4g03851 . .
Vvi3g0528 . . . . . . . . Aev03g0206 . Ahy20g1533 . Aip10g01777 . . . Amo20g1721 . . . . . . . . . Bva13g00265 Bva14g00341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu2g01755 . . . . . . . . . . . Lja2g3378 . . . . . . . . . . . . . Phco8g03296 . . Psa6g2204 . . Pste1g03366 . . . . . . . Pvu3g0123 . . . . . Spst2g02139 . . Sto2g0639 . . . . . . . . . . . . Vimu7g00357 . . . Vivi4g03852 . .
Vvi3g0529 . . . . . . . . Aev03g0205 . Ahy20g1531 . Aip10g01775 . . . Amo20g1719 . Apr3g1688 . . . . . . . . . Car06g01693 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal7g3405 . . . . . . . Mtr4g2837 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr2g3568 . . . Tsu02g03417 . . . . . . . . . . . . .
Vvi3g0530 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0531 . . . . . . . . . . Ahy20g1529 . Aip10g01768 . . . Amo20g1704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g03204 . . . . . . . . . . . . . . . . . . . . . Phac2g02413 . Phco4g01069 . . . Psa2g3738 . Pste1g02495 . . Pte14g00945 . . . . Pvu2g0225 . . . . . Spst3g03968 . . . . . . . . . . . . . . . Vimu7g02853 . . . Vivi2g03215 . .
Vvi3g0532 . . . . . . . . . . . . . . . . . . Apr3g1689 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g3380 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0523 Chr3 4481840 4484748 -
Adu Adu10g01296 Chr10 32360373 32363570 +
Aev Aev03g0210 Chr03 1644801 1647496 +
Ahy Ahy20g1543 Chr20 47044880 47048159 +
Aip Aip10g01800 Chr10 43852850 43856032 +
Apr Apr3g1685 Chr3 32462757 32465870 -
Bva Bva13g00270 Chr13 1280303 1283372 +
Bva Bva14g00346 Chr14 1717417 1720384 +
Car Car06g01697 Chr06 16736014 16738805 +
Lapu Lapu3g02450 Chr3 46351483 46354253 +
Mal Mal7g3402 Chr7 98920922 98924012 -
Mtr Mtr4g2834 Chr4 41996766 42000046 -
Phco Phco8g00049 Chr8 442121 444425 -
Pte Pte3g01841 Chr3 29270578 29273259 -
Pvu Pvu3g3024 Chr3 51936395 51939301 +
Sto Sto2g0633 Chr2 5366374 5370963 -
Sto Sto10g0209 Chr10 1759199 1768301 -
Tsu Tsu02g03414 Chr02 38170831 38173597 -
Vimu Vimu11g01076 Chr11 11436084 11439008 -
Vvi Vvi3g0524 Chr3 4489118 4491489 -
Aev Aev03g0209 Chr03 1638387 1640528 +
Aev Aev05g0613 Chr05 4217869 4219568 +
Ahy Ahy20g1540 Chr20 46499789 46502739 +
Ahy Ahy15g0678 Chr15 9107234 9109721 -
Aip Aip10g01793 Chr10 43402140 43405522 +
Aip Aip05g00691 Chr05 8788415 8790872 -
Apr Apr3g1686 Chr3 32470635 32473211 -
Bva Bva13g00269 Chr13 1274729 1277179 +
Bva Bva14g00345 Chr14 1712428 1715490 +
Car Car06g01696 Chr06 16728802 16731564 +
Car Car08g00521 Chr08 4437689 4440171 -
Dod Dod02g0671 Chr02 8738337 8741180 +
Lapu Lapu3g02449 Chr3 46339566 46342979 +
Lja Lja2g0367 Chr2 3379224 3381179 -
Mal Mal7g3403 Chr7 98948506 98950948 -
Mtr Mtr4g2835 Chr4 42012204 42015426 -
Psa Psa2g3747 Chr2 398626926 398629624 +
Pvu Pvu3g3023 Chr3 51926447 51929176 +
Sto Sto2g0634 Chr2 5378509 5380600 -
