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
Vvi3g1123 . . . . . Adu03g03242 . . . . . . . . . . . . . . . Arst3g04219 . Bach11g00765 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02881 . . . . . . . . . . . . . . . Mepo2g03470 . Mesa13g01670 . . . . . Phac2g03230 . Phco4g02436 . . . . . Pste3g03426 . . . Pte19g00828 . Pumo6g01658 . Pvu2g2189 . Rops2g01840 . Seca12g05126 . Spst3g00411 . . . . . . . Trre7g03956 . . . Vian1g03029 . Vifa1g10717 . Vimu11g03335 . Viun3g01696 . . . .
Vvi3g1124 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1125 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1126 . . . . . . Aed10g2056 . . . . . . . . . . . Apr3g1964 . . . . . . . . . . . Cca09g01431 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja6g3244 . . Mal4g4824 . . . . . . . Mtr2g0193 . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g1887 . . . . Tpr2g2814 . . . Tsu08g04278 . . . . . . . . . . Vra7g1526 .
Vvi3g1127 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1128 . Acco06g2381 . Accr5g00739 . Adu03g03240 Aed10g2058 . . . . . . . . Alju03g1017 . . Apr3g1966 . . Arst3g04217 . Bach11g00761 . Bisa07g0656 . . . . Cca09g01433 . . . . . . Enph4g0551 . Glsi11g2608 . . . . . . . . . . . . . . . . . . . . . Lapu3g02879 . Lasa7g03494 . . . . . Lele14g0500 . Lele16g1913 . Lja4g4039 Mal7g3820 . . Mepo2g03473 . Mesa13g01667 . . Mtr4g3187 . . Phac2g03227 . Phco4g02433 . . . . . Pste3g03423 . . Pte2g00714 Pte19g00827 . Pumo6g01656 . Pvu2g2186 . Rops2g01838 . Seca12g05128 . Spst3g00409 Ssu5g1889 . . . Tpr3g1634 . . Trre7g03963 Tsu02g01597 . . . . Vifa6g02222 . Vimu11g03333 . Viun3g01703 . . Vra7g1524 .
Vvi3g1129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1130 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g1132 . . . . . . . . Aev04g0799 . Ahy20g0801 . Aip10g00802 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi3g1123 Chr3 14838441 14852734 +
Adu Adu03g03242 Chr03 118786472 118787489 +
Arst Arst3g04219 Chr3 117510140 117511069 +
Bach Bach11g00765 Chr11 6192168 6194361 +
Lapu Lapu3g02881 Chr3 51799054 51801471 +
Mepo Mepo2g03470 Chr2 44350177 44351610 +
Mesa Mesa13g01670 Chr13 20056596 20057469 +
Phac Phac2g03230 Chr2 33779869 33781866 +
Phco Phco4g02436 Chr4 45546100 45547694 +
Pste Pste3g03426 Chr3 26958733 26960379 +
Pte Pte19g00828 Chr19 6686560 6689979 +
Pumo Pumo6g01658 Chr6 24552449 24554425 +
Pvu Pvu2g2189 Chr2 37486859 37488748 +
Rops Rops2g01840 Chr2 28751769 28753123 +
Seca Seca12g05126 Chr12 139253479 139254626 -
Spst Spst3g00411 Chr3 7211246 7213407 +
Trre Trre7g03956 Chr7 47809395 47810838 -
Vian Vian1g03029 Chr1 50074548 50076486 +
