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
Vvi1g1071 . . . . . . . . . . Ahy15g1887 . Aip05g01870 . . . . . Apr7g1413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal6g0798 . . . . . Lan11g0802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1072 . . . . . . Aed11g0379 . Aev05g1492 . Ahy15g1783 . Aip05g01990 . . . Amo15g0764 . Apr7g1507 . Arst5g02309 . . . . . Bva08g01514 . Car02g00762 . Cca06g00632 . . . Dod02g1662 . . . . . Gma02g01000 . . . Gso2g0918 . . . . . . . . . . . . . . . . . Lasa2g00113 . . . . . . . . . Lja2g1173 . Mal6g2140 . Mepo5g01916 . Mesa17g02166 . . . Mtr5g1663 . Phac2g01272 . Phco4g01610 . . . Psa2g2652 . Pste1g01379 . . . . . . . Pvu2g0861 . . . . . Spst2g01730 . Ssu2g1574 . Sto11g0928 . Tpr2g2002 . Trre9g02752 . Tsu05g01904 . . . . . . . . . Vivi2g02071 . . .
Vvi1g1073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1074 . . . . . Adu05g01810 Aed11g0380 . Aev05g1493 . Ahy15g1782 . Aip05g01991 . . . . . Apr7g1508 . . . . . . . Bva08g01516 Bva11g00968 Car02g00763 . Cca06g00631 . . . Dod02g1663 . . . . . Gma02g01001 Gma01g00464 . . Gso2g0919 Gso2g0919 . . . Lal22g0740 Lal18g0897 . . . . . . . . . . . . Lasa2g00111 . . . . . . . . Lja2g1175 . Mal6g2141 . . Mepo5g01917 . Mesa17g02167 . . Mtr5g1664 . . . . . . . Psa2g2651 . . . . . Pte14g00101 . . . . Pvu3g0462 . . . . . . Ssu2g1573 . . Sto6g3008 Tpr2g2003 . . Trre9g02753 Tsu05g01905 . . . . . . . . . . . . .
Vvi1g1075 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1076 . . . . . Adu05g01808 Aed11g0382 . Aev05g1495 . Ahy15g1778 . Aip05g01993 . . . . . Apr7g1509 . . . . . . . Bva08g01519 . Car02g00765 . Cca06g00629 . . . Dod02g1665 . . . . . . Gma01g00467 . . . . . . . Lal22g0738 . . . . . . . . . . . . . Lasa2g00109 . . . . . . . . Lja2g1177 . Mal6g2142 . . Mepo5g01919 . Mesa17g02170 . . Mtr5g1667 . . . . Phco8g02956 . . Psa2g2649 . . . . . . Pte12g01114 . . . Pvu3g0465 . . . . . . Ssu2g1570 . . Sto6g3006 Tpr2g2006 . . Trre9g02768 Tsu05g01909 . . . . . . . . . . . . .
Vvi1g1077 . . . . . Adu05g01807 Aed11g0383 . Aev05g1496 . Ahy15g1776 . Aip05g01995 . . . Amo15g0771 . . . . . . . . . Bva08g01520 . Car02g00766 . Cca06g00628 . . . . . . . . . Gma02g01003 . . . Gso2g0922 . . . . Lal22g0736 . . . . . . . . . . . . . Lasa2g00108 . . . . . . . . Lja2g1178 . Mal6g2143 . . Mepo5g01921 . Mesa17g02172 . . Mtr5g1668 . . . . Phco8g02955 . . Psa2g2648 . . . . . . . . . . Pvu3g0467 . . . . . . Ssu2g1569 . . Sto6g3004 Tpr2g2007 . . Trre9g02769 Tsu05g01913 . . . . . . . . . . . . .
Vvi1g1078 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1079 . . . . . . Aed11g0384 . Aev05g1502 Aev03g0404 Ahy15g1772 Ahy13g3859 Aip05g02000 Aip03g04295 . . . Amo13g4871 Apr7g1511 . . . . . . . Bva08g01521 . Car06g01878 Car07g02163 Cca06g00627 . . . Dod02g1667 Dod04g1110 . . . . Gma02g01004 Gma01g00469 . . Gso2g0923 Gso2g0923 . . . Lal22g0735 Lal18g0898 . Lal16g0827 . . . . . . . . . . . . . . . . . . . Lja2g1179 . Mal6g2144 . . . . . . . Mtr5g1669 . . . . . . . Psa2g2647 . . . . . . . . . . . . . . . . . Ssu2g1568 . Sto11g0926 Sto6g3003 Tpr2g2008 . . . Tsu05g01914 . . . . . . . . . . . . .
