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
Vvi4g1264 . . . . . . . . . . . . . . . . . . Apr3g0323 . . . Bach10g00591 . . . Bva08g00823 . . . . . . . . . . . . . . . Gma02g00461 . . . . . Lal16g1837 Lal15g1501 . . . . Lan6g1479 Lan6g1479 . . . . . . Lasa4g02274 . . . . . . . . . . Lja4g3164 . Mal5g3358 Mepo1g02109 . Mesa29g02272 . . . . Mtr8g2431 . . Phco8g00430 . . . . Psa4g2267 . . Pte14g00874 Pte12g00497 . . Pumo4g02181 . Pvu3g2671 . Rops2g03292 . Seca12g02858 . Spst3g03822 . . . Sto6g3903 . . Tpr4g4245 Trre15g02716 . . Tsu04g03484 Vian1g01818 . Vifa4g02364 . Vimu11g00705 . Viun3g03606 . Vivi1g03098 . . .
Vvi4g1265 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1266 . . . . . . . . Aev05g0446 . Ahy15g0864 . Aip05g00884 . . . . . Apr3g0324 Apr7g1079 . . . . . . Bva08g00824 . . . . . . . Dod02g0494 . . . . . . . Gma02g00460 Gma16g01223 . . . . . . Lal23g1454 . . . . . . . . . . . . . . . . . . . . . Lja2g0527 Lja4g3163 Mal6g1062 Mal5g3357 . . . . . . Mtr5g0848 Mtr8g2430 . . . . . . Psa2g3540 Psa4g2270 . . . . . . . . Pvu3g2677 . . . . . . . . . Sto6g3905 . Tpr2g1070 Tpr4g4246 . . Tsu05g00809 Tsu04g03486 . . . . . . . . . . . .
Vvi4g1267 . Acco11g2353 . Accr9g00135 . Adu05g00891 Aed11g1234 . Aev05g0445 . Ahy15g0865 . Aip05g00885 . Alju12g0014 Alju09g2360 . . . Apr7g1080 Arst3g00718 Arst5g01116 Bach10g00593 . Bisa01g2850 Bisa11g1766 Bva08g00825 . . . Cca06g01286 . Dere13g0709 Dere09g1013 Dod02g0493 . . Enph13g0874 Glsi09g0615 Glsi05g1367 Gma11g00680 Gma01g01720 . . Gso11g0632 Gso11g0632 . . . . Lal23g1455 . . . . . . . . . . Lapu2g00737 Lasa2g03399 Lasa2g03399 Lele53g0014 . . . Lele49g0103 . Lele51g0116 Lele52g0122 Lja2g0528 Lja4g3160 Mal6g1060 . . Mepo5g00963 . Mesa17g01004 . Mibi12g2050 Mtr5g0851 . . Phac2g01747 Phco8g00427 Phco4g00894 Prci5g0030 Prci10g0194 Psa2g3539 . . Pste1g02979 Pte14g00870 Pte2g01271 . Pte12g00486 . . Pvu3g2678 Pvu2g1150 . . . . Spst3g03819 Spst3g03819 . . Sto6g3906 Sto11g1504 Tpr2g1071 . . Trre9g01160 Tsu05g00810 . . . . . Vimu7g03030 Vimu7g03030 . . . . Vra11g0756 .
Vvi4g1268 . . . . . Adu05g00893 Aed11g1233 . Aev05g0443 . Ahy15g0866 . Aip05g00887 . . . . . . Apr7g1081 . Arst5g01118 . Bach4g00712 . Bisa11g1767 Bva08g00826 . . . Cca06g01285 . . Dere09g1015 Dod02g0492 . . . . Glsi05g1366 Gma11g00681 Gma01g01719 . . Gso11g0633 Gso11g0633 . . . . . . . . . . . . . . . Lapu2g00738 . Lasa2g03401 . . . . . . . . Lja2g0529 . Mal6g1057 . . Mepo5g00965 . Mesa17g01006 . . Mtr5g0853 . . Phac2g01745 . Phco4g00893 . . Psa2g3538 Psa4g2274 . Pste1g02981 . . . . . . . Pvu2g1149 . . . . . Spst2g00888 . . Sto6g3907 Sto11g1503 Tpr2g1072 . . Trre9g01162 Tsu05g00811 . . . . . . Vimu7g03031 . . . . Vra11g0757 .