Vifa Vifa1g10717 Chr1 1801273105 1801274633 -
Vimu Vimu11g03335 Chr11 53934146 53936117 +
Viun Viun3g01696 Chr3 11881467 11883379 -
Vvi Vvi3g1124 Chr3 14881928 14892855 -
Vvi Vvi3g1125 Chr3 14893223 14893704 -
Vvi Vvi3g1126 Chr3 14960929 14980463 -
Aed Aed10g2056 Chr10 24420935 24421768 -
Apr Apr3g1964 Chr3 35642175 35644590 -
Cca Cca09g01431 Chr09 37559474 37561797 -
Lja Lja6g3244 Chr6 60813387 60814997 -
Mal Mal4g4824 Chr4 127652402 127654421 -
Mtr Mtr2g0193 Chr2 1985133 1987029 +
Ssu Ssu5g1887 Chr5 55603655 55606843 -
Tpr Tpr2g2814 Chr2 32662854 32664633 -
Tsu Tsu08g04278 Chr08 60737913 60739876 -
Vra Vra7g1526 Chr7 32972153 32974319 +
Vvi Vvi3g1127 Chr3 15013569 15013835 +
Vvi Vvi3g1128 Chr3 15021733 15043473 -
Acco Acco06g2381 Chr06 19874568 19881706 +
Accr Accr5g00739 Chr5 31492566 31500286 -
Adu Adu03g03240 Chr03 118780094 118784324 +
Aed Aed10g2058 Chr10 24424776 24428782 -
Alju Alju03g1017 Chr03 37749322 37763225 +
Apr Apr3g1966 Chr3 35648219 35656093 -
Arst Arst3g04217 Chr3 117503772 117507875 +
Bach Bach11g00761 Chr11 6073658 6083882 +
Bisa Bisa07g0656 Chr07 16977946 16993221 +
Cca Cca09g01433 Chr09 37565271 37570957 -
Enph Enph4g0551 Chr4 19251658 19259400 +
Glsi Glsi11g2608 Chr11 18771342 18778284 -
Lapu Lapu3g02879 Chr3 51787338 51793813 +
Lasa Lasa7g03494 Chr7 598904590 598907114 +
Lele Lele14g0500 Chr14 16638524 16643858 +
Lele Lele16g1913 Chr16 11541700 11546966 -
Lja Lja4g4039 Chr4 73536806 73539556 -
Mal Mal7g3820 Chr7 104033302 104036137 +
Mepo Mepo2g03473 Chr2 44362356 44366460 +
Mesa Mesa13g01667 Chr13 20019473 20023755 -
Mtr Mtr4g3187 Chr4 45318628 45320950 +
Phac Phac2g03227 Chr2 33766160 33773920 +
Phco Phco4g02433 Chr4 45532767 45540163 +
Pste Pste3g03423 Chr3 26947869 26954512 +
Pte Pte2g00714 Chr2 5761427 5764831 +
Pte Pte19g00827 Chr19 6669827 6673259 +
Pumo Pumo6g01656 Chr6 24540887 24548225 +
Pvu Pvu2g2186 Chr2 37474169 37481693 +
Rops Rops2g01838 Chr2 28734989 28743001 +
Seca Seca12g05128 Chr12 139298731 139307009 -
Spst Spst3g00409 Chr3 7189119 7195221 +
Ssu Ssu5g1889 Chr5 55615574 55622977 -
Tpr Tpr3g1634 Chr3 14537769 14539783 -
Trre Trre7g03963 Chr7 47846136 47849381 +
Tsu Tsu02g01597 Chr02 14024142 14026140 -
Vifa Vifa6g02222 Chr6 789015572 789018255 -
Vimu Vimu11g03333 Chr11 53921420 53928291 +
Viun Viun3g01703 Chr3 11924619 11930801 -
Vra Vra7g1524 Chr7 32958682 32965062 +
Vvi Vvi3g1129 Chr3 15117058 15117570 -
Vvi Vvi3g1130 Chr3 15118890 15122036 +
Vvi Vvi3g1131 Chr3 15130618 15134989 -
Vvi Vvi3g1132 Chr3 15160995 15174429 +
Aev Aev04g0799 Chr04 4904575 4906167 +
Ahy Ahy20g0801 Chr20 10206199 10208051 +
Aip Aip10g00802 Chr10 9750622 9752146 +