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
Vvi1g0871 . . . . . . . . . . . . . . . . . . . . Arst5g01929 . . . . . Bva08g01291 . . . . . . . . . . . . . Gma02g00286 . . . . . . . . . . . . . . . . . . . Lapu2g01563 . Lasa2g00433 . . . . . . . . . . . . . . . . . . . . . Phac2g01113 . Phco4g01475 . . . Psa2g2468 . . Pste2g03038 Pte14g00227 . . . Pumo8g01191 . Pvu2g0758 Pvu9g1274 Rops1g00881 . . . Spst2g01445 Spst9g01277 . . Sto11g1092 . . . . . . . Vian10g01148 Vian4g01555 Vifa1g04733 Vifa2g01769 Vimu7g03756 Vimu10g02173 . . . . . .
Vvi1g0872 . . . . . . Aed11g0221 . . . . . . . . . . . Apr7g1610 . . . . . . . . . . . Cca06g00797 . . . . . . . . . . Gma01g00311 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal6g1684 . . . . . . . Mtr5g1436 . . . . . . . Psa2g2471 . . . . . . . . . . . . . . . . . Ssu2g1748 . . . Tpr2g1768 . . . Tsu05g01523 . . . . . . . . . . . . .
Vvi1g0873 . . . . Adu05g01511 . . . . . . . . . . . . . . . Arst5g01931 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu2g01562 . Lasa2g00431 . . . . . . . . . . . Mal6g1686 . . . . . . . Mtr5g1437 . Phac2g01115 . Phco4g01476 . . . . . . . . . . . . . Pvu2g0759 . . . . . Spst2g01446 . . . Sto11g1091 . Tpr2g1769 . . . . . . . . . Vimu7g03758 . . . Vivi2g01414 . . .
Vvi1g0874 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0875 . . . . . . Aed11g0222 . Aev05g1305 . Ahy15g1460 Ahy13g3721 Aip05g01538 Aip03g04162 . . . Amo13g4694 Apr7g1609 . . . . . . . . . Car02g00610 Car07g01993 Cca06g00796 . . . Dod02g1489 . . . . . Gma02g00285 Gma01g00312 . . Gso2g0268 Gso2g0268 . . . . . . Lal16g0553 Lal15g0501 . . . . . . . . . . . . . . . . . . Lja2g1001 . Mal6g1687 . . . . . . . Mtr5g1438 . . . . . . . Psa2g2490 Psa4g2928 . . . . . . . . . . . . . . . . Ssu2g1746 . Sto11g1089 . Tpr2g1771 . . . Tsu05g01527 . . . . . . . . . . . . .
Vvi1g0876 . . . . . . . . Aev05g1306 Aev03g0526 Ahy15g1461 Ahy13g3723 Aip05g01539 Aip03g04164 . . Amo15g0119 Amo13g4696 Apr7g1608 Apr3g0824 . . . . . . . . Car02g00612 Car07g01994 Cca06g00795 . . . Dod02g1490 Dod04g0025 . . . . Gma02g00284 Gma01g00313 Gma08g02732 Gma18g01212 Gso2g0267 Gso2g0267 Gso2g0267 Gso2g0267 . . . . Lal16g0554 . . . . . . . . . . . . . . . . . . . Lja2g1002 . Mal6g1689 . . . . . . . Mtr5g1439 Mtr8g1925 . . . . . . . Psa4g2929 . . . . . . . . . . . . . . . . Ssu2g1745 . Sto11g1088 . Tpr2g1772 . . . Tsu05g01528 . . . . . . . . . . . . .
Vvi1g0877 . . . . Adu05g01517 . Aed11g0223 . Aev05g1307 . Ahy15g1462 . Aip05g01540 . . . Amo15g0118 . Apr7g1607 . Arst5g01948 . . . . . . . . . Cca06g00794 . . . Dod02g1491 . . . . . Gma02g00283 Gma01g00314 . . Gso2g0266 Gso2g0266 . . . . . Lal23g1044 . . . . . . . . . . Lasa2g00421 . . . . . . . . . Lja2g1004 . Mal6g1691 . Mepo5g01626 . Mesa17g01810 . . . Mtr5g1440 . . . Phco4g01478 . . . Psa2g2495 . Pste1g02134 . . . . . Pumo8g01186 . Pvu2g0760 . Rops1g00887 . Seca10g01516 . Spst2g01449 . Ssu2g1744 . Sto11g1087 . Tpr2g1773 . . . Tsu05g01529 . Vian10g01146 . Vifa1g04761 . Vimu7g03760 . Viun2g01169 . Vivi2g01433 . . .