Sto Sto10g0211 Chr10 1773958 1775887 -
Tsu Tsu02g03415 Chr02 38195911 38199481 -
Vvi Vvi3g0525 Chr3 4502406 4509862 -
Acco Acco11g2162 Chr11 35546527 35550967 -
Accr Accr9g00310 Chr9 3502680 3507220 +
Adu Adu05g00705 Chr05 8348105 8352856 -
Aev Aev05g0612 Chr05 4205515 4210595 +
Ahy Ahy15g0679 Chr15 9149910 9154659 -
Aip Aip05g00693 Chr05 8829757 8834989 -
Alju Alju09g2166 Chr09 45087035 45091577 -
Arst Arst5g00890 Chr5 8373771 8378479 -
Bach Bach4g00549 Chr4 3728896 3733557 -
Bisa Bisa11g1555 Chr11 36229557 36235114 -
Car Car08g00522 Chr08 4452280 4457228 -
Dere Dere09g0783 Chr09 10772329 10777094 -
Dod Dod02g0670 Chr02 8722689 8729292 +
Enph Enph13g1009 Chr13 16053774 16058920 +
Glsi Glsi05g1564 Chr05 64042904 64047791 +
Lapu Lapu2g00591 Chr2 5160439 5165594 -
Lasa Lasa2g03195 Chr2 524835600 524839585 -
Lele Lele49g0247 Chr49 1432063 1436493 +
Lele Lele50g0259 Chr50 1503709 1508224 +
Lele Lele51g0257 Chr51 1458071 1462506 +
Lele Lele52g0265 Chr52 1538404 1542867 +
Lja Lja2g0368 Chr2 3389402 3394775 -
Mepo Mepo5g00795 Chr5 7594731 7599192 -
Mesa Mesa17g00799 Chr17 10277098 10281107 -
Mibi Mibi12g1873 Chr12 35090287 35094788 -
Phac Phac2g02402 Chr2 25649179 25654781 -
Phco Phco4g01076 Chr4 8645665 8649939 +
Prci Prci10g0418 Chr10 2761077 2765900 +
Psa Psa2g3743 Chr2 398462532 398467682 +
Pste Pste1g02477 Chr1 9080024 9084952 -
Pumo Pumo8g01923 Chr8 55691675 55696314 +
Pvu Pvu2g0219 Chr2 2345717 2350932 -
Rops Rops1g01748 Chr1 36304613 36310962 +
Seca Seca10g00784 Chr10 7491075 7498108 -
Spst Spst2g00714 Chr2 5963217 5967538 -
Trre Trre9g00903 Chr9 6998257 7002308 -
Vian Vian10g00615 Chr10 5886084 5890415 -
Vifa Vifa1g07073 Chr1 1091991138 1091995171 +
Vimu Vimu7g02847 Chr7 24075643 24079993 -
Viun Viun2g02074 Chr2 28960271 28964736 +
Vivi Vivi2g03221 Chr2 133857539 133861844 +
Vvi Vvi3g0526 Chr3 4514308 4520362 +
Aev Aev03g0207 Chr03 1614497 1617448 -
Aev Aev05g0611 Chr05 4199711 4202956 -
Ahy Ahy20g1534 Chr20 45659228 45663067 -
Ahy Ahy15g0681 Chr15 9166942 9171639 +
Aip Aip10g01778 Chr10 42682058 42685858 -
Aip Aip05g00695 Chr05 8846649 8851261 +
Amo Amo20g1722 Chr20 49576353 49579941 -
Apr Apr3g1687 Chr3 32490777 32494960 +
Bva Bva13g00266 Chr13 1261959 1265024 -
Bva Bva14g00343 Chr14 1696181 1699425 -
Car Car06g01694 Chr06 16691109 16694623 -
Car Car08g00523 Chr08 4462276 4466248 +
Dod Dod02g0669 Chr02 8690496 8694875 -
Lja Lja2g3376 Chr2 77126377 77130982 +
Mal Mal7g3404 Chr7 98973519 98976349 +
Mtr Mtr4g2836 Chr4 42036367 42039593 +
Psa Psa6g2202 Chr6 155447256 155450294 +
Psa Psa2g3742 Chr2 398395024 398398197 -
Sto Sto2g0636 Chr2 5409066 5412528 +
Sto Sto10g0212 Chr10 1790759 1794402 +
Tsu Tsu02g03416 Chr02 38224768 38228290 +
Vvi Vvi3g0527 Chr3 4586630 4588907 -
Adu Adu10g03043 Chr10 106434292 106436942 +
Bva Bva14g00342 Chr14 1693071 1695817 +