Vvi1g1080 . . . . . Adu05g01800 Aed11g0385 . Aev05g1503 . Ahy15g1769 . Aip05g02005 . . . Amo15g0782 . Apr7g1512 . . . . . . . Bva08g01522 . Car02g00769 . Cca06g00626 . . . Dod02g1668 . . . . . Gma02g01005 Gma01g00470 . . Gso2g0924 Gso2g0924 . . . . . . . . . . . . . . . . . Lasa2g00103 . . . . . . . . Lja2g1180 . Mal6g2151 . . Mepo5g01923 . Mesa17g02174 . . Mtr5g1670 . . . . Phco8g02952 . . Psa2g2642 . . . . . . . . . . Pvu3g0469 . . . . . . Ssu2g1567 . . Sto6g3002 Tpr2g2009 . . Trre9g02774 Tsu05g01919 . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Apr Apr7g1413 Chr7 21245503 21250235 +
Lal Lal6g0798 Chr6 5360902 5366880 +
Lan Lan11g0802 Chr11 7568009 7573902 +
Vvi Vvi1g1071 Chr1 12291234 12293328 +
Ahy Ahy15g1887 Chr15 78669915 78674666 -
Aip Aip05g01870 Chr05 50729039 50733802 +
Apr Apr7g1413 Chr7 21245503 21250235 +
Lal Lal6g0798 Chr6 5360902 5366880 +
Lan Lan11g0802 Chr11 7568009 7573902 +
Vvi Vvi1g1072 Chr1 12361725 12366038 -
Aed Aed11g0379 Chr11 3224885 3228820 -
Aev Aev05g1492 Chr05 11210776 11213889 -
Ahy Ahy15g1783 Chr15 59835951 59838952 +
Aip Aip05g01990 Chr05 67819769 67821603 -
Amo Amo15g0764 Chr15 52478586 52481847 -
Apr Apr7g1507 Chr7 22273801 22277075 -
Arst Arst5g02309 Chr5 47617905 47620515 +
Bva Bva08g01514 Chr08 7979342 7981398 -
Car Car02g00762 Chr02 10647699 10663205 -
Cca Cca06g00632 Chr06 17929524 17932713 +
Dod Dod02g1662 Chr02 20715469 20718618 -
Gma Gma02g01000 Chr02 10725834 10729852 -
Gso Gso2g0918 Chr2 10516189 10520280 -
Lasa Lasa2g00113 Chr2 7756187 7758338 +
Lja Lja2g1173 Chr2 11162090 11165330 -
Mal Mal6g2140 Chr6 50029352 50032922 -
Mepo Mepo5g01916 Chr5 21183775 21187232 -
Mesa Mesa17g02166 Chr17 31506292 31515961 -
Mtr Mtr5g1663 Chr5 18269131 18273222 -
Phac Phac2g01272 Chr2 9573165 9579018 +
Phco Phco4g01610 Chr4 15562788 15569717 +
Psa Psa2g2652 Chr2 303820888 303823049 +
Pste Pste1g01379 Chr1 4383198 4388604 -
Pvu Pvu2g0861 Chr2 12822821 12828352 +
Spst Spst2g01730 Chr2 16249921 16257995 +
Ssu Ssu2g1574 Chr2 63410496 63413533 +
Sto Sto11g0928 Chr11 9777543 9780588 +
Tpr Tpr2g2002 Chr2 23910272 23913724 -
Trre Trre9g02752 Chr9 34834621 34836880 -
Tsu Tsu05g01904 Chr05 20959244 20962479 -
Vivi Vivi2g02071 Chr2 97134844 97137678 -
Vvi Vvi1g1073 Chr1 12389409 12392723 +
Vvi Vvi1g1074 Chr1 12397202 12403404 -
Adu Adu05g01810 Chr05 47390472 47392543 +
Aed Aed11g0380 Chr11 3229588 3232556 -
Aev Aev05g1493 Chr05 11220194 11222287 -
Ahy Ahy15g1782 Chr15 59776781 59779735 +
Aip Aip05g01991 Chr05 67884929 67887092 -
Apr Apr7g1508 Chr7 22278903 22281637 -
Bva Bva08g01516 Chr08 7985330 7990285 -
Bva Bva11g00968 Chr11 11577517 11582155 +
Car Car02g00763 Chr02 10664043 10666917 -
Cca Cca06g00631 Chr06 17922233 17925007 +
Dod Dod02g1663 Chr02 20727720 20730651 -
Gma Gma02g01001 Chr02 10731656 10734297 -
