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
Vvi18g1176 . . . . . . . Aed9g0239 . . . . . . . . . . . Apr5g1638 . . . . . . Bva06g01935 . . . . Cca07g00294 . . . . . . . . Gma04g00248 . . . Gso4g0232 . . . Lal4g0078 Lal17g0066 Lal21g0124 . . . Lan14g0943 Lan14g0943 Lan14g0943 . . . . . . . . . . . . . . . Lja1g3526 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Vra5g1635
Vvi18g1177 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1178 . . . . . . . . . . . . . Aip06g00076 . . . . . . . . Bach12g00117 . . . . Bva10g00890 Car04g03567 . . . Dere04g0113 . . Dod08g2251 . . Glsi08g2010 . . Gma06g00227 . . . . . . . . . . . . . . . . . . Lapu9g02278 . . . . . . . . . . . . . Mal1g6003 . . . . . . . Mtr1g0683 . . . Phco7g00309 . . . . . Pste2g00720 . . . . . . . Pvu9g0154 . Rops10g02446 . . . Spst9g00305 . . . . Sto9g3680 Tpr1g3845 . . . Tsu01g00241 . Vian4g02373 . . . Vimu10g03463 . Viun9g03647 . Vivi4g05877 . . .
Vvi18g1179 . . . . . Adu03g00554 Aed11g0065 Aed9g0238 . Aev07g0707 . Ahy16g0087 . Aip06g00075 . . . . Apr9g0560 Apr5g1639 . Arst3g00733 . . . . . Bva10g00891 Car04g03568 . Cca05g00340 Cca07g00293 . . . Dod08g2252 . . . . . . . . . . . . . . . Lal8g0548 . . . . . . . . . Lapu11g00817 . Lasa7g02200 . . . . . . . . . Lja5g3300 Mal1g6004 . . Mepo2g02399 . Mesa13g02665 . . Mtr1g0684 . . Phac11g00564 . Phco9g00436 . . . . . Pste1g01574 . . . . . Pumo11g01886 . Pvu11g0393 . Rops3g00475 . Seca6g00793 . Spst2g02600 Ssu5g0083 . Sto5g0162 . Tpr1g3848 . . Trre7g02685 Tsu01g00240 . . Vian5g01551 . . . Vimu5g02434 . Viun11g02518 . Vivi5g02883 Vra6g2053 .
Vvi18g1180 Acco10g1571 . Accr4g01178 . . . . Aed9g0237 . . . . . . Alju08g1213 . . . . Apr5g1640 . . Bach12g00116 . Bisa09g2025 . Bva06g01934 Bva10g00892 . Car05g03257 . Cca07g00292 Dere04g0112 . . . Enph1g1062 . Glsi08g2012 . Gma04g00246 Gma06g00225 . . Gso4g0230 Gso4g0230 . . Lal4g0077 Lal17g0064 . . . . Lan14g0944 Lan14g0944 . . . . Lapu9g02279 . Lasa5g04508 . Lele01g0968 Lele02g0971 Lele03g0965 Lele04g0965 . . . . Lja1g3524 . . Mal2g0499 Mepo3g07872 . . . Mibi05g1125 . . Mtr3g4250 . . Phco7g00307 . Prci8g0417 . . Psa5g0340 Pste2g00714 . Pte3g01404 . . . . . Pvu9g0155 . Rops10g02448 . Seca4g00463 . Spst9g00304 . . . Sto5g0161 Sto9g3681 . Tpr7g0251 Trre5g05657 . . Tsu07g00278 Vian4g02374 . Vifa2g04478 . Vimu10g03464 . Viun9g03651 . Vivi3g00577 . . Vra5g1636
Vvi18g1181 . . . . . . . . . . . . . . . . . . Apr9g0561 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal1g6021 . . . . . . . Mtr1g0686 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr1g3849 . . . Tsu01g00238 . . . . . . . . . . . . .
Vvi18g1182 . . . . . . Aed11g0064 . . . . . . . . . . . . . . . . . . . . . Car04g03569 . Cca05g00341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g3301 Mal7g0848 . . . . . . . Mtr4g0751 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g0082 . . Sto9g3682 Tpr4g1001 . . . Tsu06g00712 . . . . . . . . . . . Vra6g2052 .
