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
Vvi2g0742 . . . . . . . . . . . . . . . . . . . Apr10g1690 . . . . . . . . . Car07g01331 . . . . . . . . . . . . Gma05g01146 Gma17g01403 . . . . . . Lal23g0775 . . . . . . . . . . . . . . . . . . . . . . Lja4g2665 . Mal5g3764 . . . . . . . Mtr4g3496 . . . . . . . Psa4g1856 . . . . . . . . . . . . . . . . . . . . . Tpr4g3893 . . . Tsu04g02254 . . . . . . . . . . . .
Vvi2g0743 . . . . . . Aed11g1538 . . . . . . . . . . . . . . . . . . . . . . . Cca06g01598 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g3949 . . . . . . . . . . . . . . . . . Ssu2g2638 . . . . . . . . . . . . . . . . . . . Vra11g0461 .
Vvi2g0744 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0745 . . . . . . . . . . . . . . . . . . . Apr10g1691 . . . . . . . . . . . . . . . . . . . . . . . Gma17g01402 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja4g2662 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0746 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0747 . . . . . . . . . . . . . . . . . . . Apr10g1692 . . . . . . . . . . . . . . . . . . . . Gma01g02029 . Gma05g00668 Gma17g01401 Gso1g1715 . Gso1g1715 Gso1g1715 . . . . . . . . . . . . . . . . . . . . . . . . . Lja4g2660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0748 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0750 Acco11g1946 . Accr9g00503 . Adu05g00525 . Aed11g1528 Aed6g0668 Aev05g0775 . . . Aip05g00500 . Alju09g1946 . . . Apr7g0788 . Arst5g00659 . Bach4g00389 Bach10g00342 Bisa11g1303 . Bva08g00453 Bva11g01866 Car08g00382 . Cca06g01586 Cca11g01478 Dere09g0543 . Dod02g0860 . Enph13g1162 . Glsi05g1762 . Gma01g02016 Gma11g00394 . Gma17g01424 Gso1g1704 Gso1g1704 . Gso1g1704 . Lal16g0282 . Lal15g0818 . . . . . . . . Lapu2g00455 . Lasa2g02992 Lasa2g02992 Lele49g0408 Lele50g0438 Lele51g0417 Lele52g0435 . . . . Lja2g0200 . Mal6g1457 . Mepo5g00584 . Mesa17g00609 . Mibi12g1681 . Mtr5g0518 . Phac2g00770 . Phco4g01244 Phco8g00900 Prci10g0653 . Psa2g3942 . Pste1g01652 Pste7g00790 Pte14g01055 Pte12g00262 Pte14g01055 Pte12g00262 Pumo8g02082 Pumo4g01807 Pvu2g0072 Pvu3g2374 Rops1g01938 Rops2g04388 Seca10g00585 Seca10g00585 Spst3g04166 Spst3g04166 Ssu2g2628 Ssu6g1740 Sto6g3535 . Tpr2g5613 . Trre9g00663 . Tsu05g00479 . Vian10g00469 Vian1g01529 Vifa1g07544 . Vimu7g02686 Vimu7g02686 Viun2g02253 Viun3g04010 Vivi2g03573 . Vra11g0473 Vra7g1278