Vvi1g0878 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva08g01351 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g4363 . . . . . . . . . . . . . . . . . .
Vvi1g0879 . Acco04g2630 . Accr8g00128 . Adu01g01918 . . . . . . . . . Alju06g2600 . . . . . Arst1g02532 . . . Bisa08g1929 . . . . . . . Dere03g0826 . . . Enph6g0636 . Glsi02g0742 . . . . . . . . . . . . . . . . . . . . . Lapu3g01092 . Lasa4g03167 . . . . Lele21g1815 Lele22g1792 Lele23g0192 Lele24g1752 . . . . . Mepo1g01358 . . . Mibi09g0222 . . . Phac3g03032 . Phco8g01259 . Prci4g2919 . . . Pste6g02312 . . . . . . . Pvu3g2039 . . . . . Spst3g04608 . . . . . . . Trre15g02805 . . . . . . . Vimu7g00709 . . . Vivi1g02090 . .
Vvi1g0880 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva08g01352 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g2891 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi1g0871 Chr1 9295425 9299394 +
Arst Arst5g01929 Chr5 25498517 25502216 +
Bva Bva08g01291 Chr08 6732649 6735487 -
Gma Gma02g00286 Chr02 2987304 2991039 -
Lapu Lapu2g01563 Chr2 29077788 29081039 -
Lasa Lasa2g00433 Chr2 56875879 56896769 -
Phac Phac2g01113 Chr2 7520039 7525458 +
Phco Phco4g01475 Chr4 13313105 13315565 +
Psa Psa2g2468 Chr2 282663048 282669743 -
Pste Pste2g03038 Chr2 30380876 30384505 +
Pte Pte14g00227 Chr14 9838616 9841310 -
Pumo Pumo8g01191 Chr8 43207770 43212544 -
Pvu Pvu2g0758 Chr2 10534259 10536865 +
Pvu Pvu9g1274 Chr9 18356925 18360571 +
Rops Rops1g00881 Chr1 21315584 21319036 +
Spst Spst2g01445 Chr2 13245869 13249722 +
Spst Spst9g01277 Chr9 12223813 12229086 +
Sto Sto11g1092 Chr11 11008865 11011181 -
Vian Vian10g01148 Chr10 18739817 18741203 -
Vian Vian4g01555 Chr4 30843687 30847026 -
Vifa Vifa1g04733 Chr1 740579079 740580017 +
Vifa Vifa2g01769 Chr2 456647210 456649588 -
Vimu Vimu7g03756 Chr7 33010047 33011923 +
Vimu Vimu10g02173 Chr10 31907391 31908536 -
Vvi Vvi1g0872 Chr1 9302997 9306029 +
Aed Aed11g0221 Chr11 1835337 1838245 +
Apr Apr7g1610 Chr7 23245819 23249370 -
Cca Cca06g00797 Chr06 20834507 20837336 -
Gma Gma01g00311 Chr01 3632798 3636825 +
Mal Mal6g1684 Chr6 31863424 31945483 +
Mtr Mtr5g1436 Chr5 15119515 15123054 +
Psa Psa2g2471 Chr2 282809985 282825065 -
Ssu Ssu2g1748 Chr2 67704430 67707866 -
Tpr Tpr2g1768 Chr2 20945919 20952512 +
Tsu Tsu05g01523 Chr05 14758643 14769044 +
Vvi Vvi1g0873 Chr1 9309061 9312724 +
Adu Adu05g01511 Chr05 25572662 25580092 +
Arst Arst5g01931 Chr5 25498520 25502216 +
Lapu Lapu2g01562 Chr2 29063048 29070705 -
Lasa Lasa2g00431 Chr2 56225525 56235057 -
Mal Mal6g1686 Chr6 32048605 32054884 +
Mtr Mtr5g1437 Chr5 15129185 15134954 +
Phac Phac2g01115 Chr2 7544416 7547643 +
Phco Phco4g01476 Chr4 13324537 13330842 +
Pvu Pvu2g0759 Chr2 10559694 10566192 +
Spst Spst2g01446 Chr2 13249848 13253475 +
Sto Sto11g1091 Chr11 11004122 11005740 -
Tpr Tpr2g1769 Chr2 20965154 20971952 +