Lal Lal1g0270 Chr1 1584942 1586270 +
Lan Lan13g0270 Chr13 1710077 1715681 +
Lapu Lapu2g01754 Chr2 31222717 31227128 -
Lja Lja2g3377 Chr2 77132801 77141886 -
Mepo Mepo4g01247 Chr4 16038899 16043654 -
Mesa Mesa1g01373 Chr1 18896742 18898778 -
Phco Phco8g03295 Chr8 47593810 47595992 -
Psa Psa6g2203 Chr6 155452131 155458326 -
Pste Pste1g03634 Chr1 17351226 17355138 -
Pumo Pumo8g00200 Chr8 6313248 6317553 +
Pvu Pvu3g0124 Chr3 1128083 1131598 +
Rops Rops1g00237 Chr1 6824801 6829522 -
Seca Seca10g05326 Chr10 121440349 121454158 +
Spst Spst2g02138 Chr2 20325534 20327768 -
Sto Sto2g0638 Chr2 5414028 5415958 -
Trre Trre1g01322 Chr1 9905391 9907112 -
Vian Vian10g01807 Chr10 29902247 29904379 -
Vifa Vifa3g03851 Chr3 1134843236 1134844993 +
Vimu Vimu7g00356 Chr7 4076021 4085207 -
Viun Viun2g00244 Chr2 4791411 4795505 +
Vivi Vivi4g03851 Chr4 157847425 157850125 -
Vvi Vvi3g0528 Chr3 4593424 4601048 -
Aev Aev03g0206 Chr03 1609829 1613162 +
Ahy Ahy20g1533 Chr20 45654801 45658397 +
Aip Aip10g01777 Chr10 42677708 42681251 +
Amo Amo20g1721 Chr20 49571796 49575338 +
Bva Bva13g00265 Chr13 1254798 1261810 +
Bva Bva14g00341 Chr14 1687842 1692499 +
Lapu Lapu2g01755 Chr2 31230481 31235026 -
Lja Lja2g3378 Chr2 77155957 77176196 -
Phco Phco8g03296 Chr8 47597277 47601776 -
Psa Psa6g2204 Chr6 155565988 155571543 -
Pste Pste1g03366 Chr1 15511691 15517740 +
Pvu Pvu3g0123 Chr3 1121249 1127162 +
Spst Spst2g02139 Chr2 20329642 20338556 -
Sto Sto2g0639 Chr2 5418073 5423398 -
Vimu Vimu7g00357 Chr7 4087296 4092480 -
Vivi Vivi4g03852 Chr4 157852334 157858171 -
Vvi Vvi3g0529 Chr3 4602584 4617416 -
Aev Aev03g0205 Chr03 1595214 1608834 +
Ahy Ahy20g1531 Chr20 45550137 45565676 +
Aip Aip10g01775 Chr10 42574722 42590366 +
Amo Amo20g1719 Chr20 49467328 49482756 +
Apr Apr3g1688 Chr3 32497077 32513484 -
Car Car06g01693 Chr06 16675536 16691008 +
Mal Mal7g3405 Chr7 98977383 98993194 -
Mtr Mtr4g2837 Chr4 42040006 42054700 -
Tpr Tpr2g3568 Chr2 38823986 38835895 -
Tsu Tsu02g03417 Chr02 38228858 38254640 -
Vvi Vvi3g0530 Chr3 4625594 4625857 -
Vvi Vvi3g0531 Chr3 4640645 4641638 -
Ahy Ahy20g1529 Chr20 45083464 45096642 +
Aip Aip10g01768 Chr10 42143423 42152910 +
Amo Amo20g1704 Chr20 48854167 48867198 +
Lasa Lasa2g03204 Chr2 525034581 525035542 -
Phac Phac2g02413 Chr2 25738580 25743575 -
Phco Phco4g01069 Chr4 8578746 8580394 +
Psa Psa2g3738 Chr2 398251382 398257752 +
Pste Pste1g02495 Chr1 9245382 9246110 -
Pte Pte14g00945 Chr14 31123819 31125230 -
Pvu Pvu2g0225 Chr2 2408866 2410730 -
Spst Spst3g03968 Chr3 90122925 90131406 -
Vimu Vimu7g02853 Chr7 24130065 24131287 -
Vivi Vivi2g03215 Chr2 133717975 133719440 +
Vvi Vvi3g0532 Chr3 4643010 4644218 -
Apr Apr3g1689 Chr3 32539474 32541716 -
Lja Lja2g3380 Chr2 77224226 77231684 -
Pte Pte14g00945 Chr14 31123819 31125230 -
Pste Pste1g03366 Chr1 15511691 15517740 +
Tpr Tpr2g3568 Chr2 38823986 38835895 -