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
Vvi2g0652 . . . . . . . . Aev05g0822 . Ahy15g0454 . Aip05g00451 . . . . . Apr7g0746 . . . . . . . . Bva11g01915 . . . . . . Dod02g0909 . . . . . . . . . . . . . Lal15g0234 . . . . Lal23g1254 Lan18g0930 . . . . Lan18g0930 . . . . . . . . . . . . Lja2g0159 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0653 . . . . . Adu01g01303 . . Aev05g0821 Aev01g0413 Ahy15g0455 Ahy11g1222 Aip05g00453 Aip01g01295 . . . . . Apr10g1670 . Arst1g01732 . Bach10g00300 . . Bva08g00396 Bva11g01914 . Car07g01301 . Cca11g01523 . . Dod02g0908 Dod05g1295 . . . . . . Gma05g00637 Gma17g01373 . . . . . . . . Lal16g0868 . . . . . . . . . . . . . . . . . . . . . . Mal5g3796 . Mepo1g01691 . . . . . Mtr4g3524 . Phac3g03531 . Phco8g00847 . . . Psa4g1792 . Pste7g00664 . . . Pte12g00224 . Pumo4g01756 . Pvu3g2332 . Rops2g04345 . Seca12g02123 . Spst3g04215 . Ssu6g1692 Sto6g3471 . . Tpr5g2565 . Trre15g03467 . Tsu04g02289 . . . Vifa4g02823 . . . Viun3g04063 . Vivi1g02604 . .
Vvi2g0654 . . . . . . Aed11g1568 Aed6g0617 Aev05g0820 Aev01g0414 Ahy15g0456 Ahy11g1220 Aip05g00454 Aip01g01288 . . . Amo11g1137 Apr7g0748 Apr10g1671 . . . . . . Bva08g00397 Bva11g01913 . Car07g01302 Cca06g01639 Cca11g01522 . . Dod02g0906 Dod05g1294 . . . . Gma01g02061 Gma11g00355 Gma05g00638 Gma17g01374 Gso1g1736 Gso1g1736 Gso1g1736 Gso1g1736 . . Lal23g0757 Lal15g0852 Lal16g0867 Lal23g1255 . . . . . . . . . . . . . . . . . . Lja2g0160 . Mal6g1500 Mal5g3795 . . . . . . Mtr5g0476 Mtr4g3523 . . . . . . Psa2g3990 Psa4g1795 . . . . . . . . . . . . . . . . Ssu2g2672 Ssu6g1693 Sto6g3472 Sto11g1859 Tpr2g5573 Tpr5g2564 . . Tsu05g00446 Tsu04g02288 . . . . . . . . . . Vra11g0430 Vra7g1317
Vvi2g0655 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0656 . Acco12g1721 . Accr10g00340 . Adu01g01300 Aed11g1567 Aed6g0619 . Aev01g0415 . Ahy11g1214 . Aip01g01286 . Alju12g0413 . . Apr7g0749 Apr10g1673 . Arst1g01721 . Bach10g00302 . Bisa01g1023 Bva08g00398 Bva11g01912 Car08g00351 Car07g01303 Cca06g01638 Cca11g01520 . . . Dod05g1291 . Enph14g0310 . Glsi09g0254 Gma01g02060 Gma11g00356 Gma05g00639 Gma17g01375 Gso1g1735 Gso1g1735 Gso1g1735 Gso1g1735 . . Lal23g0759 . Lal16g0866 Lal23g1256 . . . . . . . Lapu3g01388 . Lasa4g02742 . . . . Lele53g0292 Lele54g0290 Lele55g1196 Lele56g1150 Lja2g0161 . Mal6g1499 Mal5g3794 . Mepo1g01694 . . . Mibi10g0370 Mtr5g0477 Mtr4g3522 . Phac3g03534 . Phco8g00849 . Prci5g0434 . Psa4g1797 . Pste7g00670 . . Pte14g01012 Pte12g00226 . Pumo4g01759 . Pvu3g2335 . Rops2g04347 . Seca12g02127 . Spst3g04212 Ssu2g2671 Ssu6g1694 Sto6g3474 Sto11g1858 Tpr2g5574 Tpr4g3864 . Trre15g03471 Tsu05g00447 Tsu04g02285 . Vian1g01486 . Vifa4g02821 . Vimu7g02639 . Viun3g04061 . . Vra11g0431 Vra7g1316
