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
Vvi16g1069 . . . . . . . . . . . . . . . . . . . Apr6g0294 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1070 . . . . . . . . . Aev09g2162 . Ahy19g3598 . Aip09g04057 . . . . . . . . . . . . . . . . . . . . . Dod06g0861 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g0687 . . . . . . . . . . . . . . . . Psa6g4446 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1071 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cca02g02192 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Vra8g2176 .
Vvi16g1072 . . . . . Adu09g02316 . . . . . . . . . . . . . . . Arst9g03053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal12g0073 . . . . . . . . Lapu7g01975 . Lasa6g04012 . . . . . . . . . . . . . Mepo4g04181 . Mesa1g04560 . . . . . Phac7g01182 . Phco6g02400 . . . . . Pste4g02745 . . . . . . . Pvu7g0799 . Rops6g02651 . Seca8g07322 . Spst10g00900 . . . . . . . Trre1g05308 . . . Vian3g00687 . Vifa3g02834 . Vimu3g02968 . Viun7g03158 . Vivi1g04478 . .
Vvi16g1073 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1074 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1075 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma10g02172 . . . Gso10g2036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal1g2124 . . . . . . . Mtr1g3682 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr1g0822 . . . Tsu01g04348 . . . . . . . . . . . . .
Vvi16g1076 . . . . . . Aed1g2328 . . . . . . . . . . . . . . . . . . . . . . . Cca02g02190 . . . . . . . . . Gma20g01541 . . . Gso20g1322 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu7g0855 . . . . . . . . . . . . . . . . . . . Vra8g2175 .
Vvi16g1077 Acco01g0195 . Accr1g00002 . Adu05g03458 Adu09g02315 . . Aev05g2832 Aev09g2161 Ahy15g3622 Ahy19g3599 Aip05g03937 Aip09g04058 Alju02g3708 . . . . Apr6g0609 Arst5g04443 Arst9g03052 Bach1g00042 . Bisa01g0828 . Bva03g02486 . . . . Cca08g00760 Dere06g1266 . Dod02g2956 Dod06g0862 Enph12g0847 . Glsi01g1418 . Gma10g02171 . . . Gso10g2035 . . . Lal1g0864 Lal2g0969 . . . . Lan13g0956 Lan13g0956 . . . . Lapu4g00762 Lapu7g01974 Lasa1g02777 Lasa6g04011 Lele45g0124 Lele46g0148 Lele47g1173 Lele48g1308 . . . . Lja2g2707 Lja5g0689 Mal1g2125 . Mepo5g04015 Mepo4g04180 Mesa22g01276 Mesa1g04559 Mibi01g3464 . Mtr1g3681 . . Phac7g01184 Phco5g00854 Phco6g02399 Prci14g2231 . Psa6g4443 . Pste9g01076 Pste4g02743 Pte16g00337 . Pte16g00337 . Pumo6g02490 . Pvu4g1081 Pvu7g0800 Rops5g01020 . Seca10g03749 . Spst4g03302 Spst10g00899 . Ssu9g0023 Sto10g2297 . Tpr1g0823 . Trre11g00956 Trre1g05306 Tsu01g04347 . Vian8g00954 . . . . Vimu3g02967 Viun4g01975 . Vivi2g05174 Vivi1g04479 . .