Vvi2g0751 Acco11g1948 . . . Adu05g00526 . Aed11g1527 . Aev05g0774 . Ahy15g0495 . Aip05g00501 . . . . . Apr7g0789 . Arst5g00660 . Bach4g00390 . Bisa11g1304 . Bva08g00454 Bva11g01865 Car08g00383 . Cca06g01585 . Dere09g0545 . Dod02g0859 . . . . . Gma01g02015 Gma11g00395 . . . . . . Lal15g0214 Lal16g0281 . . . . . . . . . . Lapu2g00456 . Lasa2g02994 . . . . . . . . . Lja2g0201 . Mal6g1456 . Mepo5g00585 . Mesa17g00610 . . . Mtr5g0519 . Phac2g00769 . Phco4g01243 . Prci10g0651 . Psa2g3941 . . . . Pte12g00263 . . Pumo8g02081 . Pvu2g0073 . Rops1g01937 . Seca10g00587 . Spst2g00537 . Ssu2g2627 . Sto6g3537 . Tpr2g5615 . Trre9g00668 . Tsu05g00481 . Vian10g00470 . Vifa1g07541 . Vimu7g02687 . Viun2g02252 . Vivi2g03572 . Vra11g0474 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0742 Chr2 7100905 7117055 -
Apr Apr10g1690 Chr10 29700477 29704519 -
Car Car07g01331 Chr07 12287181 12291699 -
Gma Gma05g01146 Chr05 32586425 32590002 -
Gma Gma17g01403 Chr17 13112993 13117023 +
Lal Lal23g0775 Chr23 10268200 10272117 +
Lja Lja4g2665 Chr4 36447659 36451257 +
Mal Mal5g3764 Chr5 105781076 105785239 +
Mtr Mtr4g3496 Chr4 48584361 48589068 +
Psa Psa4g1856 Chr4 132527304 132530815 +
Tpr Tpr4g3893 Chr4 45184729 45192260 -
Tsu Tsu04g02254 Chr04 25113601 25120393 +
Vvi Vvi2g0743 Chr2 7118206 7119533 +
Aed Aed11g1538 Chr11 19607519 19609006 +
Cca Cca06g01598 Chr06 31152060 31154017 +
Psa Psa2g3949 Chr2 412683555 412684964 +
Ssu Ssu2g2638 Chr2 86278327 86279643 +
Vra Vra11g0461 Chr11 3414515 3415817 -
Vvi Vvi2g0744 Chr2 7122552 7123992 -
Vvi Vvi2g0745 Chr2 7149568 7159643 -
Apr Apr10g1691 Chr10 29713699 29718908 -
Gma Gma17g01402 Chr17 13096510 13111652 +
Lja Lja4g2662 Chr4 36301456 36307386 +
Vvi Vvi2g0746 Chr2 7180186 7183125 -
Vvi Vvi2g0747 Chr2 7184234 7189008 +
Apr Apr10g1692 Chr10 29754611 29759513 +
Gma Gma01g02029 Chr01 55711981 55718617 +
Gma Gma05g00668 Chr05 7493090 7499192 -
Gma Gma17g01401 Chr17 13064129 13070091 -
Gso Gso1g1715 Chr1 53910370 53916938 +
Gso Gso1g1715 Chr1 53910370 53916938 +
Gso Gso1g1715 Chr1 53910370 53916938 +
Lja Lja4g2660 Chr4 36199074 36206136 -
Vvi Vvi2g0748 Chr2 7190996 7216881 -
Vvi Vvi2g0749 Chr2 7229647 7230780 +
Vvi Vvi2g0750 Chr2 7241834 7242586 +
Acco Acco11g1946 Chr11 33736344 33736949 +
Accr Accr9g00503 Chr9 5680559 5681164 -
Adu Adu05g00525 Chr05 5540244 5541522 +
Aed Aed11g1528 Chr11 19541825 19542535 -
Aed Aed6g0668 Chr6 5774948 5775851 +
Aev Aev05g0775 Chr05 5426949 5427740 -
Aip Aip05g00500 Chr05 5757777 5759054 +
Alju Alju09g1946 Chr09 43277454 43278059 +
Apr Apr7g0788 Chr7 14839096 14839830 +
