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
Vvi1g1341 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva05g00031 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja4g1066 . . . . . . . . . . . . . . . . . Psa7g1829 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1342 . . . . Adu03g04517 . . . . . . . . . . . . . . . Arst3g05972 . . . Bisa07g0393 . . Bva05g00032 . . . . Dere02g3394 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02593 . Lasa7g03918 . . . . . . . . . . Lja4g1067 . . Mepo2g03845 . Mesa13g01296 . . . . . Phac2g02751 . Phco4g02047 . . . . Psa7g1812 Pste3g02710 . . . . . Pumo6g01278 . Pvu2g1809 . Rops2g01373 . Seca12g05681 . Spst3g00129 . . . . . . . Trre7g04503 . . . Vian1g02698 . Vifa6g01247 . Vimu11g01829 . Viun3g02288 . Vivi5g05606 . . .
Vvi1g1343 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa5g2212 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1344 . . . . Adu03g04516 . . . . . . . . . . . . . . . Arst3g05970 . . . . . . . . . . . . . . . . . . . . . . Gma18g00083 . . . . . . . . . . . . . . . . Lapu3g02594 . . . . . . . . . . . . Lja4g1068 . . . . . . . . Mtr3g2823 . . . Phco4g02048 . . . Psa5g2213 . Pste3g02707 . . . . . . . Pvu2g1810 . . . . . Spst3g00128 . . . . . Tpr2g4692 . . . Tsu07g02733 . . . . . Vimu11g01826 . . . . . . .
Vvi1g1345 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02595 . Lasa7g03917 . . . . . . . . . . Lja4g1069 . . Mepo2g03844 . Mesa13g01297 . . . . . Phac2g02753 . Phco4g02049 . . . . . . . . . . . . . Pvu2g1812 . . . . . . . . . Sto11g1211 . . . Trre7g04502 . . . . . . . . . . . . . . .
Vvi1g1346 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1347 . . . . Adu03g04514 . . . . . . . . . . . . . . . Arst3g05968 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02596 . . . . . . . . . . . . Lja4g1070 . . . . . . . . . . . . Phco4g02050 . . . Psa5g2214 . Pste3g02701 . . . . . Pumo6g01281 . Pvu2g1813 . Rops2g01376 . Seca12g05676 . Spst3g00127 . . . . . . . . . . . Vian1g02702 . Vifa2g02475 . Vimu11g01823 . Viun3g02294 . . . . .
Vvi1g1348 . . . . . . . . . . . Ahy20g1001 . Aip10g01056 . . . Amo20g0930 . . Arst10g00921 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa5g02634 . . . . . . . . . . . . . Mepo3g06240 . Mesa9g03687 . . . . . . . Phco2g02957 . . . Psa5g2215 . Pste7g02379 . . Pte2g01372 . . Pumo1g00432 . Pvu1g2678 . Rops11g03744 . Seca6g01737 . Spst1g01914 . . . . . . . Trre5g03137 . . . Vian2g03166 . Vifa2g02476 . Vimu6g01537 . Viun1g03433 . Vivi3g03328 . . .
Vvi1g1349 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1350 . . . . . . . . . . . Ahy20g1000 . Aip10g01055 . . . Amo20g0414 . . . Arst6g03099 . . . . . . . . . . . . . Dod04g0592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja4g1071 . . . . . . . . . . . . . . . . . . . . . . . . . . . Pvu8g1548 . . . . . . . . . . . . . . . . . . . . . Vimu6g03845 . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Lapu Lapu3g02593 Chr3 48280283 48283475 -
Dod Dod04g0592 Chr04 8460663 8463798 +
Vvi Vvi1g1341 Chr1 19607521 19610788 -
Bva Bva05g00031 Chr05 152509 156701 -
Lja Lja4g1066 Chr4 9241632 9245970 -
Psa Psa7g1829 Chr7 132343945 132350772 -
Vvi Vvi1g1342 Chr1 19616036 19617692 -
Adu Adu03g04517 Chr03 134541464 134544763 +
Arst Arst3g05972 Chr3 133304656 133307956 +
Bisa Bisa07g0393 Chr07 10291755 10295886 +
Bva Bva05g00032 Chr05 158964 161519 -
Dere Dere02g3394 Chr02 43123850 43127579 +
Lapu Lapu3g02593 Chr3 48280283 48283475 -
Lasa Lasa7g03918 Chr7 625599502 625601102 +
Lja Lja4g1067 Chr4 9250625 9253933 -
Mepo Mepo2g03845 Chr2 47660079 47663543 +
Mesa Mesa13g01296 Chr13 15425686 15428233 -
Phac Phac2g02751 Chr2 29080605 29083915 -
Phco Phco4g02047 Chr4 40637781 40640094 -
Psa Psa7g1812 Chr7 130737199 130740318 +
Pste Pste3g02710 Chr3 19915665 19918898 +