Vvi2g0657 . . . . . Adu01g01299 . Aed6g0620 . Aev01g0416 . Ahy11g1213 . Aip01g01285 . . . Amo11g1134 . Apr10g1674 . Arst1g01718 . . . . Bva08g00399 Bva11g01911 . Car07g01304 . Cca11g01519 . . . Dod05g1290 . . . . . . Gma05g00640 Gma17g01376 . . . . . . Lal23g0760 . Lal16g0865 . . . . . . . . Lapu3g01389 . Lasa4g02738 . . . . . . . . . . . Mal5g3793 . Mepo1g01695 . . . . . Mtr4g3521 . . . Phco8g00850 . . . Psa4g1810 . Pste7g00672 . . Pte14g01013 . . Pumo4g01760 . Pvu3g2336 . Rops2g04348 . Seca12g02128 . Spst3g04211 . Ssu6g1695 Sto6g3475 . . Tpr4g3866 . Trre15g03472 . Tsu04g02284 . Vian1g01487 . Vifa4g02819 . Vimu11g00235 . Viun3g04060 . . . Vra7g1315
Vvi2g0658 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g3989 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0659 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g3987 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0661 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cca06g01634 . . . . . . . . . . . . . . . . . Lal15g0232 . . . . . Lan18g0933 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g3986 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Vra11g0434 .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0652 Chr2 5723377 5725314 -
Aev Aev05g0822 Chr05 5784189 5788210 +
Ahy Ahy15g0454 Chr15 5263300 5267654 -
Aip Aip05g00451 Chr05 5045678 5049555 -
Apr Apr7g0746 Chr7 14334332 14338009 -
Bva Bva11g01915 Chr11 16525497 16529316 +
Dod Dod02g0909 Chr02 11714368 11718731 +
Lal Lal15g0234 Chr15 1613451 1618822 +
Lal Lal23g1254 Chr23 13655177 13662455 -
Lan Lan18g0930 Chr18 14527669 14533380 -
Lan Lan18g0930 Chr18 14527669 14533380 -
Lja Lja2g0159 Chr2 1301962 1305703 -
Vvi Vvi2g0653 Chr2 5758099 5775361 +
Adu Adu01g01303 Chr01 30875271 30884280 -
Aev Aev05g0821 Chr05 5776692 5778914 -
Aev Aev01g0413 Chr01 3469960 3473978 +
Ahy Ahy15g0455 Chr15 5278371 5282612 +
Ahy Ahy11g1222 Chr11 39192976 39198411 -
Aip Aip05g00453 Chr05 5067318 5071178 +
Aip Aip01g01295 Chr01 37048178 37053769 -
Apr Apr10g1670 Chr10 29404889 29408932 +
Arst Arst1g01732 Chr1 31280234 31285765 -
Bach Bach10g00300 Chr10 2078078 2081346 +
Bva Bva08g00396 Chr08 1974947 1979333 +
Bva Bva11g01914 Chr11 16518696 16522630 -
Car Car07g01301 Chr07 11904503 11909692 +
Cca Cca11g01523 Chr11 38357722 38362557 -
Dod Dod02g0908 Chr02 11690170 11693662 -
Dod Dod05g1295 Chr05 36500308 36505170 -
Gma Gma05g00637 Chr05 6875596 6877772 +
Gma Gma17g01373 Chr17 12629898 12634268 +
Lal Lal16g0868 Chr16 5695529 5702866 -
Mal Mal5g3796 Chr5 106523497 106527535 -
Mepo Mepo1g01691 Chr1 16666841 16671936 +
Mtr Mtr4g3524 Chr4 48983419 48989235 -