Gma Gma01g00464 Chr01 6100633 6102714 -
Gso Gso2g0919 Chr2 10521710 10524284 -
Gso Gso2g0919 Chr2 10521710 10524284 -
Lal Lal22g0740 Chr22 5287171 5297373 +
Lal Lal18g0897 Chr18 11634496 11642512 -
Lasa Lasa2g00111 Chr2 7752943 7755317 +
Lja Lja2g1175 Chr2 11168613 11170958 -
Mal Mal6g2141 Chr6 50034248 50037033 -
Mepo Mepo5g01917 Chr5 21187892 21191505 -
Mesa Mesa17g02167 Chr17 31516882 31519672 -
Mtr Mtr5g1664 Chr5 18273761 18277152 -
Psa Psa2g2651 Chr2 303817684 303820028 +
Pte Pte14g00101 Chr14 4040407 4044023 +
Pvu Pvu3g0462 Chr3 5129342 5133303 -
Ssu Ssu2g1573 Chr2 63406344 63408267 +
Sto Sto6g3008 Chr6 37175320 37184519 +
Tpr Tpr2g2003 Chr2 23914214 23917772 -
Trre Trre9g02753 Chr9 34838003 34841073 -
Tsu Tsu05g01905 Chr05 20962955 20966965 -
Vvi Vvi1g1075 Chr1 12404428 12404707 +
Vvi Vvi1g1076 Chr1 12409357 12410092 -
Adu Adu05g01808 Chr05 47289007 47292100 +
Aed Aed11g0382 Chr11 3239004 3240714 -
Aev Aev05g1495 Chr05 11232672 11234238 -
Ahy Ahy15g1778 Chr15 59532573 59535800 +
Aip Aip05g01993 Chr05 68100870 68103679 -
Apr Apr7g1509 Chr7 22289050 22292862 -
Bva Bva08g01519 Chr08 7997382 7998176 -
Car Car02g00765 Chr02 10686279 10688436 -
Cca Cca06g00629 Chr06 17898512 17899651 +
Dod Dod02g1665 Chr02 20746834 20748662 -
Gma Gma01g00467 Chr01 6133026 6135194 -
Lal Lal22g0738 Chr22 5279117 5280640 +
Lasa Lasa2g00109 Chr2 7497641 7498329 +
Lja Lja2g1177 Chr2 11177629 11179882 -
Mal Mal6g2142 Chr6 50080656 50082414 -
Mepo Mepo5g01919 Chr5 21210847 21212266 -
Mesa Mesa17g02170 Chr17 31556477 31558506 -
Mtr Mtr5g1667 Chr5 18326351 18328699 -
Phco Phco8g02956 Chr8 43439846 43441403 +
Psa Psa2g2649 Chr2 303679286 303680483 +
Pte Pte12g01114 Chr12 28894515 28896311 +
Pvu Pvu3g0465 Chr3 5152163 5154501 -
Ssu Ssu2g1570 Chr2 63386591 63388119 +
Sto Sto6g3006 Chr6 37170243 37171632 +
Tpr Tpr2g2006 Chr2 23943905 23945674 -
Trre Trre9g02768 Chr9 35056903 35058080 -
Tsu Tsu05g01909 Chr05 21033924 21035215 -
Vvi Vvi1g1077 Chr1 12436843 12437317 +
Adu Adu05g01807 Chr05 47282564 47285822 -
Aed Aed11g0383 Chr11 3241428 3243289 +
Aev Aev05g1496 Chr05 11240767 11243104 +
Ahy Ahy15g1776 Chr15 59502858 59505963 -
Aip Aip05g01995 Chr05 68129004 68132006 +
Amo Amo15g0771 Chr15 53257732 53260943 -
Bva Bva08g01520 Chr08 7998486 8001516 +
Car Car02g00766 Chr02 10690604 10697307 +
Cca Cca06g00628 Chr06 17866964 17872415 -
Gma Gma02g01003 Chr02 10755528 10761106 +
Gso Gso2g0922 Chr2 10557924 10562981 +
Lal Lal22g0736 Chr22 5274921 5277558 -
Lasa Lasa2g00108 Chr2 7396063 7398538 -
Lja Lja2g1178 Chr2 11188028 11190441 +
Mal Mal6g2143 Chr6 50093277 50098703 +
Mepo Mepo5g01921 Chr5 21256376 21261275 +
Mesa Mesa17g02172 Chr17 31606432 31607429 +
Mtr Mtr5g1668 Chr5 18345620 18349977 +
Phco Phco8g02955 Chr8 43430966 43439001 -
Psa Psa2g2648 Chr2 303649457 303652183 -
Pvu Pvu3g0467 Chr3 5168048 5175759 +