Vvi18g1183 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal1g6022 . . . . . . . Mtr1g0687 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr1g3851 . . . . . . . . . . . . . . . . .
Vvi18g1184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g3302 Mal7g0846 . . . . . . . Mtr4g0747 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g3683 . . . . . . . . . . . . . . . . . .
Vvi18g1185 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal7g0844 . . . . . . . Mtr4g0746 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr4g0995 . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Adu Adu03g00554 Chr03 5244816 5248848 +
Arst Arst3g00733 Chr3 5250797 5254868 +
Lapu Lapu11g00817 Chr11 10949056 10953250 +
Lasa Lasa7g02200 Chr7 503602015 503604540 +
Mepo Mepo2g02399 Chr2 33769141 33773173 +
Mesa Mesa13g02665 Chr13 31173924 31177422 -
Phac Phac11g00564 Chr11 3851234 3855468 -
Phco Phco9g00436 Chr9 3147098 3150328 -
Pste Pste1g01574 Chr1 4884249 4887985 -
Pumo Pumo11g01886 Chr11 50598557 50602155 +
Pvu Pvu11g0393 Chr11 3309634 3313584 -
Rops Rops3g00475 Chr3 6044719 6050618 -
Seca Seca6g00793 Chr6 26940578 26945325 -
Spst Spst2g02600 Chr2 25755402 25758554 +
Trre Trre7g02685 Chr7 22843332 22846159 -
Vian Vian5g01551 Chr5 38072545 38075763 +
Vimu Vimu5g02434 Chr5 34961981 34965222 +
Viun Viun11g02518 Chr11 38552582 38556571 +
Vivi Vivi5g02883 Chr5 116591824 116594843 +
Acco Acco10g1571 Chr10 29299912 29306007 -
Vvi Vvi18g1176 Chr18 11730595 11731579 +
Aed Aed9g0239 Chr9 1720695 1725200 -
Apr Apr5g1638 Chr5 20021550 20025612 +
Bva Bva06g01935 Chr06 13108650 13112035 -
Cca Cca07g00294 Chr07 3881498 3882660 -
Gma Gma04g00248 Chr04 2155016 2156178 -
Gso Gso4g0232 Chr4 2116298 2120438 -
Lal Lal4g0078 Chr4 462096 465423 -
Lal Lal17g0066 Chr17 385941 389213 -
Lal Lal21g0124 Chr21 849913 853241 -
Lan Lan14g0943 Chr14 15839289 15842364 +
Lan Lan14g0943 Chr14 15839289 15842364 +
Lan Lan14g0943 Chr14 15839289 15842364 +
Lja Lja1g3526 Chr1 43947255 43949396 -
Vra Vra5g1635 Chr5 22781828 22785815 +
Vvi Vvi18g1177 Chr18 11734395 11741869 +
Vvi Vvi18g1178 Chr18 11741937 11743126 +
Aip Aip06g00076 Chr06 750116 750829 -
Bach Bach12g00117 Chr12 822728 823870 -
Bva Bva10g00890 Chr10 6774793 6778677 +
Car Car04g03567 Chr04 64810201 64810983 +
Dere Dere04g0113 Chr04 1190196 1191342 -
Dod Dod08g2251 Chr08 50311777 50315620 +
Glsi Glsi08g2010 Chr08 14180032 14181173 +
Gma Gma06g00227 Chr06 2038854 2047760 -
Lapu Lapu9g02278 Chr9 37358832 37363283 +
Mal Mal1g6003 Chr1 137972114 137973269 +
Mtr Mtr1g0683 Chr1 7670626 7674297 +
Phco Phco7g00309 Chr7 2173972 2175136 -
Pste Pste2g00720 Chr2 7580688 7585800 -
Pvu Pvu9g0154 Chr9 2377757 2381806 +