Phac Phac3g03531 Chr3 35608933 35615131 +
Phco Phco8g00847 Chr8 8607906 8613328 +
Psa Psa4g1792 Chr4 126536084 126540526 +
Pste Pste7g00664 Chr7 6077048 6082481 +
Pte Pte12g00224 Chr12 1788524 1793182 +
Pumo Pumo4g01756 Chr4 23101824 23106634 +
Pvu Pvu3g2332 Chr3 44639561 44645503 +
Rops Rops2g04345 Chr2 79225938 79230483 +
Seca Seca12g02123 Chr12 26740297 26745086 +
Spst Spst3g04215 Chr3 93607315 93612588 -
Ssu Ssu6g1692 Chr6 28465896 28470013 +
Sto Sto6g3471 Chr6 40355708 40359722 +
Tpr Tpr5g2565 Chr5 47684692 47689188 -
Trre Trre15g03467 Chr15 41290426 41294308 +
Tsu Tsu04g02289 Chr04 25565302 25573984 -
Vifa Vifa4g02823 Chr4 903578208 903582044 -
Viun Viun3g04063 Chr3 48301417 48307535 -
Vivi Vivi1g02604 Chr1 54769233 54773666 +
Vvi Vvi2g0654 Chr2 5786291 5790565 +
Aed Aed11g1568 Chr11 19861690 19864513 -
Aed Aed6g0617 Chr6 5240725 5251029 +
Aev Aev05g0820 Chr05 5771843 5774332 -
Aev Aev01g0414 Chr01 3479949 3482447 +
Ahy Ahy15g0456 Chr15 5305773 5308094 +
Ahy Ahy11g1220 Chr11 38892911 38896269 -
Aip Aip05g00454 Chr05 5088845 5091183 +
Aip Aip01g01288 Chr01 36778621 36781758 -
Amo Amo11g1137 Chr11 36308434 36311841 -
Apr Apr7g0748 Chr7 14353683 14359561 +
Apr Apr10g1671 Chr10 29418728 29421363 +
Bva Bva08g00397 Chr08 1983075 1986303 +
Bva Bva11g01913 Chr11 16515518 16518078 -
Car Car07g01302 Chr07 11910700 11913940 +
Cca Cca06g01639 Chr06 31635265 31638566 -
Cca Cca11g01522 Chr11 38336333 38338891 -
Dod Dod02g0906 Chr02 11672139 11676266 -
Dod Dod05g1294 Chr05 36486855 36490634 -
Gma Gma01g02061 Chr01 56003376 56006438 -
Gma Gma11g00355 Chr11 2836368 2838879 +
Gma Gma05g00638 Chr05 6884688 6887807 +
Gma Gma17g01374 Chr17 12646432 12649496 +
Gso Gso1g1736 Chr1 54188650 54191424 -
Gso Gso1g1736 Chr1 54188650 54191424 -
Gso Gso1g1736 Chr1 54188650 54191424 -
Gso Gso1g1736 Chr1 54188650 54191424 -
Lal Lal23g0757 Chr23 10158103 10161298 +
Lal Lal15g0852 Chr15 6391174 6405850 -
Lal Lal16g0867 Chr16 5689566 5692854 -
Lal Lal23g1255 Chr23 13663528 13672330 +
Lja Lja2g0160 Chr2 1311288 1314420 +
Mal Mal6g1500 Chr6 27959240 27961783 -
Mal Mal5g3795 Chr5 106517487 106520701 -
Mtr Mtr5g0476 Chr5 4364590 4367487 +
Mtr Mtr4g3523 Chr4 48979056 48982742 -
Psa Psa2g3990 Chr2 414667748 414670610 -
Psa Psa4g1795 Chr4 126600627 126604037 +
Ssu Ssu2g2672 Chr2 86925607 86927847 -
Ssu Ssu6g1693 Chr6 28484551 28486644 +
Sto Sto6g3472 Chr6 40362982 40365052 +
Sto Sto11g1859 Chr11 17352628 17357307 -
Tpr Tpr2g5573 Chr2 64451262 64454245 +
Tpr Tpr5g2564 Chr5 47680175 47683505 -
Tsu Tsu05g00446 Chr05 3360593 3364120 +
Tsu Tsu04g02288 Chr04 25560131 25563891 -
Vra Vra11g0430 Chr11 3119184 3121421 +
Vra Vra7g1317 Chr7 30062942 30066731 -