Vvi4g1269 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1270 . . . . . . Aed11g1232 . Aev05g0442 Aev08g0224 Ahy15g0867 Ahy17g2317 Aip05g00888 Aip07g02473 . . . . Apr3g0326 Apr7g1082 . . . . . . Bva08g00827 . . . Cca06g01284 . . . Dod02g0491 . . . . . Gma11g00682 Gma01g01718 Gma02g00459 Gma16g01221 Gso11g0634 Gso11g0634 Gso11g0634 Gso11g0634 . Lal15g1502 Lal23g1456 . . . . . . . . . . . . . . . . . . . . . Lja2g0532 Lja4g3159 Mal6g1055 Mal5g3356 . . . . . . Mtr5g0854 Mtr8g2429 . . . . . . Psa2g3535 . . . . . . . . . . . . . . . . . . . Sto6g3908 . Tpr2g1073 Tpr4g4247 . . Tsu05g00812 Tsu04g03487 . . . . . . . . . . Vra11g0758 .
Vvi4g1271 . . . . . . . . . Aev08g0223 Ahy15g0869 Ahy17g2316 Aip05g00891 Aip07g02472 . . . . . . . . . . . . Bva08g00828 . . . . . . . Dod02g0488 . . . . . Gma11g00683 Gma01g01717 Gma02g00458 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g0533 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3910 . . . . . . . . . . . . . . . . . . .
Vvi4g1272 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa4g2287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1273 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Lal Lal15g1501 Chr15 17133304 17137240 +
Vvi Vvi4g1264 Chr4 19589675 19597229 +
Apr Apr3g0323 Chr3 6424487 6428197 +
Bach Bach10g00591 Chr10 4222530 4224381 +
Bva Bva08g00823 Chr08 4231987 4234829 +
Gma Gma02g00461 Chr02 4643669 4646926 -
Lal Lal16g1837 Chr16 17459358 17462344 +
Lal Lal15g1501 Chr15 17133304 17137240 +
Lan Lan6g1479 Chr6 21652216 21655384 -
Lan Lan6g1479 Chr6 21652216 21655384 -
Lasa Lasa4g02274 Chr4 451089487 451091639 -
Lja Lja4g3164 Chr4 59804495 59808857 -
Mal Mal5g3358 Chr5 97370854 97373301 -
Mepo Mepo1g02109 Chr1 21709337 21713460 +
Mesa Mesa29g02272 Chr29 31241288 31244124 +
Mtr Mtr8g2431 Chr8 34747146 34751215 -
Phco Phco8g00430 Chr8 3924379 3927256 -
Psa Psa4g2267 Chr4 184703817 184707392 +
Pte Pte14g00874 Chr14 30149010 30151343 -
Pte Pte12g00497 Chr12 4478705 4481155 +
Pumo Pumo4g02181 Chr4 32033608 32037096 +
Pvu Pvu3g2671 Chr3 48755599 48759290 +
Rops Rops2g03292 Chr2 60211447 60214932 -
Seca Seca12g02858 Chr12 52220847 52224401 +
Spst Spst3g03822 Chr3 88205839 88208487 -
Sto Sto6g3903 Chr6 43269473 43271193 +
Tpr Tpr4g4245 Chr4 49594622 49598245 +
Trre Trre15g02716 Chr15 22997870 22999679 -
Tsu Tsu04g03484 Chr04 44021381 44024121 +
Vian Vian1g01818 Chr1 21520295 21522402 +
Vifa Vifa4g02364 Chr4 710937200 710939023 -
Vimu Vimu11g00705 Chr11 7524817 7527163 +
Viun Viun3g03606 Chr3 42797694 42801100 -
Vivi Vivi1g03098 Chr1 68334169 68336728 +