Arst Arst5g00659 Chr5 5565509 5566914 +
Bach Bach4g00389 Chr4 2588255 2588971 +
Bach Bach10g00342 Chr10 2386766 2387440 +
Bisa Bisa11g1303 Chr11 32123010 32123648 +
Bva Bva08g00453 Chr08 2325025 2325735 +
Bva Bva11g01866 Chr11 16242419 16243147 -
Car Car08g00382 Chr08 3104154 3104911 +
Cca Cca06g01586 Chr06 31016020 31016941 -
Cca Cca11g01478 Chr11 37392595 37394030 -
Dere Dere09g0543 Chr09 8302544 8303182 +
Dod Dod02g0860 Chr02 11039580 11041083 -
Enph Enph13g1162 Chr13 17377420 17378031 -
Glsi Glsi05g1762 Chr05 65414391 65414918 -
Gma Gma01g02016 Chr01 55574414 55575166 -
Gma Gma11g00394 Chr11 3219692 3220474 +
Gma Gma17g01424 Chr17 13411372 13412067 +
Gso Gso1g1704 Chr1 53772051 53773441 -
Gso Gso1g1704 Chr1 53772051 53773441 -
Gso Gso1g1704 Chr1 53772051 53773441 -
Lal Lal16g0282 Chr16 1685948 1686679 -
Lal Lal15g0818 Chr15 6005998 6006858 -
Lapu Lapu2g00455 Chr2 3801169 3802670 +
Lasa Lasa2g02992 Chr2 516673739 516674443 +
Lasa Lasa2g02992 Chr2 516673739 516674443 +
Lele Lele49g0408 Chr49 2364700 2365371 -
Lele Lele50g0438 Chr50 2496917 2497591 -
Lele Lele51g0417 Chr51 2404795 2405457 -
Lele Lele52g0435 Chr52 2568604 2569266 -
Lja Lja2g0200 Chr2 1734090 1734845 +
Mal Mal6g1457 Chr6 26667672 26668442 -
Mepo Mepo5g00584 Chr5 5249111 5249960 +
Mesa Mesa17g00609 Chr17 7185246 7185788 +
Mibi Mibi12g1681 Chr12 32913982 32914665 +
Mtr Mtr5g0518 Chr5 4836125 4837218 +
Phac Phac2g00770 Chr2 4748286 4749808 -
Phco Phco4g01244 Chr4 10515285 10516043 -
Phco Phco8g00900 Chr8 9237257 9237898 +
Prci Prci10g0653 Chr10 4356874 4358351 -
Psa Psa2g3942 Chr2 412379762 412381061 -
Pste Pste1g01652 Chr1 5069802 5070515 +
Pste Pste7g00790 Chr7 7209734 7210495 +
Pte Pte14g01055 Chr14 32203794 32204516 +
Pte Pte12g00262 Chr12 2110455 2111836 +
Pte Pte14g01055 Chr14 32203794 32204516 +
Pte Pte12g00262 Chr12 2110455 2111836 +
Pumo Pumo8g02082 Chr8 57753228 57754503 -
Pumo Pumo4g01807 Chr4 24290050 24291263 +
Pvu Pvu2g0072 Chr2 805396 806931 +
Pvu Pvu3g2374 Chr3 45149792 45152206 +
Rops Rops1g01938 Chr1 39400679 39401380 -
Rops Rops2g04388 Chr2 79997847 79998437 +
Seca Seca10g00585 Chr10 5332028 5332747 +
Seca Seca10g00585 Chr10 5332028 5332747 +
Spst Spst3g04166 Chr3 92999689 93000321 -
Spst Spst3g04166 Chr3 92999689 93000321 -
Ssu Ssu2g2628 Chr2 86069053 86069778 -
Ssu Ssu6g1740 Chr6 29402735 29403502 +
Sto Sto6g3535 Chr6 40850090 40856188 +
Tpr Tpr2g5613 Chr2 64953112 64954297 +
Trre Trre9g00663 Chr9 4804797 4805588 +
Tsu Tsu05g00479 Chr05 3727593 3728513 +