Vvi16g1078 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cca06g01830 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu2g2907 . . . . . . . . . . . . . . . . . . . Vra11g0246
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Cca Cca06g01830 Chr06 33704692 33709033 -
Ssu Ssu2g2907 Chr2 90411559 90413532 -
Vra Vra11g0246 Chr11 1673642 1678032 +
Adu Adu09g02315 Chr09 110071057 110075671 -
Arst Arst9g03052 Chr9 107969070 107973523 -
Vvi Vvi16g1069 Chr16 19082053 19085375 -
Apr Apr6g0294 Chr6 3060242 3063272 +
Vvi Vvi16g1070 Chr16 19092228 19092645 -
Aev Aev09g2162 Chr09 24578079 24587901 +
Ahy Ahy19g3598 Chr19 158571094 158581214 +
Aip Aip09g04057 Chr09 146858628 146867903 +
Dod Dod06g0861 Chr06 10697158 10710178 -
Lja Lja5g0687 Chr5 6175691 6189474 -
Psa Psa6g4446 Chr6 390831706 390845408 +
Vvi Vvi16g1071 Chr16 19098149 19101465 -
Cca Cca02g02192 Chr02 42436622 42438874 +
Vra Vra8g2176 Chr8 40135980 40139185 +
Vvi Vvi16g1072 Chr16 19111517 19118799 -
Adu Adu09g02316 Chr09 110085969 110095231 -
Arst Arst9g03053 Chr9 107983662 107993321 -
Lal Lal12g0073 Chr12 471978 481530 -
Lapu Lapu7g01975 Chr7 35997181 36006727 +
Lasa Lasa6g04012 Chr6 611780565 611792557 +
Mepo Mepo4g04181 Chr4 51730626 51741505 +
Mesa Mesa1g04560 Chr1 71520516 71531455 +
Phac Phac7g01182 Chr7 7591840 7601452 -
Phco Phco6g02400 Chr6 45381051 45390184 +
Pste Pste4g02745 Chr4 19395886 19406348 +
Pvu Pvu7g0799 Chr7 7251003 7260664 -
Rops Rops6g02651 Chr6 47731429 47741834 +
Seca Seca8g07322 Chr8 169882997 169897181 +
Spst Spst10g00900 Chr10 9816166 9825488 +
Trre Trre1g05308 Chr1 59014637 59023968 +
Vian Vian3g00687 Chr3 7020398 7030057 -
Vifa Vifa3g02834 Chr3 796481107 796499464 +
Vimu Vimu3g02968 Chr3 43769262 43778956 +
Viun Viun7g03158 Chr7 34221111 34230783 +
Vivi Vivi1g04478 Chr1 95293925 95305698 -
Vvi Vvi16g1073 Chr16 19119406 19119983 -
Vvi Vvi16g1074 Chr16 19120410 19123943 -
Vvi Vvi16g1075 Chr16 19135104 19148022 -
Gma Gma10g02172 Chr10 49257604 49266621 +
Gso Gso10g2036 Chr10 47378775 47386266 +
Mal Mal1g2124 Chr1 27759787 27771371 -
Mtr Mtr1g3682 Chr1 48503192 48514383 +
Tpr Tpr1g0822 Chr1 6863208 6874145 -
Tsu Tsu01g04348 Chr01 51423330 51433793 +
Vvi Vvi16g1076 Chr16 19148901 19149867 -
Aed Aed1g2328 Chr1 19303902 19313073 -
Cca Cca02g02190 Chr02 42425457 42434026 +
Gma Gma20g01541 Chr20 42440572 42449706 -
Gso Gso20g1322 Chr20 43252705 43262167 -
Ssu Ssu7g0855 Chr7 17521774 17531716 -
Vra Vra8g2175 Chr8 40123787 40132510 +
Vvi Vvi16g1077 Chr16 19150904 19157096 +
Acco Acco01g0195 Chr01 2185536 2192369 -
Accr Accr1g00002 Chr1 30348 124039 -
Adu Adu05g03458 Chr05 107059845 107064434 +
Adu Adu09g02315 Chr09 110071057 110075671 -
Aev Aev05g2832 Chr05 29334068 29337909 -
Aev Aev09g2161 Chr09 24572325 24576380 -
Ahy Ahy15g3622 Chr15 158987889 158992540 +
Ahy Ahy19g3599 Chr19 158582172 158586961 +