Vvi Vvi4g1265 Chr4 19605101 19606877 +
Vvi Vvi4g1266 Chr4 19607770 19615813 -
Aev Aev05g0446 Chr05 3098105 3102209 +
Ahy Ahy15g0864 Chr15 12558703 12562980 -
Aip Aip05g00884 Chr05 12172387 12177740 -
Apr Apr3g0324 Chr3 6431118 6437111 -
Apr Apr7g1079 Chr7 17757874 17764241 -
Bva Bva08g00824 Chr08 4234890 4240039 -
Dod Dod02g0494 Chr02 6446321 6451189 +
Gma Gma02g00460 Chr02 4639225 4643148 +
Gma Gma16g01223 Chr16 30047075 30052850 +
Lal Lal23g1454 Chr23 14907292 14913100 -
Lja Lja2g0527 Chr2 4760354 4766682 +
Lja Lja4g3163 Chr4 59797143 59803206 +
Mal Mal6g1062 Chr6 16001128 16005128 +
Mal Mal5g3357 Chr5 97363605 97369761 +
Mtr Mtr5g0848 Chr5 8350570 8355093 -
Mtr Mtr8g2430 Chr8 34740246 34746499 +
Psa Psa2g3540 Chr2 386682745 386686126 +
Psa Psa4g2270 Chr4 184823213 184828629 -
Pvu Pvu3g2677 Chr3 48779028 48784205 -
Sto Sto6g3905 Chr6 43277672 43282233 -
Tpr Tpr2g1070 Chr2 12548146 12553068 -
Tpr Tpr4g4246 Chr4 49598805 49605186 -
Tsu Tsu05g00809 Chr05 6894399 6899287 -
Tsu Tsu04g03486 Chr04 44029572 44036325 -
Vvi Vvi4g1267 Chr4 19619418 19622085 -
Acco Acco11g2353 Chr11 36921741 36923816 -
Accr Accr9g00135 Chr9 1544192 1546272 +
Adu Adu05g00891 Chr05 11289148 11291650 -
Aed Aed11g1234 Chr11 17528833 17531821 +
Aev Aev05g0445 Chr05 3094671 3096263 +
Ahy Ahy15g0865 Chr15 12581570 12583983 -
Aip Aip05g00885 Chr05 12196072 12200144 -
Alju Alju12g0014 Chr12 276967 278926 -
Alju Alju09g2360 Chr09 46620338 46622437 -
Apr Apr7g1080 Chr7 17768395 17771443 -
Arst Arst3g00718 Chr3 5110874 5113754 -
Arst Arst5g01116 Chr5 11313248 11315579 -
Bach Bach10g00593 Chr10 4235126 4237692 -
Bisa Bisa01g2850 Chr01 57408113 57410231 -
Bisa Bisa11g1766 Chr11 39350662 39353386 -
Bva Bva08g00825 Chr08 4241202 4243920 -
Cca Cca06g01286 Chr06 27540532 27543928 +
Dere Dere13g0709 Chr13 8931529 8933675 -
Dere Dere09g1013 Chr09 13040534 13042599 -
Dod Dod02g0493 Chr02 6439872 6443003 +
Enph Enph13g0874 Chr13 14913066 14915686 +
Glsi Glsi09g0615 Chr09 4264881 4266911 -
Glsi Glsi05g1367 Chr05 62717805 62719974 +
Gma Gma11g00680 Chr11 5679949 5683681 -
Gma Gma01g01720 Chr01 52898828 52901897 +
Gso Gso11g0632 Chr11 5634181 5637440 -
Gso Gso11g0632 Chr11 5634181 5637440 -
Lal Lal23g1455 Chr23 14914968 14916678 -
Lapu Lapu2g00737 Chr2 6526709 6531168 -
Lasa Lasa2g03399 Chr2 533695757 533697255 -
Lasa Lasa2g03399 Chr2 533695757 533697255 -
Lele Lele53g0014 Chr53 160540 162988 -
Lele Lele49g0103 Chr49 640654 641822 +
Lele Lele51g0116 Chr51 669438 671692 +
Lele Lele52g0122 Chr52 717140 719254 +
Lja Lja2g0528 Chr2 4767128 4770807 -
Lja Lja4g3160 Chr4 59731619 59734093 +