Vimu Vimu7g03758 Chr7 33026548 33027794 +
Vivi Vivi2g01414 Chr2 60813508 60826940 -
Vvi Vvi1g0874 Chr1 9335985 9336206 -
Vvi Vvi1g0875 Chr1 9337386 9338233 -
Aed Aed11g0222 Chr11 1840306 1841905 -
Aev Aev05g1305 Chr05 9256563 9257932 -
Ahy Ahy15g1460 Chr15 27343210 27344928 -
Ahy Ahy13g3721 Chr13 136117348 136119021 -
Aip Aip05g01538 Chr05 26228695 26230369 -
Aip Aip03g04162 Chr03 125601309 125602945 -
Amo Amo13g4694 Chr13 144635501 144637478 -
Apr Apr7g1609 Chr7 23237182 23238393 +
Car Car02g00610 Chr02 7715691 7716614 -
Car Car07g01993 Chr07 23348158 23350349 -
Cca Cca06g00796 Chr06 20831943 20833071 +
Dod Dod02g1489 Chr02 17871190 17873948 -
Gma Gma02g00285 Chr02 2980239 2981389 +
Gma Gma01g00312 Chr01 3640249 3642264 -
Gso Gso2g0268 Chr2 2884662 2885783 +
Gso Gso2g0268 Chr2 2884662 2885783 +
Lal Lal16g0553 Chr16 3572787 3573665 -
Lal Lal15g0501 Chr15 3469171 3470221 -
Lja Lja2g1001 Chr2 9441455 9442702 -
Mal Mal6g1687 Chr6 32056592 32058123 -
Mtr Mtr5g1438 Chr5 15139816 15150226 -
Psa Psa2g2490 Chr2 288175655 288176747 +
Psa Psa4g2928 Chr4 234954825 234955943 -
Ssu Ssu2g1746 Chr2 67673223 67675286 +
Sto Sto11g1089 Chr11 10993027 10993671 +
Tpr Tpr2g1771 Chr2 20995150 20996398 -
Tsu Tsu05g01527 Chr05 14789835 14791197 -
Vvi Vvi1g0876 Chr1 9342575 9344861 +
Aev Aev05g1306 Chr05 9260515 9263400 +
Aev Aev03g0526 Chr03 3852310 3853913 -
Ahy Ahy15g1461 Chr15 27352585 27356345 +
Ahy Ahy13g3723 Chr13 136127488 136129696 +
Aip Aip05g01539 Chr05 26233185 26241595 +
Aip Aip03g04164 Chr03 125612369 125613961 +
Amo Amo15g0119 Chr15 4543992 4546979 +
Amo Amo13g4696 Chr13 144646234 144648134 +
Apr Apr7g1608 Chr7 23228765 23242758 -
Apr Apr3g0824 Chr3 21578131 21580964 +
Car Car02g00612 Chr02 7736137 7739720 +
Car Car07g01994 Chr07 23364913 23368031 +
Cca Cca06g00795 Chr06 20819901 20825175 -
Dod Dod02g1490 Chr02 17880560 17883595 +
Dod Dod04g0025 Chr04 381690 384908 -
Gma Gma02g00284 Chr02 2967709 2971344 -
Gma Gma01g00313 Chr01 3652444 3656688 +
Gma Gma08g02732 Chr08 42884129 42888668 +
Gma Gma18g01212 Chr18 19139792 19145111 -
Gso Gso2g0267 Chr2 2872833 2876549 -
Gso Gso2g0267 Chr2 2872833 2876549 -
Gso Gso2g0267 Chr2 2872833 2876549 -
Gso Gso2g0267 Chr2 2872833 2876549 -
Lal Lal16g0554 Chr16 3576134 3583278 +
Lja Lja2g1002 Chr2 9447525 9451650 +
Mal Mal6g1689 Chr6 32077127 32079631 +
Mtr Mtr5g1439 Chr5 15154246 15157168 +
Mtr Mtr8g1925 Chr8 29001175 29003432 +
Psa Psa4g2929 Chr4 234968513 234975590 -
Ssu Ssu2g1745 Chr2 67654614 67658821 -
Sto Sto11g1088 Chr11 10988684 10991331 -
Tpr Tpr2g1772 Chr2 21000064 21003718 +
Tsu Tsu05g01528 Chr05 14797659 14801126 +
Vvi Vvi1g0877 Chr1 9345791 9354107 -
Adu Adu05g01517 Chr05 25619853 25626593 -
Aed Aed11g0223 Chr11 1845937 1856157 -
Aev Aev05g1307 Chr05 9264684 9267401 -
Ahy Ahy15g1462 Chr15 27353633 27359731 -