Aip Aip05g03937 Chr05 147597591 147601973 +
Aip Aip09g04058 Chr09 146872750 146877292 +
Alju Alju02g3708 Chr02 55877220 55881876 +
Apr Apr6g0609 Chr6 8757489 8766554 -
Arst Arst5g04443 Chr5 105735575 105740158 +
Arst Arst9g03052 Chr9 107969070 107973523 -
Bach Bach1g00042 Chr1 443271 448512 -
Bisa Bisa01g0828 Chr01 13385514 13391046 +
Bva Bva03g02486 Chr03 20994085 20999850 +
Cca Cca08g00760 Chr08 14917917 14921318 -
Dere Dere06g1266 Chr06 24829479 24834744 -
Dod Dod02g2956 Chr02 62641673 62647105 -
Dod Dod06g0862 Chr06 10716841 10723032 +
Enph Enph12g0847 Chr12 15167694 15173733 -
Glsi Glsi01g1418 Chr01 72462830 72469902 -
Gma Gma10g02171 Chr10 49250308 49255305 -
Gso Gso10g2035 Chr10 47371611 47376671 -
Lal Lal1g0864 Chr1 6073824 6084011 -
Lal Lal2g0969 Chr2 6514224 6519850 +
Lan Lan13g0956 Chr13 13549290 13556759 -
Lan Lan13g0956 Chr13 13549290 13556759 -
Lapu Lapu4g00762 Chr4 18414614 18422047 +
Lapu Lapu7g01974 Chr7 35988926 35995398 -
Lasa Lasa1g02777 Chr1 542726283 542730981 -
Lasa Lasa6g04011 Chr6 611610042 611613770 -
Lele Lele45g0124 Chr45 1155135 1160079 -
Lele Lele46g0148 Chr46 889400 894283 -
Lele Lele47g1173 Chr47 17194575 17199572 +
Lele Lele48g1308 Chr48 17312388 17316898 +
Lja Lja2g2707 Chr2 39304221 39311260 +
Lja Lja5g0689 Chr5 6191333 6196325 +
Mal Mal1g2125 Chr1 27776137 27780466 +
Mepo Mepo5g04015 Chr5 50175091 50183359 +
Mepo Mepo4g04180 Chr4 51722839 51727939 -
Mesa Mesa22g01276 Chr22 24778171 24786252 +
Mesa Mesa1g04559 Chr1 71512698 71516875 -
Mibi Mibi01g3464 Chr01 60564704 60570301 +
Mtr Mtr1g3681 Chr1 48495047 48499623 -
Phac Phac7g01184 Chr7 7608255 7614233 +
Phco Phco5g00854 Chr5 11620725 11625852 -
Phco Phco6g02399 Chr6 45374324 45380153 -
Prci Prci14g2231 Chr14 29280328 29286979 +
Psa Psa6g4443 Chr6 390696078 390702984 -
Pste Pste9g01076 Chr9 7789666 7796580 -
Pste Pste4g02743 Chr4 19379067 19384702 -
Pte Pte16g00337 Chr16 4457092 4462538 +
Pte Pte16g00337 Chr16 4457092 4462538 +
Pumo Pumo6g02490 Chr6 57597870 57607628 -
Pvu Pvu4g1081 Chr4 30140220 30146311 +
Pvu Pvu7g0800 Chr7 7262364 7268257 +
Rops Rops5g01020 Chr5 20556248 20565988 -
Seca Seca10g03749 Chr10 74590805 74604767 -
Spst Spst4g03302 Chr4 72875552 72882814 +
Spst Spst10g00899 Chr10 9809001 9816050 -
Ssu Ssu9g0023 Chr9 2912566 2921528 -
Sto Sto10g2297 Chr10 33098509 33105420 -
Tpr Tpr1g0823 Chr1 6875199 6879621 +
Trre Trre11g00956 Chr11 8366978 8373108 +
Trre Trre1g05306 Chr1 59009130 59013115 -
Tsu Tsu01g04347 Chr01 51418349 51422272 -
Vian Vian8g00954 Chr8 24259778 24265476 -
Vimu Vimu3g02967 Chr3 43761263 43765794 -
Viun Viun4g01975 Chr4 35011977 35017585 -
Vivi Vivi2g05174 Chr2 174338448 174343207 +
Vivi Vivi1g04479 Chr1 95364575 95368590 +
Vvi Vvi16g1078 Chr16 19158746 19160854 -
Cca Cca06g01830 Chr06 33704692 33709033 -
Ssu Ssu2g2907 Chr2 90411559 90413532 -
Vra Vra11g0246 Chr11 1673642 1678032 +