Mal Mal6g1060 Chr6 15958945 15961228 +
Mepo Mepo5g00963 Chr5 9360167 9363046 -
Mesa Mesa17g01004 Chr17 12784150 12785618 -
Mibi Mibi12g2050 Chr12 36891246 36893328 -
Mtr Mtr5g0851 Chr5 8372370 8375326 -
Phac Phac2g01747 Chr2 19506014 19509228 +
Phco Phco8g00427 Chr8 3881695 3883435 +
Phco Phco4g00894 Chr4 7045351 7046704 +
Prci Prci5g0030 Chr5 898830 901454 -
Prci Prci10g0194 Chr10 1274601 1277850 +
Psa Psa2g3539 Chr2 386656323 386658929 +
Pste Pste1g02979 Chr1 13077827 13080952 -
Pte Pte14g00870 Chr14 30132735 30134954 +
Pte Pte2g01271 Chr2 14433181 14434072 +
Pte Pte12g00486 Chr12 4392314 4392884 +
Pvu Pvu3g2678 Chr3 48801087 48803925 -
Pvu Pvu2g1150 Chr2 22653997 22656628 +
Spst Spst3g03819 Chr3 88160147 88162744 +
Spst Spst3g03819 Chr3 88160147 88162744 +
Sto Sto6g3906 Chr6 43285777 43286751 -
Sto Sto11g1504 Chr11 14256976 14257831 +
Tpr Tpr2g1071 Chr2 12554929 12557951 -
Trre Trre9g01160 Chr9 9349905 9352210 -
Tsu Tsu05g00810 Chr05 6903092 6906224 -
Vimu Vimu7g03030 Chr7 25543693 25545553 -
Vimu Vimu7g03030 Chr7 25543693 25545553 -
Vra Vra11g0756 Chr11 6151563 6153584 -
Vvi Vvi4g1268 Chr4 19631730 19632571 -
Adu Adu05g00893 Chr05 11312446 11313807 -
Aed Aed11g1233 Chr11 17525883 17527369 +
Aev Aev05g0443 Chr05 3089088 3090195 +
Ahy Ahy15g0866 Chr15 12603956 12605239 -
Aip Aip05g00887 Chr05 12221976 12223349 -
Apr Apr7g1081 Chr7 17772840 17779683 -
Arst Arst5g01118 Chr5 11336436 11337595 -
Bach Bach4g00712 Chr4 4720706 4721649 -
Bisa Bisa11g1767 Chr11 39357383 39359161 -
Bva Bva08g00826 Chr08 4245213 4246326 -
Cca Cca06g01285 Chr06 27536926 27538690 +
Dere Dere09g1015 Chr09 13045496 13046255 -
Dod Dod02g0492 Chr02 6429934 6431730 +
Glsi Glsi05g1366 Chr05 62715616 62716401 +
Gma Gma11g00681 Chr11 5685512 5686929 -
Gma Gma01g01719 Chr01 52894497 52896810 +
Gso Gso11g0633 Chr11 5639616 5641158 -
Gso Gso11g0633 Chr11 5639616 5641158 -
Lapu Lapu2g00738 Chr2 6532040 6533687 -
Lasa Lasa2g03401 Chr2 533729360 533730544 -
Lja Lja2g0529 Chr2 4773129 4774845 -
Mal Mal6g1057 Chr6 15885733 15887123 +
Mepo Mepo5g00965 Chr5 9387769 9389131 -
Mesa Mesa17g01006 Chr17 12811078 12812105 -
Mtr Mtr5g0853 Chr5 8396690 8398307 -
Phac Phac2g01745 Chr2 19503060 19504684 +
Phco Phco4g00893 Chr4 7042164 7043244 +
Psa Psa2g3538 Chr2 386589025 386590884 +
Psa Psa4g2274 Chr4 185157592 185158337 +
Pste Pste1g02981 Chr1 13083043 13084615 -
Pvu Pvu2g1149 Chr2 22651130 22652347 +
Spst Spst2g00888 Chr2 7575159 7576091 -
Sto Sto6g3907 Chr6 43288245 43289007 -
Sto Sto11g1503 Chr11 14252330 14253586 +
Tpr Tpr2g1072 Chr2 12563779 12565646 -