Vian Vian10g00469 Chr10 4316963 4317706 +
Vian Vian1g01529 Chr1 16990564 16991217 +
Vifa Vifa1g07544 Chr1 1170746568 1170747290 +
Vimu Vimu7g02686 Chr7 22611988 22613522 +
Vimu Vimu7g02686 Chr7 22611988 22613522 +
Viun Viun2g02253 Chr2 30191246 30192749 -
Viun Viun3g04010 Chr3 47630508 47632017 -
Vivi Vivi2g03573 Chr2 143904981 143906284 +
Vra Vra11g0473 Chr11 3508481 3510107 +
Vra Vra7g1278 Chr7 29477996 29479634 -
Vvi Vvi2g0751 Chr2 7296781 7304428 +
Acco Acco11g1948 Chr11 33762710 33765764 +
Adu Adu05g00526 Chr05 5564016 5567204 +
Aed Aed11g1527 Chr11 19531515 19534419 -
Aev Aev05g0774 Chr05 5412369 5415091 -
Ahy Ahy15g0495 Chr15 5969829 5972942 +
Aip Aip05g00501 Chr05 5776774 5779954 +
Apr Apr7g0789 Chr7 14849084 14852625 +
Arst Arst5g00660 Chr5 5589442 5592608 +
Bach Bach4g00390 Chr4 2596653 2600013 +
Bisa Bisa11g1304 Chr11 32137893 32141674 +
Bva Bva08g00454 Chr08 2333284 2337270 +
Bva Bva11g01865 Chr11 16235632 16237618 -
Car Car08g00383 Chr08 3120148 3123965 +
Cca Cca06g01585 Chr06 30993252 30998088 -
Dere Dere09g0545 Chr09 8316693 8320164 +
Dod Dod02g0859 Chr02 11019829 11022773 -
Gma Gma01g02015 Chr01 55556054 55558053 -
Gma Gma11g00395 Chr11 3234794 3238262 +
Lal Lal15g0214 Chr15 1464647 1472053 -
Lal Lal16g0281 Chr16 1676650 1680817 -
Lapu Lapu2g00456 Chr2 3812916 3817315 +
Lasa Lasa2g02994 Chr2 516750882 516754095 +
Lja Lja2g0201 Chr2 1743446 1747578 +
Mal Mal6g1456 Chr6 26639001 26642972 -
Mepo Mepo5g00585 Chr5 5263680 5267881 +
Mesa Mesa17g00610 Chr17 7200019 7205070 +
Mtr Mtr5g0519 Chr5 4852438 4857107 +
Phac Phac2g00769 Chr2 4728022 4732426 -
Phco Phco4g01243 Chr4 10492296 10497006 -
Prci Prci10g0651 Chr10 4345967 4350682 -
Psa Psa2g3941 Chr2 412297749 412305204 -
Pte Pte12g00263 Chr12 2122161 2126151 +
Pumo Pumo8g02081 Chr8 57737541 57740106 -
Pvu Pvu2g0073 Chr2 822329 827426 +
Rops Rops1g01937 Chr1 39373866 39378849 -
Seca Seca10g00587 Chr10 5352511 5353771 +
Spst Spst2g00537 Chr2 4331924 4335417 +
Ssu Ssu2g2627 Chr2 86031672 86036281 -
Sto Sto6g3537 Chr6 40874016 40878511 +
Tpr Tpr2g5615 Chr2 64974198 64978279 +
Trre Trre9g00668 Chr9 4823534 4826130 +
Tsu Tsu05g00481 Chr05 3747297 3749981 +
Vian Vian10g00470 Chr10 4327118 4331107 +
Vifa Vifa1g07541 Chr1 1169585522 1169587622 -
Vimu Vimu7g02687 Chr7 22621291 22625479 +
Viun Viun2g02252 Chr2 30177962 30182206 -
Vivi Vivi2g03572 Chr2 143836823 143839346 -
Vra Vra11g0474 Chr11 3518254 3522596 +
Gma Gma17g01401 Chr17 13064129 13070091 -
Gma Gma05g00668 Chr05 7493090 7499192 -