Vvi Vvi2g0655 Chr2 5798065 5798307 +
Vvi Vvi2g0656 Chr2 5804364 5806981 -
Acco Acco12g1721 Chr12 28359132 28361109 -
Accr Accr10g00340 Chr10 5540365 5542356 +
Adu Adu01g01300 Chr01 30761371 30763932 +
Aed Aed11g1567 Chr11 19858633 19861144 +
Aed Aed6g0619 Chr6 5259893 5263292 -
Aev Aev01g0415 Chr01 3488170 3491051 -
Ahy Ahy11g1214 Chr11 38824711 38827967 +
Aip Aip01g01286 Chr01 36723331 36725893 +
Alju Alju12g0413 Chr12 5031749 5033887 +
Apr Apr7g0749 Chr7 14358427 14363406 -
Apr Apr10g1673 Chr10 29426568 29429816 -
Arst Arst1g01721 Chr1 31162609 31165096 +
Bach Bach10g00302 Chr10 2089335 2091657 -
Bisa Bisa01g1023 Chr01 17363922 17365893 +
Bva Bva08g00398 Chr08 1987405 1990827 -
Bva Bva11g01912 Chr11 16509806 16512802 +
Car Car08g00351 Chr08 2740719 2743646 -
Car Car07g01303 Chr07 11919148 11921319 -
Cca Cca06g01638 Chr06 31631156 31634303 +
Cca Cca11g01520 Chr11 38327891 38330785 +
Dod Dod05g1291 Chr05 36477999 36480297 +
Enph Enph14g0310 Chr14 5217389 5219981 -
Glsi Glsi09g0254 Chr09 1810288 1812394 -
Gma Gma01g02060 Chr01 55998849 56001941 +
Gma Gma11g00356 Chr11 2841138 2844690 -
Gma Gma05g00639 Chr05 6915184 6919052 -
Gma Gma17g01375 Chr17 12653979 12657363 -
Gso Gso1g1735 Chr1 54183845 54186977 +
Gso Gso1g1735 Chr1 54183845 54186977 +
Gso Gso1g1735 Chr1 54183845 54186977 +
Gso Gso1g1735 Chr1 54183845 54186977 +
Lal Lal23g0759 Chr23 10163620 10168862 -
Lal Lal16g0866 Chr16 5685773 5688226 +
Lal Lal23g1256 Chr23 13672819 13675443 -
Lapu Lapu3g01388 Chr3 15523109 15525703 -
Lasa Lasa4g02742 Chr4 520289891 520291846 -
Lele Lele53g0292 Chr53 2441637 2443580 +
Lele Lele54g0290 Chr54 2461855 2463797 +
Lele Lele55g1196 Chr55 18575011 18577339 -
Lele Lele56g1150 Chr56 14944719 14946660 -
Lja Lja2g0161 Chr2 1316732 1319750 -
Mal Mal6g1499 Chr6 27942795 27946353 +
Mal Mal5g3794 Chr5 106509860 106512331 +
Mepo Mepo1g01694 Chr1 16682140 16684879 -
Mibi Mibi10g0370 Chr10 5950106 5952481 +
Mtr Mtr5g0477 Chr5 4367805 4370768 -
Mtr Mtr4g3522 Chr4 48971440 48973956 +
Phac Phac3g03534 Chr3 35625640 35630184 -
Phco Phco8g00849 Chr8 8626944 8629685 -
Prci Prci5g0434 Chr5 5715843 5718248 +
Psa Psa4g1797 Chr4 126615859 126617562 -
Pste Pste7g00670 Chr7 6109184 6112487 -
Pte Pte14g01012 Chr14 31763669 31764217 -
Pte Pte12g00226 Chr12 1802675 1805212 -
Pumo Pumo4g01759 Chr4 23130807 23133500 -
Pvu Pvu3g2335 Chr3 44657913 44660920 -
Rops Rops2g04347 Chr2 79248243 79251142 -
Seca Seca12g02127 Chr12 26835011 26838859 -
Spst Spst3g04212 Chr3 93592251 93594766 +
Ssu Ssu2g2671 Chr2 86913481 86916141 +
Ssu Ssu6g1694 Chr6 28491964 28494698 -
Sto Sto6g3474 Chr6 40368391 40370679 -
Sto Sto11g1858 Chr11 17350099 17355809 +
Tpr Tpr2g5574 Chr2 64455403 64458331 -