Pumo Pumo6g01278 Chr6 16960560 16964059 -
Pvu Pvu2g1809 Chr2 32662357 32664893 -
Rops Rops2g01373 Chr2 19646043 19649239 -
Seca Seca12g05681 Chr12 148378571 148381340 +
Spst Spst3g00129 Chr3 2287873 2290213 +
Trre Trre7g04503 Chr7 53003827 53005992 +
Vian Vian1g02698 Chr1 40759493 40761543 -
Vifa Vifa6g01247 Chr6 407076435 407077867 -
Vimu Vimu11g01829 Chr11 25433796 25435862 +
Viun Viun3g02288 Chr3 20249855 20252792 -
Vivi Vivi5g05606 Chr5 159144779 159147071 -
Vvi Vvi1g1343 Chr1 19621573 19632384 +
Psa Psa5g2212 Chr5 173880050 173886272 +
Vvi Vvi1g1344 Chr1 19633078 19637462 -
Adu Adu03g04516 Chr03 134525750 134527198 +
Arst Arst3g05970 Chr3 133289214 133291230 +
Gma Gma18g00083 Chr18 663814 666125 -
Lapu Lapu3g02594 Chr3 48290565 48293865 -
Lja Lja4g1068 Chr4 9256905 9259956 -
Mtr Mtr3g2823 Chr3 42206338 42209261 -
Phco Phco4g02048 Chr4 40651986 40655252 -
Psa Psa5g2213 Chr5 173886540 173888946 -
Pste Pste3g02707 Chr3 19895114 19898112 +
Pvu Pvu2g1810 Chr2 32671986 32675310 -
Spst Spst3g00128 Chr3 2254603 2257157 +
Tpr Tpr2g4692 Chr2 52284602 52288112 -
Tsu Tsu07g02733 Chr07 32020070 32023162 -
Vimu Vimu11g01826 Chr11 25345243 25346974 +
Vvi Vvi1g1345 Chr1 19639325 19648549 -
Lapu Lapu3g02595 Chr3 48295028 48304602 -
Lasa Lasa7g03917 Chr7 625513807 625528411 +
Lja Lja4g1069 Chr4 9260802 9268112 -
Mepo Mepo2g03844 Chr2 47649952 47657352 +
Mesa Mesa13g01297 Chr13 15431834 15439391 -
Phac Phac2g02753 Chr2 29095831 29105713 -
Phco Phco4g02049 Chr4 40655475 40664647 -
Pvu Pvu2g1812 Chr2 32683274 32686315 -
Sto Sto11g1211 Chr11 12028498 12033795 +
Trre Trre7g04502 Chr7 52976754 52984018 +
Vvi Vvi1g1346 Chr1 19653128 19663329 +
Vvi Vvi1g1347 Chr1 19670873 19678713 -
Adu Adu03g04514 Chr03 134511773 134517948 +
Arst Arst3g05968 Chr3 133275330 133280341 +
Lapu Lapu3g02596 Chr3 48308389 48315895 -
Lja Lja4g1070 Chr4 9269097 9275729 -
Phco Phco4g02050 Chr4 40678908 40684783 -
Psa Psa5g2214 Chr5 173958247 173963252 -
Pste Pste3g02701 Chr3 19864698 19872815 +
Pumo Pumo6g01281 Chr6 16984257 16991602 -
Pvu Pvu2g1813 Chr2 32693663 32700906 -
Rops Rops2g01376 Chr2 19666777 19673112 -
Seca Seca12g05676 Chr12 148334128 148347141 +
Spst Spst3g00127 Chr3 2232646 2238976 +
Vian Vian1g02702 Chr1 40853673 40859473 -
Vifa Vifa2g02475 Chr2 648253624 648258128 -
Vimu Vimu11g01823 Chr11 25268877 25278932 +
Viun Viun3g02294 Chr3 20320334 20327351 -
Vvi Vvi1g1348 Chr1 19685434 19688176 +
Ahy Ahy20g1001 Chr20 14639887 14641686 +
Aip Aip10g01056 Chr10 13976127 13977755 +
Amo Amo20g0930 Chr20 15496095 15500220 +
Arst Arst10g00921 Chr10 8433035 8540311 +
Lasa Lasa5g02634 Chr5 493946172 493948525 +
Mepo Mepo3g06240 Chr3 76546802 76550575 +
Mesa Mesa9g03687 Chr9 68485459 68488746 +
Phco Phco2g02957 Chr2 58457251 58460351 -
Psa Psa5g2215 Chr5 173980391 173983525 +
Pste Pste7g02379 Chr7 22534654 22558592 -
Pte Pte2g01372 Chr2 20235839 20239322 -
Pumo Pumo1g00432 Chr1 5977013 5979339 -
Pvu Pvu1g2678 Chr1 51492682 51496171 -
Rops Rops11g03744 Chr11 71148712 71151296 +
Seca Seca6g01737 Chr6 72143937 72145445 +
Spst Spst1g01914 Chr1 27395532 27398097 +
Trre Trre5g03137 Chr5 26782360 26785435 +
Vian Vian2g03166 Chr2 52135677 52138303 -
Vifa Vifa2g02476 Chr2 649120100 649122691 +
Vimu Vimu6g01537 Chr6 14419364 14419711 +
Viun Viun1g03433 Chr1 41360579 41363418 -
Vivi Vivi3g03328 Chr3 56180239 56183346 -
Vvi Vvi1g1349 Chr1 19699502 19701180 -
Vvi Vvi1g1350 Chr1 19703167 19710688 -
Ahy Ahy20g1000 Chr20 14603795 14611794 -
Aip Aip10g01055 Chr10 13941321 13943934 -
Amo Amo20g0414 Chr20 5199177 5207085 +
Arst Arst6g03099 Chr6 97032821 97037921 -
Dod Dod04g0592 Chr04 8460663 8463798 +
Lja Lja4g1071 Chr4 9280258 9283852 -
Pvu Pvu8g1548 Chr8 30893063 30900877 +
Vimu Vimu6g03845 Chr6 37329488 37331497 +
Sto Sto11g1211 Chr11 12028498 12033795 +