Rops Rops10g02446 Chr10 42790249 42795327 +
Spst Spst9g00305 Chr9 2881877 2883018 -
Sto Sto9g3680 Chr9 35192474 35193604 +
Tpr Tpr1g3845 Chr1 42470889 42474612 +
Tsu Tsu01g00241 Chr01 1970772 1974462 -
Vian Vian4g02373 Chr4 40431986 40433148 +
Vimu Vimu10g03463 Chr10 44412456 44413939 +
Viun Viun9g03647 Chr9 41871516 41875465 +
Vivi Vivi4g05877 Chr4 195501122 195504445 +
Vvi Vvi18g1179 Chr18 11745491 11746246 -
Adu Adu03g00554 Chr03 5244816 5248848 +
Aed Aed11g0065 Chr11 505670 512425 -
Aed Aed9g0238 Chr9 1714374 1718290 -
Aev Aev07g0707 Chr07 4590326 4593023 -
Ahy Ahy16g0087 Chr16 835042 839030 -
Aip Aip06g00075 Chr06 743581 746375 -
Apr Apr9g0560 Chr9 7931038 7934139 +
Apr Apr5g1639 Chr5 20028725 20032361 +
Arst Arst3g00733 Chr3 5250797 5254868 +
Bva Bva10g00891 Chr10 6781361 6784747 +
Car Car04g03568 Chr04 64816186 64820051 +
Cca Cca05g00340 Chr05 7343324 7347196 +
Cca Cca07g00293 Chr07 3872714 3875872 -
Dod Dod08g2252 Chr08 50319479 50323903 +
Lal Lal8g0548 Chr8 3784668 3788628 -
Lapu Lapu11g00817 Chr11 10949056 10953250 +
Lasa Lasa7g02200 Chr7 503602015 503604540 +
Lja Lja5g3300 Chr5 63948356 63952685 +
Mal Mal1g6004 Chr1 137985034 137988385 +
Mepo Mepo2g02399 Chr2 33769141 33773173 +
Mesa Mesa13g02665 Chr13 31173924 31177422 -
Mtr Mtr1g0684 Chr1 7688837 7692553 +
Phac Phac11g00564 Chr11 3851234 3855468 -
Phco Phco9g00436 Chr9 3147098 3150328 -
Pste Pste1g01574 Chr1 4884249 4887985 -
Pumo Pumo11g01886 Chr11 50598557 50602155 +
Pvu Pvu11g0393 Chr11 3309634 3313584 -
Rops Rops3g00475 Chr3 6044719 6050618 -
Seca Seca6g00793 Chr6 26940578 26945325 -
Spst Spst2g02600 Chr2 25755402 25758554 +
Ssu Ssu5g0083 Chr5 1840488 1843128 -
Sto Sto5g0162 Chr5 933905 938201 -
Tpr Tpr1g3848 Chr1 42534239 42538672 +
Trre Trre7g02685 Chr7 22843332 22846159 -
Tsu Tsu01g00240 Chr01 1933486 1937609 -
Vian Vian5g01551 Chr5 38072545 38075763 +
Vimu Vimu5g02434 Chr5 34961981 34965222 +
Viun Viun11g02518 Chr11 38552582 38556571 +
Vivi Vivi5g02883 Chr5 116591824 116594843 +
Vra Vra6g2053 Chr6 37159446 37162882 -
Vvi Vvi18g1180 Chr18 11750211 11760799 +
Acco Acco10g1571 Chr10 29299912 29306007 -
Accr Accr4g01178 Chr4 11205076 11211632 +
Aed Aed9g0237 Chr9 1707368 1713236 -
Alju Alju08g1213 Chr08 9144617 9151411 +
Apr Apr5g1640 Chr5 20035026 20042833 +
Bach Bach12g00116 Chr12 813591 819503 -
Bisa Bisa09g2025 Chr09 32421570 32427880 +
Bva Bva06g01934 Chr06 13100355 13106513 -
Bva Bva10g00892 Chr10 6785718 6791254 +
Car Car05g03257 Chr05 77312749 77318524 +
Cca Cca07g00292 Chr07 3850718 3862663 -
Dere Dere04g0112 Chr04 1172827 1179333 -
Enph Enph1g1062 Chr1 36865477 36872254 -
Glsi Glsi08g2012 Chr08 14187184 14192944 +
Gma Gma04g00246 Chr04 2129289 2136826 -
Gma Gma06g00225 Chr06 2018786 2026693 -
