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
Vvi3g0003 . Acco08g2003 . . . . . Aed9g0090 . . . . . . . Alju10g1982 . . . . . . . . . Bisa02g2608 Bva13g00159 Bva14g00231 . . Cca04g00397 Cca07g00110 . Dere07g1906 . . . Enph8g1347 . . . . . Gma12g00362 . . . . . Lal2g0131 Lal9g0146 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mibi07g1860 . . . Phac11g00134 . . . . . . . Pste1g00498 . . Pte1g01079 . . . . Pvu11g0109 . . . . . Spst2g02926 . . Sto2g0766 . . . . . . . . . . . . Vimu5g02770 . . . . Vra2g0379 Vra5g1790
Vvi3g0004 . . . . . . . Aed9g0090 . . . . . . . . . . . Apr5g1791 Arst8g00102 . . . . . Bva13g00158 Bva14g00230 . . . Cca07g00110 . . . . . . . . Gma04g00089 Gma06g00084 . . Gso4g0084 Gso4g0084 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco7g00128 . . . . . . . . . . . . . Pvu9g0050 . Rops10g02623 . Seca4g00168 . . . . . Sto2g0767 . . . . . . . . . . . Vimu10g03651 . . . . . . Vra5g1790
Vvi3g0005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g0141 . . . . . . . . . . . . . . . . . .
Vvi3g0007 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g00229 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g0768 . . . . . . . . . . . . . . . . . . .
Vvi3g0008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0009 . . . . . . . Aed9g0089 . . . . . . . . . . . Apr5g1792 . . . . . . Bva13g00157 Bva14g00228 . . . Cca07g00109 . . . . . . . . Gma04g00088 Gma06g00083 . . Gso4g0083 Gso4g0083 . . . . . . . . . . . . . . Lapu9g02428 . Lasa5g04720 . . . . . . . . . Lja1g2326 . . . Mepo3g07999 . . . . . . . Phac9g02036 . Phco7g00124 . . . . . . . . . . . . . Pvu9g0047 . Rops10g02624 . . . Spst9g00116 . . . Sto2g0769 Sto10g0140 . . Trre5g05899 . . . Vian4g02544 . Vifa2g04738 . Vimu10g03656 . Viun9g03885 . Vivi3g00627 . . Vra5g1793
Vvi3g0010 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g00156 Bva14g00227 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g0770 . . . . . . . . . . . . . . . . . . .
Vvi3g0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Bva Bva13g00159 Chr13 779708 783777 -
Bva Bva14g00231 Chr14 1205794 1211007 -
Gma Gma04g00089 Chr04 784995 788210 +
Gma Gma06g00084 Chr06 758686 761587 +
Gso Gso4g0084 Chr4 770167 774486 +
Gso Gso4g0084 Chr4 770167 774486 +
Vvi Vvi3g0003 Chr3 26344 40225 +
Acco Acco08g2003 Chr08 34279705 34285456 +
Aed Aed9g0090 Chr9 656564 675460 +
Alju Alju10g1982 Chr10 38819405 38825363 +
Bisa Bisa02g2608 Chr02 66096157 66103428 +
Bva Bva13g00159 Chr13 779708 783777 -
Bva Bva14g00231 Chr14 1205794 1211007 -
Cca Cca04g00397 Chr04 3999092 4001373 -
Cca Cca07g00110 Chr07 1406483 1410369 +
Dere Dere07g1906 Chr07 31826967 31833390 +
Enph Enph8g1347 Chr8 21934744 21939382 -
Gma Gma12g00362 Chr12 2981086 2982527 -
Lal Lal2g0131 Chr2 801166 810380 +
Lal Lal9g0146 Chr9 939200 939682 -
Mibi Mibi07g1860 Chr07 39087802 39096028 +
Phac Phac11g00134 Chr11 888572 895347 +
Pste Pste1g00498 Chr1 1607776 1612291 -
