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
Vvi5g0144 . . . . Adu01g02604 . . . . . . . . . . . . . . Apr1g2108 Arst1g03373 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa4g03838 . . . . . . . . . . . . . . . . . . . . . . . Phco8g02199 . . . Psa1g3581 . . . . . . . Pumo4g00406 . Pvu3g1137 . Rops2g04923 . Seca12g00377 . Spst3g02996 . . . . . . . . . . . Vian1g00311 . Vifa4g04005 . Vimu11g01264 . Viun3g05688 . Vivi1g01074 . . .
Vvi5g0145 . . . . . . Aed6g2349 . . . . . . . . . . . . . . . . . . . Bva05g01318 . Car07g00533 Car01g00971 Cca11g02736 . . . . . . . . . . Gma07g02353 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja6g2276 . Mal4g3725 . . . . . . . Mtr2g1256 . . . . . . Psa1g3580 . . . . . . . . . . . . . . . . . Ssu6g0362 . Sto3g0863 . . Tpr5g2047 . . . . . . . . . . . . . . Vra7g2807 .
Vvi5g0146 . . . . Adu01g02605 . . . . . . . . . . . . . Apr9g2278 . Arst1g03375 . Bach5g01098 . . . Bva05g01319 . . . . . . . . . . . . . . . . . . . . . . . Lal19g1121 . . . . . . . . . . . Lasa4g03837 . . . . . . . . . . . . . . . . . . . . . . . Phco8g02203 . . . Psa1g3579 . Pste6g04061 . . . . . Pumo4g00404 . Pvu3g1134 . Rops2g04920 . Seca12g00376 . Spst3g02999 . . . . . . . . . . . Vian1g00309 . Vifa4g04000 . Vimu7g01754 . Viun3g05690 . Vivi1g01079 . . .
Vvi5g0147 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g0148 . . . . . . . . Aev01g2909 . Ahy11g2608 . Aip01g02861 . . . . . . . . . . . . . Bva05g01320 . . Car01g01031 . . . . Dod05g2638 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja6g2275 . Mal4g3724 . . . . . . . Mtr2g1257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tsu07g01788 . . . . . . . . . . . .
Vvi5g0149 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g0150 . . . . . . . Aed4g0671 . Aev04g1126 . Ahy14g0978 . Aip04g01066 . . . Amo14g1376 Apr9g2277 . . . . . . . Bva05g01321 . . . . Cca08g01723 . . . Dod03g1273 . . . . . . . . . . . . . . Lal19g1120 . . . . . . . . . Lapu3g00311 . . . . . . . . . . . . . . . . . . . . . . . . . Phco8g02204 . . . Psa1g3573 . . . . . . . . . Pvu3g1133 . . . . . Spst3g03000 . . . . . . . . . . . . . . . Vimu11g01269 . . . Vivi1g01081 . . Vra5g0097
Vvi5g0151 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g0152 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva05g01323 . . . . . . . . . . . . . Gma17g00280 . . . Gso17g0244 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal4g3719 . . . . . . . Mtr2g1258 . . . . . . . Psa4g0582 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g0153 . . . . Adu01g02606 . . Aed4g0672 Aev01g2910 Aev04g1128 Ahy11g2607 Ahy14g0981 Aip01g02860 Aip04g01068 . . . Amo14g1379 Apr9g2276 . Arst1g03376 . . . . . Bva05g02625 . . Car01g00974 . Cca08g01722 . . Dod05g2639 . . . . . . . . . . . . . . . Lal19g1119 . . . . . . . . . . . Lasa4g03835 . . . . . . . . . . . . Mal4g3717 . . . . . . . Mtr2g1260 . . Phco8g02205 . . . Psa1g3570 . Pste6g04062 . . . . . . . Pvu3g1132 . . . . . Spst3g03001 . . Ssu1g1280 . . . Tpr5g2045 . . . Tsu07g01790 . . . . Vimu7g01755 . . . Vivi1g01083 . . Vra5g0098