Gso Gso4g0230 Chr4 2092073 2099872 -
Gso Gso4g0230 Chr4 2092073 2099872 -
Lal Lal4g0077 Chr4 455178 460753 -
Lal Lal17g0064 Chr17 374184 380542 -
Lan Lan14g0944 Chr14 15843728 15849901 +
Lan Lan14g0944 Chr14 15843728 15849901 +
Lapu Lapu9g02279 Chr9 37365781 37373582 +
Lasa Lasa5g04508 Chr5 668360166 668365831 +
Lele Lele01g0968 Chr01 5599739 5604401 +
Lele Lele02g0971 Chr02 5902056 5906941 +
Lele Lele03g0965 Chr03 5617833 5622510 +
Lele Lele04g0965 Chr04 5961020 5965890 +
Lja Lja1g3524 Chr1 43927160 43933976 -
Mal Mal2g0499 Chr2 5820193 5826270 -
Mepo Mepo3g07872 Chr3 91746620 91753422 -
Mibi Mibi05g1125 Chr05 13627204 13633126 +
Mtr Mtr3g4250 Chr3 56356116 56362854 +
Phco Phco7g00307 Chr7 2161529 2167604 -
Prci Prci8g0417 Chr8 2648921 2655560 +
Psa Psa5g0340 Chr5 24434637 24440364 +
Pste Pste2g00714 Chr2 7508437 7515928 -
Pte Pte3g01404 Chr3 12263140 12268801 +
Pvu Pvu9g0155 Chr9 2391557 2398218 +
Rops Rops10g02448 Chr10 42803256 42810399 +
Seca Seca4g00463 Chr4 7448632 7456688 -
Spst Spst9g00304 Chr9 2858682 2872490 -
Sto Sto5g0161 Chr5 927182 932315 -
Sto Sto9g3681 Chr9 35200596 35206971 +
Tpr Tpr7g0251 Chr7 2044112 2051450 -
Trre Trre5g05657 Chr5 56654466 56659911 +
Tsu Tsu07g00278 Chr07 2132393 2138554 -
Vian Vian4g02374 Chr4 40437319 40443424 +
Vifa Vifa2g04478 Chr2 1316027444 1316033095 +
Vimu Vimu10g03464 Chr10 44416762 44422853 +
Viun Viun9g03651 Chr9 41880530 41887067 +
Vivi Vivi3g00577 Chr3 9524381 9530309 +
Vra Vra5g1636 Chr5 22787593 22794135 +
Vvi Vvi18g1181 Chr18 11761857 11763067 -
Apr Apr9g0561 Chr9 7934090 7938352 -
Mal Mal1g6021 Chr1 138261430 138263494 -
Mtr Mtr1g0686 Chr1 7697765 7701329 -
Tpr Tpr1g3849 Chr1 42539360 42547109 -
Tsu Tsu01g00238 Chr01 1904186 1929905 +
Vvi Vvi18g1182 Chr18 11767728 11769317 -
Aed Aed11g0064 Chr11 505670 509494 +
Car Car04g03569 Chr04 64820920 64823151 -
Cca Cca05g00341 Chr05 7378817 7380797 -
Lja Lja5g3301 Chr5 63953989 63956402 -
Mal Mal7g0848 Chr7 22967014 22969106 +
Mtr Mtr4g0751 Chr4 9512666 9515724 -
Ssu Ssu5g0082 Chr5 1832896 1836194 +
Sto Sto9g3682 Chr9 35209722 35211328 -
Tpr Tpr4g1001 Chr4 9602270 9607266 +
Tsu Tsu06g00712 Chr06 6208800 6210200 +
Vra Vra6g2052 Chr6 37153222 37156233 +
Vvi Vvi18g1183 Chr18 11774368 11775969 -
Mal Mal1g6022 Chr1 138285660 138287866 +
Mtr Mtr1g0687 Chr1 7704813 7708261 -
Tpr Tpr1g3851 Chr1 42556767 42561731 -
Vvi Vvi18g1184 Chr18 11779385 11781003 -
Lja Lja5g3302 Chr5 63964391 63967179 -
Mal Mal7g0846 Chr7 22759675 22762427 +
Mtr Mtr4g0747 Chr4 9477704 9484748 -
Sto Sto9g3683 Chr9 35214875 35216195 -
Vvi Vvi18g1185 Chr18 11784344 11785492 -
Mal Mal7g0844 Chr7 22533727 22535518 -
Mtr Mtr4g0746 Chr4 9464098 9467400 +
Tpr Tpr4g0995 Chr4 9550963 9552952 -