Aip Aip05g01540 Chr05 26243555 26244632 -
Amo Amo15g0118 Chr15 4543548 4550496 -
Apr Apr7g1607 Chr7 23226261 23229395 +
Arst Arst5g01948 Chr5 25668129 25673943 -
Cca Cca06g00794 Chr06 20817499 20825186 +
Dod Dod02g1491 Chr02 17884817 17886442 -
Gma Gma02g00283 Chr02 2959551 2967015 +
Gma Gma01g00314 Chr01 3657215 3662663 -
Gso Gso2g0266 Chr2 2864447 2872476 +
Gso Gso2g0266 Chr2 2864447 2872476 +
Lal Lal23g1044 Chr23 12197985 12200148 +
Lasa Lasa2g00421 Chr2 53006299 53008201 +
Lja Lja2g1004 Chr2 9452583 9454387 -
Mal Mal6g1691 Chr6 32083779 32086974 -
Mepo Mepo5g01626 Chr5 17281492 17285281 -
Mesa Mesa17g01810 Chr17 25825620 25828937 -
Mtr Mtr5g1440 Chr5 15161161 15165696 -
Phco Phco4g01478 Chr4 13341776 13345036 -
Psa Psa2g2495 Chr2 288913440 288914069 +
Pste Pste1g02134 Chr1 6790354 6791157 -
Pumo Pumo8g01186 Chr8 43179328 43186430 +
Pvu Pvu2g0760 Chr2 10574343 10582768 -
Rops Rops1g00887 Chr1 21392726 21393427 -
Seca Seca10g01516 Chr10 16429414 16436623 -
Spst Spst2g01449 Chr2 13266607 13269563 -
Ssu Ssu2g1744 Chr2 67652617 67653715 +
Sto Sto11g1087 Chr11 10985353 10987364 +
Tpr Tpr2g1773 Chr2 21000818 21006133 -
Tsu Tsu05g01529 Chr05 14798233 14803563 -
Vian Vian10g01146 Chr10 18637437 18640579 +
Vifa Vifa1g04761 Chr1 744018732 744020508 -
Vimu Vimu7g03760 Chr7 33063372 33066359 -
Viun Viun2g01169 Chr2 22587937 22595432 +
Vivi Vivi2g01433 Chr2 62163143 62165872 -
Vvi Vvi1g0878 Chr1 9369279 9379357 +
Bva Bva08g01351 Chr08 7080239 7085595 +
Sto Sto6g4363 Chr6 46199961 46206318 +
Vvi Vvi1g0879 Chr1 9381769 9382394 +
Acco Acco04g2630 Chr04 43158651 43159179 -
Accr Accr8g00128 Chr8 1776586 1777112 +
Adu Adu01g01918 Chr01 83582567 83585664 -
Alju Alju06g2600 Chr06 53008114 53008640 -
Arst Arst1g02532 Chr1 83815898 83818549 -
Bisa Bisa08g1929 Chr08 46489272 46490447 +
Dere Dere03g0826 Chr03 12805297 12806056 -
Enph Enph6g0636 Chr6 9563324 9565011 -
Glsi Glsi02g0742 Chr02 4836600 4837238 -
Lapu Lapu3g01092 Chr3 11731207 11732296 +
Lasa Lasa4g03167 Chr4 571168166 571168615 -
Lele Lele21g1815 Chr21 25767630 25768056 -
Lele Lele22g1792 Chr22 23083667 23084073 -
Lele Lele23g0192 Chr23 1252066 1253001 +
Lele Lele24g1752 Chr24 22729602 22731292 -
Mepo Mepo1g01358 Chr1 13441427 13442402 +
Mibi Mibi09g0222 Chr09 2787479 2788198 +
Phac Phac3g03032 Chr3 31635878 31637273 +
Phco Phco8g01259 Chr8 13178274 13179081 -
Prci Prci4g2919 Chr4 41007715 41008323 -
Pste Pste6g02312 Chr6 11187615 11189304 -
Pvu Pvu3g2039 Chr3 41001933 41003038 +
Spst Spst3g04608 Chr3 97889356 97890006 -
Trre Trre15g02805 Chr15 24028788 24029847 +
Vimu Vimu7g00709 Chr7 7083424 7084046 -
Vivi Vivi1g02090 Chr1 44280206 44280966 +
Vvi Vvi1g0880 Chr1 9395296 9396993 +
Bva Bva08g01352 Chr08 7089239 7090964 +
Psa Psa2g2891 Chr2 334933451 334936250 +
Pte Pte14g00227 Chr14 9838616 9841310 -
Vimu Vimu7g03756 Chr7 33010047 33011923 +