Trre Trre9g01162 Chr9 9358738 9360444 -
Tsu Tsu05g00811 Chr05 6911409 6919213 -
Vimu Vimu7g03031 Chr7 25546814 25548571 -
Vra Vra11g0757 Chr11 6155092 6156870 -
Vvi Vvi4g1269 Chr4 19635144 19636740 -
Vvi Vvi4g1270 Chr4 19638019 19645915 +
Aed Aed11g1232 Chr11 17513510 17521414 -
Aev Aev05g0442 Chr05 3078817 3083219 -
Aev Aev08g0224 Chr08 1260102 1265503 -
Ahy Ahy15g0867 Chr15 12640516 12647420 +
Ahy Ahy17g2317 Chr17 111538559 111544100 -
Aip Aip05g00888 Chr05 12250878 12257855 +
Aip Aip07g02473 Chr07 103586537 103591229 -
Apr Apr3g0326 Chr3 6502362 6508466 +
Apr Apr7g1082 Chr7 17784880 17793125 +
Bva Bva08g00827 Chr08 4252454 4259416 +
Cca Cca06g01284 Chr06 27516085 27524309 -
Dod Dod02g0491 Chr02 6416462 6424192 -
Gma Gma11g00682 Chr11 5695778 5702874 +
Gma Gma01g01718 Chr01 52871002 52877432 -
Gma Gma02g00459 Chr02 4622665 4629334 -
Gma Gma16g01221 Chr16 29983248 29989119 -
Gso Gso11g0634 Chr11 5647874 5656609 +
Gso Gso11g0634 Chr11 5647874 5656609 +
Gso Gso11g0634 Chr11 5647874 5656609 +
Gso Gso11g0634 Chr11 5647874 5656609 +
Lal Lal15g1502 Chr15 17142511 17148558 +
Lal Lal23g1456 Chr23 14921298 14927104 +
Lja Lja2g0532 Chr2 4790951 4796974 +
Lja Lja4g3159 Chr4 59714849 59722865 +
Mal Mal6g1055 Chr6 15847571 15853151 -
Mal Mal5g3356 Chr5 97352768 97359268 +
Mtr Mtr5g0854 Chr5 8412820 8418835 +
Mtr Mtr8g2429 Chr8 34726735 34734444 +
Psa Psa2g3535 Chr2 386414749 386420881 -
Sto Sto6g3908 Chr6 43295005 43300360 +
Tpr Tpr2g1073 Chr2 12578699 12585153 +
Tpr Tpr4g4247 Chr4 49617012 49624899 -
Tsu Tsu05g00812 Chr05 6931313 6936728 +
Tsu Tsu04g03487 Chr04 44059357 44067282 -
Vra Vra11g0758 Chr11 6167165 6173843 +
Vvi Vvi4g1271 Chr4 19652846 19656238 +
Aev Aev08g0223 Chr08 1254653 1258072 -
Ahy Ahy15g0869 Chr15 12682255 12687038 +
Ahy Ahy17g2316 Chr17 111518078 111521864 -
Aip Aip05g00891 Chr05 12293921 12295285 +
Aip Aip07g02472 Chr07 103568567 103572293 -
Bva Bva08g00828 Chr08 4263985 4268098 +
Dod Dod02g0488 Chr02 6406670 6408613 -
Gma Gma11g00683 Chr11 5709131 5712649 +
Gma Gma01g01717 Chr01 52860466 52863855 -
Gma Gma02g00458 Chr02 4610781 4614173 -
Lja Lja2g0533 Chr2 4800485 4804250 +
Sto Sto6g3910 Chr6 43311097 43314483 +
Vvi Vvi4g1272 Chr4 19659930 19661398 -
Psa Psa4g2287 Chr4 186216422 186221783 -
Vvi Vvi4g1273 Chr4 19662608 19665583 -
Aev Aev08g0224 Chr08 1260102 1265503 -
Ahy Ahy17g2317 Chr17 111538559 111544100 -
Aip Aip07g02473 Chr07 103586537 103591229 -
Gma Gma16g01221 Chr16 29983248 29989119 -
Aev Aev08g0223 Chr08 1254653 1258072 -
Ahy Ahy17g2316 Chr17 111518078 111521864 -
Aip Aip07g02472 Chr07 103568567 103572293 -