Ssu Ssu2g1569 Chr2 63356880 63376503 -
Sto Sto6g3004 Chr6 37166076 37168894 -
Tpr Tpr2g2007 Chr2 23951235 23959343 +
Trre Trre9g02769 Chr9 35064835 35069478 +
Tsu Tsu05g01913 Chr05 21074706 21079604 +
Vvi Vvi1g1078 Chr1 12438188 12440338 -
Vvi Vvi1g1079 Chr1 12442134 12443186 -
Aed Aed11g0384 Chr11 3244845 3245195 -
Aev Aev05g1502 Chr05 11308434 11309907 -
Aev Aev03g0404 Chr03 2913605 2914712 +
Ahy Ahy15g1772 Chr15 59403518 59405203 +
Ahy Ahy13g3859 Chr13 138011508 138012846 -
Aip Aip05g02000 Chr05 68215468 68217261 -
Aip Aip03g04295 Chr03 127375755 127376994 -
Amo Amo13g4871 Chr13 147550031 147551323 -
Apr Apr7g1511 Chr7 22304193 22306562 -
Bva Bva08g01521 Chr08 8002890 8004263 -
Car Car06g01878 Chr06 18726320 18728138 +
Car Car07g02163 Chr07 29673795 29675840 -
Cca Cca06g00627 Chr06 17863987 17866234 +
Dod Dod02g1667 Chr02 20829700 20831302 -
Dod Dod04g1110 Chr04 31613764 31615277 -
Gma Gma02g01004 Chr02 10763351 10764712 -
Gma Gma01g00469 Chr01 6165572 6167483 -
Gso Gso2g0923 Chr2 10564994 10566869 -
Gso Gso2g0923 Chr2 10564994 10566869 -
Lal Lal22g0735 Chr22 5270595 5272064 +
Lal Lal18g0898 Chr18 11644781 11647121 -
Lal Lal16g0827 Chr16 5339253 5341712 +
Lja Lja2g1179 Chr2 11193076 11194661 -
Mal Mal6g2144 Chr6 50100741 50102251 -
Mtr Mtr5g1669 Chr5 18352404 18354061 -
Psa Psa2g2647 Chr2 303646617 303648531 +
Ssu Ssu2g1568 Chr2 63352950 63354096 +
Sto Sto11g0926 Chr11 9766746 9768307 +
Sto Sto6g3003 Chr6 37159791 37161222 +
Tpr Tpr2g2008 Chr2 23961001 23962958 -
Tsu Tsu05g01914 Chr05 21082411 21084144 -
Vvi Vvi1g1080 Chr1 12480755 12504384 +
Adu Adu05g01800 Chr05 46722820 46734274 -
Aed Aed11g0385 Chr11 3251863 3261513 +
Aev Aev05g1503 Chr05 11342401 11351528 +
Ahy Ahy15g1769 Chr15 59091798 59101717 -
Aip Aip05g02005 Chr05 68500048 68509048 +
Amo Amo15g0782 Chr15 53586210 53596372 +
Apr Apr7g1512 Chr7 22311552 22321414 +
Bva Bva08g01522 Chr08 8006954 8016770 +
Car Car02g00769 Chr02 10746054 10755062 +
Cca Cca06g00626 Chr06 17839229 17854103 -
Dod Dod02g1668 Chr02 20841258 20851318 +
Gma Gma02g01005 Chr02 10787447 10797002 +
Gma Gma01g00470 Chr01 6189629 6199899 +
Gso Gso2g0924 Chr2 10587592 10597695 +
Gso Gso2g0924 Chr2 10587592 10597695 +
Lasa Lasa2g00103 Chr2 7081137 7090022 -
Lja Lja2g1180 Chr2 11197912 11206152 -
Mal Mal6g2151 Chr6 50470798 50479652 +
Mepo Mepo5g01923 Chr5 21303822 21313474 +
Mesa Mesa17g02174 Chr17 31677582 31686953 +
Mtr Mtr5g1670 Chr5 18379119 18388701 +
Phco Phco8g02952 Chr8 43405998 43414810 -
Psa Psa2g2642 Chr2 302797165 302806635 -
Pvu Pvu3g0469 Chr3 5192205 5202540 +
Ssu Ssu2g1567 Chr2 63321137 63329119 -
Sto Sto6g3002 Chr6 37133752 37143125 -
Tpr Tpr2g2009 Chr2 23975171 23984241 +
Trre Trre9g02774 Chr9 35122466 35130951 +
Tsu Tsu05g01919 Chr05 21202098 21210588 +
Car Car07g02163 Chr07 29673795 29675840 -