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi5g0144 Chr5 1246986 1247594 -
Adu Adu01g02604 Chr01 95335529 95336520 +
Apr Apr1g2108 Chr1 30596805 30602567 +
Arst Arst1g03373 Chr1 94809962 94810919 +
Lasa Lasa4g03838 Chr4 628630786 628631334 +
Phco Phco8g02199 Chr8 23569374 23569949 -
Psa Psa1g3581 Chr1 306397415 306398506 -
Pumo Pumo4g00406 Chr4 5426485 5427753 -
Pvu Pvu3g1137 Chr3 27185562 27186300 -
Rops Rops2g04923 Chr2 88618709 88621080 -
Seca Seca12g00377 Chr12 3287876 3288830 -
Spst Spst3g02996 Chr3 79612414 79613001 +
Vian Vian1g00311 Chr1 2755789 2756331 +
Vifa Vifa4g04005 Chr4 1279363877 1279364353 +
Vimu Vimu11g01264 Chr11 13919686 13920384 +
Viun Viun3g05688 Chr3 62477790 62485457 +
Vivi Vivi1g01074 Chr1 23008971 23009584 -
Vvi Vvi5g0145 Chr5 1251186 1260753 +
Aed Aed6g2349 Chr6 25318751 25319607 +
Bva Bva05g01318 Chr05 6939860 6950659 +
Car Car07g00533 Chr07 4722787 4724466 +
Car Car01g00971 Chr01 9091687 9093157 +
Cca Cca11g02736 Chr11 54749402 54750458 +
Gma Gma07g02353 Chr07 46244948 46246109 +
Lja Lja6g2276 Chr6 51652838 51653754 -
Mal Mal4g3725 Chr4 109651277 109653573 -
Mtr Mtr2g1256 Chr2 13580577 13582017 +
Psa Psa1g3580 Chr1 306354540 306355699 -
Ssu Ssu6g0362 Chr6 5742647 5743286 -
Sto Sto3g0863 Chr3 5952679 5953350 +
Tpr Tpr5g2047 Chr5 40878738 40880222 -
Vra Vra7g2807 Chr7 48304527 48305581 +
Vvi Vvi5g0146 Chr5 1263801 1264384 +
Adu Adu01g02605 Chr01 95351827 95352387 +
Apr Apr9g2278 Chr9 30510452 30511342 -
Arst Arst1g03375 Chr1 94836456 94837160 +
Bach Bach5g01098 Chr5 7860993 7862611 +
Bva Bva05g01319 Chr05 6942300 6953433 +
Lal Lal19g1121 Chr19 14797431 14798247 -
Lasa Lasa4g03837 Chr4 628286920 628287396 +
Phco Phco8g02203 Chr8 23603537 23604113 -
Psa Psa1g3579 Chr1 306299655 306300533 -
Pste Pste6g04061 Chr6 29905539 29906394 +
Pumo Pumo4g00404 Chr4 5377474 5378457 -
Pvu Pvu3g1134 Chr3 27140302 27141134 +
Rops Rops2g04920 Chr2 88589935 88590941 -
Seca Seca12g00376 Chr12 3281318 3282834 -
Spst Spst3g02999 Chr3 79632596 79633185 +
Vian Vian1g00309 Chr1 2728812 2737086 -
Vifa Vifa4g04000 Chr4 1278169968 1278170709 -
Vimu Vimu7g01754 Chr7 16170746 16172941 +
Viun Viun3g05690 Chr3 62492194 62493027 -
Vivi Vivi1g01079 Chr1 23108586 23109351 -
Vvi Vvi5g0147 Chr5 1268820 1269511 +
Vvi Vvi5g0148 Chr5 1271452 1272235 +
Aev Aev01g2909 Chr01 31141921 31142507 +
Ahy Ahy11g2608 Chr11 142276376 142277435 -
