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
Vvi16g1029 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g5718 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1030 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1032 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1033 . . . . . . . . . . . . . . . . . . . Apr6g0304 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1034 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma16g00279 . . . Gso16g0253 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1037 . . . . . Adu09g02326 Aed1g2316 Aed11g1750 . Aev09g2859 . Ahy19g2864 . Aip09g03332 . . . . . . . Arst9g03067 . . . . Bva03g01295 Bva04g01203 . . Cca02g02204 Cca06g01826 . . . . . . . . Gma10g02183 . . . Gso10g2052 . . . . . . . Lal12g0071 Lal13g0061 . . . . . . . Lapu7g02001 . Lasa6g04022 . . . . . . . . . Lja5g0678 Mal1g2112 . . Mepo4g04193 . Mesa1g04578 . . Mtr1g3693 . . Phac7g01157 . Phco6g02427 . . Psa6g4459 . . Pste4g02807 . . Pte16g00332 Pte9g00404 . . . Pvu7g0774 . Rops6g02672 . Seca8g07332 . Spst10g00915 Ssu7g0842 Ssu2g2902 . . Tpr1g0811 . . Trre1g05329 Tsu01g04362 . . Vian3g00676 . Vifa3g02852 . Vimu3g02985 . Viun7g03181 . Vivi1g04461 Vra8g2189 Vra11g0250
Vvi16g1038 . . . . . Adu09g02324 Aed1g2317 . . Aev09g2179 Ahy17g2696 Ahy19g3591 Aip07g02941 Aip09g04050 . . Amo17g2607 . . . . Arst9g03066 . . . . Bva12g01988 . . . Cca02g02203 . . . . Dod06g0849 . . . . Gma10g02182 . . . Gso10g2051 . . . . . . Lal24g0061 . Lal13g0062 . . . . . . . Lapu7g02000 . Lasa6g04020 . . . . . . . . . Lja5g0679 Mal1g2114 . . Mepo4g04190 . Mesa1g04571 . . Mtr1g3691 . . Phac7g01158 . Phco6g02425 . . Psa6g4456 . . Pste4g02803 . . . Pte9g00405 . . . Pvu7g0775 . Rops6g02671 . Seca8g07330 . Spst10g00913 Ssu7g0843 . Sto10g2317 . Tpr1g0813 . . Trre1g05324 Tsu01g04358 . . Vian3g00677 . Vifa3g02850 . Vimu3g02983 . Viun7g03180 . Vivi1g04463 Vra8g2188 .
   
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Select Species Gene Chromosome Start End Strand
Aed Aed11g1750 Chr11 21019089 21020877 -
Cca Cca06g01826 Chr06 33682257 33684055 -
Ssu Ssu2g2902 Chr2 90341163 90342465 -
Vra Vra11g0250 Chr11 1717959 1720481 +
Aev Aev09g2859 Chr09 28754102 28759718 +
Ahy Ahy19g2864 Chr19 151035433 151042800 -
Aip Aip09g03332 Chr09 139723182 139730380 -
Gma Gma16g00279 Chr16 2954730 2955629 -
Vvi Vvi16g1029 Chr16 18629753 18632196 -
Lja Lja1g5718 Chr1 101331722 101333765 +
Vvi Vvi16g1030 Chr16 18632633 18635667 +
Vvi Vvi16g1031 Chr16 18657394 18658860 +
Vvi Vvi16g1032 Chr16 18658927 18659532 +
Vvi Vvi16g1033 Chr16 18687027 18687767 +
Apr Apr6g0304 Chr6 3179646 3180893 +
Vvi Vvi16g1034 Chr16 18692112 18696266 +
Vvi Vvi16g1035 Chr16 18698075 18698719 +
Gma Gma16g00279 Chr16 2954730 2955629 -
Gso Gso16g0253 Chr16 2914305 2915334 -
Vvi Vvi16g1036 Chr16 18721720 18722355 +
Vvi Vvi16g1037 Chr16 18732482 18733566 -
Adu Adu09g02326 Chr09 110210423 110211731 +
Aed Aed1g2316 Chr1 19194284 19196409 -
Aed Aed11g1750 Chr11 21019089 21020877 -
Aev Aev09g2859 Chr09 28754102 28759718 +
Ahy Ahy19g2864 Chr19 151035433 151042800 -
Aip Aip09g03332 Chr09 139723182 139730380 -
Arst Arst9g03067 Chr9 108108314 108109672 +
Bva Bva03g01295 Chr03 12635082 12636795 +
Bva Bva04g01203 Chr04 8232529 8234259 -
Cca Cca02g02204 Chr02 42549121 42550011 +
Cca Cca06g01826 Chr06 33682257 33684055 -