Tpr Tpr4g3864 Chr4 44795124 44798027 -
Trre Trre15g03471 Chr15 41313673 41316261 -
Tsu Tsu05g00447 Chr05 3364552 3366974 -
Tsu Tsu04g02285 Chr04 25521280 25524459 +
Vian Vian1g01486 Chr1 16427052 16429550 -
Vifa Vifa4g02821 Chr4 903237137 903238997 +
Vimu Vimu7g02639 Chr7 22227261 22229674 -
Viun Viun3g04061 Chr3 48286965 48289396 +
Vra Vra11g0431 Chr11 3123221 3125888 -
Vra Vra7g1316 Chr7 30056528 30059236 +
Vvi Vvi2g0657 Chr2 5811627 5820367 -
Adu Adu01g01299 Chr01 30747603 30751670 +
Aed Aed6g0620 Chr6 5277819 5281294 -
Aev Aev01g0416 Chr01 3510052 3514498 -
Ahy Ahy11g1213 Chr11 38815167 38819302 +
Aip Aip01g01285 Chr01 36712279 36716616 +
Amo Amo11g1134 Chr11 36232434 36236561 +
Apr Apr10g1674 Chr10 29435639 29439124 -
Arst Arst1g01718 Chr1 31148814 31152877 +
Bva Bva08g00399 Chr08 1993773 1998024 -
Bva Bva11g01911 Chr11 16502971 16506904 +
Car Car07g01304 Chr07 11927953 11932291 -
Cca Cca11g01519 Chr11 38316310 38320700 +
Dod Dod05g1290 Chr05 36461760 36465761 +
Gma Gma05g00640 Chr05 6925104 6926323 -
Gma Gma17g01376 Chr17 12666424 12670376 -
Lal Lal23g0760 Chr23 10172624 10175987 -
Lal Lal16g0865 Chr16 5678993 5683879 +
Lapu Lapu3g01389 Chr3 15529676 15533803 -
Lasa Lasa4g02738 Chr4 519523231 519526607 +
Mal Mal5g3793 Chr5 106480400 106484234 +
Mepo Mepo1g01695 Chr1 16691089 16696193 -
Mtr Mtr4g3521 Chr4 48956969 48962266 +
Phco Phco8g00850 Chr8 8635528 8638407 -
Psa Psa4g1810 Chr4 127925351 127929292 +
Pste Pste7g00672 Chr7 6119717 6123920 -
Pte Pte14g01013 Chr14 31767169 31770862 -
Pumo Pumo4g01760 Chr4 23137887 23141245 -
Pvu Pvu3g2336 Chr3 44665257 44668806 -
Rops Rops2g04348 Chr2 79255333 79258921 -
Seca Seca12g02128 Chr12 26841524 26843926 -
Spst Spst3g04211 Chr3 93584779 93588296 +
Ssu Ssu6g1695 Chr6 28499448 28504035 -
Sto Sto6g3475 Chr6 40374491 40378160 -
Tpr Tpr4g3866 Chr4 44813565 44818332 -
Trre Trre15g03472 Chr15 41323743 41327744 -
Tsu Tsu04g02284 Chr04 25511882 25516614 +
Vian Vian1g01487 Chr1 16435477 16438905 -
Vifa Vifa4g02819 Chr4 900827866 900831161 +
Vimu Vimu11g00235 Chr11 2278772 2282266 -
Viun Viun3g04060 Chr3 48280309 48284125 +
Vra Vra7g1315 Chr7 30047750 30051397 +
Vvi Vvi2g0658 Chr2 5827251 5866553 -
Psa Psa2g3989 Chr2 414612993 414615550 +
Vvi Vvi2g0659 Chr2 5887055 5890114 -
Psa Psa2g3987 Chr2 414550133 414603090 +
Vvi Vvi2g0660 Chr2 5893215 5900307 -
Vvi Vvi2g0661 Chr2 5915695 5994281 -
Cca Cca06g01634 Chr06 31543022 31559320 -
Lal Lal15g0232 Chr15 1560561 1606703 -
Lan Lan18g0933 Chr18 14550013 14603488 +
Psa Psa2g3986 Chr2 414543444 414548638 +
Vra Vra11g0434 Chr11 3163467 3220059 +
Gma Gma17g01374 Chr17 12646432 12649496 +
Gma Gma05g00638 Chr05 6884688 6887807 +