Aip Aip01g02861 Chr01 130531272 130532072 -
Bva Bva05g01320 Chr05 6946267 6947114 -
Car Car01g01031 Chr01 9859612 9861305 +
Dod Dod05g2638 Chr05 52602355 52611201 +
Lja Lja6g2275 Chr6 51639269 51641254 -
Mal Mal4g3724 Chr4 109647675 109648851 -
Mtr Mtr2g1257 Chr2 13586850 13587774 +
Tsu Tsu07g01788 Chr07 17686069 17687478 +
Vvi Vvi5g0149 Chr5 1282363 1288085 +
Vvi Vvi5g0150 Chr5 1288628 1289093 +
Aed Aed4g0671 Chr4 5634914 5639456 +
Aev Aev04g1126 Chr04 7105224 7106456 +
Ahy Ahy14g0978 Chr14 16330762 16332040 +
Aip Aip04g01066 Chr04 15569088 15570481 +
Amo Amo14g1376 Chr14 22951664 22953078 +
Apr Apr9g2277 Chr9 30505298 30506241 -
Bva Bva05g01321 Chr05 6950800 6959791 +
Cca Cca08g01723 Chr08 49116198 49117836 -
Dod Dod03g1273 Chr03 16156880 16158515 +
Lal Lal19g1120 Chr19 14780576 14803474 +
Lapu Lapu3g00311 Chr3 3092842 3093401 +
Phco Phco8g02204 Chr8 23606846 23607416 +
Psa Psa1g3573 Chr1 306179428 306180796 -
Pvu Pvu3g1133 Chr3 27040486 27041443 -
Spst Spst3g03000 Chr3 79649457 79650043 +
Vimu Vimu11g01269 Chr11 13973953 13974845 +
Vivi Vivi1g01081 Chr1 23123718 23124448 -
Vra Vra5g0097 Chr5 786553 787438 +
Vvi Vvi5g0151 Chr5 1289188 1289244 +
Vvi Vvi5g0152 Chr5 1296092 1296707 +
Bva Bva05g01323 Chr05 6956785 6959791 +
Gma Gma17g00280 Chr17 2255730 2256292 -
Gso Gso17g0244 Chr17 2213623 2214474 -
Mal Mal4g3719 Chr4 109608590 109609555 -
Mtr Mtr2g1258 Chr2 13591923 13593314 +
Psa Psa4g0582 Chr4 35072479 35073210 -
Vvi Vvi5g0153 Chr5 1298448 1299094 +
Adu Adu01g02606 Chr01 95358568 95359419 +
Aed Aed4g0672 Chr4 5640700 5641316 +
Aev Aev01g2910 Chr01 31146070 31146990 +
Aev Aev04g1128 Chr04 7123181 7124594 +
Ahy Ahy11g2607 Chr11 142255797 142256794 -
Ahy Ahy14g0981 Chr14 16388738 16391154 +
Aip Aip01g02860 Chr01 130461047 130493309 -
Aip Aip04g01068 Chr04 15621309 15634125 +
Amo Amo14g1379 Chr14 22995634 22999989 +
Apr Apr9g2276 Chr9 30500651 30501380 -
Arst Arst1g03376 Chr1 94843101 94844348 +
Bva Bva05g02625 Chr05 21699263 21700121 +
Car Car01g00974 Chr01 9103360 9104732 +
Cca Cca08g01722 Chr08 49114535 49115396 -
Dod Dod05g2639 Chr05 52634392 52635409 +
Lal Lal19g1119 Chr19 14780476 14793269 -
Lasa Lasa4g03835 Chr4 628178758 628179509 -
Mal Mal4g3717 Chr4 109595759 109596797 -
Mtr Mtr2g1260 Chr2 13608492 13610297 +
Phco Phco8g02205 Chr8 23617872 23618443 +
Psa Psa1g3570 Chr1 306150432 306151575 -
Pste Pste6g04062 Chr6 29921939 29926216 +
Pvu Pvu3g1132 Chr3 27013976 27014992 -
Spst Spst3g03001 Chr3 79655528 79656092 +
Ssu Ssu1g1280 Chr1 28241094 28241902 +
Tpr Tpr5g2045 Chr5 40840428 40841930 -
Tsu Tsu07g01790 Chr07 17721096 17721976 +
Vimu Vimu7g01755 Chr7 16180507 16181362 +
Vivi Vivi1g01083 Chr1 23130326 23131123 -
Vra Vra5g0098 Chr5 789269 790037 +
Seca Seca12g00377 Chr12 3287876 3288830 -