Gma Gma10g02183 Chr10 49425770 49427316 +
Gso Gso10g2052 Chr10 47541089 47542798 +
Lal Lal12g0071 Chr12 459350 460894 -
Lal Lal13g0061 Chr13 378484 379880 -
Lapu Lapu7g02001 Chr7 36255631 36256899 +
Lasa Lasa6g04022 Chr6 612488538 612489573 +
Lja Lja5g0678 Chr5 6096635 6098112 -
Mal Mal1g2112 Chr1 27630047 27631155 -
Mepo Mepo4g04193 Chr4 51827637 51828962 +
Mesa Mesa1g04578 Chr1 71722271 71723364 +
Mtr Mtr1g3693 Chr1 48609554 48611007 +
Phac Phac7g01157 Chr7 7285798 7288530 -
Phco Phco6g02427 Chr6 45691047 45692071 +
Psa Psa6g4459 Chr6 391304066 391306997 +
Pste Pste4g02807 Chr4 19763637 19764888 +
Pte Pte16g00332 Chr16 4361516 4362421 -
Pte Pte9g00404 Chr9 4859688 4861661 -
Pvu Pvu7g0774 Chr7 6962320 6964291 -
Rops Rops6g02672 Chr6 48085625 48087159 +
Seca Seca8g07332 Chr8 170035137 170037554 +
Spst Spst10g00915 Chr10 9943008 9944078 +
Ssu Ssu7g0842 Chr7 16934703 16935461 -
Ssu Ssu2g2902 Chr2 90341163 90342465 -
Tpr Tpr1g0811 Chr1 6783060 6784588 -
Trre Trre1g05329 Chr1 59162022 59163105 +
Tsu Tsu01g04362 Chr01 51516073 51517680 +
Vian Vian3g00676 Chr3 6841294 6842351 -
Vifa Vifa3g02852 Chr3 801051065 801052106 +
Vimu Vimu3g02985 Chr3 43910615 43911658 +
Viun Viun7g03181 Chr7 34379322 34381324 +
Vivi Vivi1g04461 Chr1 95077297 95082519 -
Vra Vra8g2189 Chr8 40279695 40281265 +
Vra Vra11g0250 Chr11 1717959 1720481 +
Vvi Vvi16g1038 Chr16 18741352 18742994 +
Adu Adu09g02324 Chr09 110169559 110171036 -
Aed Aed1g2317 Chr1 19201118 19203646 +
Aev Aev09g2179 Chr09 24668158 24669735 -
Ahy Ahy17g2696 Chr17 124530916 124533603 -
Ahy Ahy19g3591 Chr19 158518560 158520156 +
Aip Aip07g02941 Chr07 115668241 115672118 -
Aip Aip09g04050 Chr09 146767912 146769381 +
Amo Amo17g2607 Chr17 125370209 125373964 -
Arst Arst9g03066 Chr9 108067848 108068945 -
Bva Bva12g01988 Chr12 15739152 15744876 -
Cca Cca02g02203 Chr02 42537127 42539045 -
Dod Dod06g0849 Chr06 10558541 10560973 +
Gma Gma10g02182 Chr10 49406724 49412259 -
Gso Gso10g2051 Chr10 47527884 47530825 -
Lal Lal24g0061 Chr24 375963 378405 +
Lal Lal13g0062 Chr13 383553 385060 +
Lapu Lapu7g02000 Chr7 36243379 36245869 -
Lasa Lasa6g04020 Chr6 612233531 612235533 -
Lja Lja5g0679 Chr5 6104078 6106719 +
Mal Mal1g2114 Chr1 27647288 27649336 +
Mepo Mepo4g04190 Chr4 51809222 51811110 -
Mesa Mesa1g04571 Chr1 71657723 71659741 -
Mtr Mtr1g3691 Chr1 48589672 48592004 -
Phac Phac7g01158 Chr7 7300531 7302954 +
Phco Phco6g02425 Chr6 45675776 45677981 -
Psa Psa6g4456 Chr6 391153721 391156200 -
Pste Pste4g02803 Chr4 19746129 19748540 -
Pte Pte9g00405 Chr9 4872848 4874427 +
Pvu Pvu7g0775 Chr7 6978392 6980784 +
Rops Rops6g02671 Chr6 48071348 48074050 -
Seca Seca8g07330 Chr8 170020991 170023546 -
Spst Spst10g00913 Chr10 9930321 9932529 -
Ssu Ssu7g0843 Chr7 16962881 16965279 +
Sto Sto10g2317 Chr10 33369043 33371142 -
Tpr Tpr1g0813 Chr1 6801364 6803752 +
Trre Trre1g05324 Chr1 59118191 59120419 -
Tsu Tsu01g04358 Chr01 51493282 51495483 -
Vian Vian3g00677 Chr3 6852866 6855079 +
Vifa Vifa3g02850 Chr3 799939151 799940979 -
Vimu Vimu3g02983 Chr3 43900807 43903299 -
Viun Viun7g03180 Chr7 34371099 34373766 -
Vivi Vivi1g04463 Chr1 95119746 95121936 +
Vra Vra8g2188 Chr8 40270865 40273435 -
Bva Bva12g01988 Chr12 15739152 15744876 -
Ahy Ahy17g2696 Chr17 124530916 124533603 -
Aip Aip07g02941 Chr07 115668241 115672118 -
Amo Amo17g2607 Chr17 125370209 125373964 -