Pte Pte1g01079 Chr1 28719928 28720836 +
Pvu Pvu11g0109 Chr11 809821 816500 +
Spst Spst2g02926 Chr2 29007830 29012132 -
Sto Sto2g0766 Chr2 6556691 6561801 +
Vimu Vimu5g02770 Chr5 37260645 37261043 -
Vra Vra2g0379 Chr2 2944615 2946896 -
Vra Vra5g1790 Chr5 23931325 23935307 -
Vvi Vvi3g0004 Chr3 41298 46508 -
Aed Aed9g0090 Chr9 656564 675460 +
Apr Apr5g1791 Chr5 21222679 21226834 -
Arst Arst8g00102 Chr8 1136090 1138695 -
Bva Bva13g00158 Chr13 775002 779059 +
Bva Bva14g00230 Chr14 1200199 1204398 +
Cca Cca07g00110 Chr07 1406483 1410369 +
Gma Gma04g00089 Chr04 784995 788210 +
Gma Gma06g00084 Chr06 758686 761587 +
Gso Gso4g0084 Chr4 770167 774486 +
Gso Gso4g0084 Chr4 770167 774486 +
Phco Phco7g00128 Chr7 851828 854853 +
Pvu Pvu9g0050 Chr9 877380 880404 +
Rops Rops10g02623 Chr10 45430748 45435772 -
Seca Seca4g00168 Chr4 2576100 2581324 -
Sto Sto2g0767 Chr2 6566166 6570133 -
Vimu Vimu10g03651 Chr10 45673038 45676635 -
Vra Vra5g1790 Chr5 23931325 23935307 -
Vvi Vvi3g0005 Chr3 69711 75526 -
Vvi Vvi3g0006 Chr3 76147 76494 -
Sto Sto10g0141 Chr10 1125525 1129302 +
Vvi Vvi3g0007 Chr3 78495 93933 +
Bva Bva14g00229 Chr14 1192034 1192729 -
Sto Sto2g0768 Chr2 6583630 6592859 +
Vvi Vvi3g0008 Chr3 111028 116884 +
Vvi Vvi3g0009 Chr3 120160 122718 +
Aed Aed9g0089 Chr9 649455 653680 -
Apr Apr5g1792 Chr5 21231333 21235173 +
Bva Bva13g00157 Chr13 768946 772845 -
Bva Bva14g00228 Chr14 1186521 1189386 -
Cca Cca07g00109 Chr07 1392602 1397873 -
Gma Gma04g00088 Chr04 777229 780727 -
Gma Gma06g00083 Chr06 751084 755087 -
Gso Gso4g0083 Chr4 763445 767162 -
Gso Gso4g0083 Chr4 763445 767162 -
Lapu Lapu9g02428 Chr9 38716852 38722721 +
Lasa Lasa5g04720 Chr5 691424261 691427131 +
Lja Lja1g2326 Chr1 26931425 26935766 +
Mepo Mepo3g07999 Chr3 92822931 92828492 +
Phac Phac9g02036 Chr9 19026171 19027156 +
Phco Phco7g00124 Chr7 829000 834227 -
Pvu Pvu9g0047 Chr9 855696 860624 -
Rops Rops10g02624 Chr10 45442424 45446987 +
Spst Spst9g00116 Chr9 936844 941738 -
Sto Sto2g0769 Chr2 6596339 6600194 +
Sto Sto10g0140 Chr10 1119439 1120513 -
Trre Trre5g05899 Chr5 58567702 58571660 +
Vian Vian4g02544 Chr4 41942338 41947392 -
Vifa Vifa2g04738 Chr2 1395333757 1395336993 +
Vimu Vimu10g03656 Chr10 45699274 45699827 +
Viun Viun9g03885 Chr9 43127339 43130875 +
Vivi Vivi3g00627 Chr3 10475994 10488999 -
Vra Vra5g1793 Chr5 23954144 23959326 +
Vvi Vvi3g0010 Chr3 126532 137261 -
Bva Bva13g00156 Chr13 762835 768403 +
Bva Bva14g00227 Chr14 1179680 1185942 +
Sto Sto2g0770 Chr2 6601588 6607044 -
Vvi Vvi3g0011 Chr3 138993 139274 +
Vvi Vvi3g0012 Chr3 145900 146562 +
Sto Sto2g0767 Chr2 6566166 6570133 -
Sto Sto2g0766 Chr2 6556691 6561801 +
Gma Gma12g00362 Chr12 2981086 2982527 -
Aed Aed9g0090 Chr9 656564 675460 +
Arst Arst8g00102 Chr8 1136090 1138695 -
Cca Cca07g00110 Chr07 1406483 1410369 +
Gma Gma04g00089 Chr04 784995 788210 +
Gso Gso4g0084 Chr4 770167 774486 +
Gso Gso4g0084 Chr4 770167 774486 +
Vra Vra5g1790 Chr5 23931325 23935307 -
Gma Gma06g00084 Chr06 758686 761587 +