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
Vvi16g1249 . . . . . . . . . . . . . . . . . . Apr1g0588 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal4g0548 . . . . . . . . . . . . . . . . . . . . . . Lja1g4701 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1250 Acco10g2606 . Accr4g00175 . . . . . . . . . . . Alju08g0176 . . . Apr1g0589 . . . . . Bisa09g0842 . Bva12g01868 Bva06g03057 . . . . Dere04g1298 . . . Enph1g1871 . Glsi08g0887 . . . . . . . . . . . . . . . . . . . . . . . . . Lele01g0139 Lele02g0144 Lele03g0148 Lele04g0141 . . . . Lja1g4702 . . . . . . . Mibi05g0147 . . . . . Phco7g01527 . Prci15g0218 . . . . . . . . . . . Pvu9g0405 . . . . . . . . . Sto9g2669 Sto5g1375 . . . . . . . . . . . . . . Vivi3g02674 . . .
Vvi16g1251 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva12g01869 Bva06g03056 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g2671 . . . . . . . . . . . . . . . . . . .
Vvi16g1252 . . . . . . . . . . . . . . . . . . Apr1g0590 . . . . . . . Bva12g01871 Bva06g03054 . . . . . . . . . . . . . . . . . . . . . Lal4g0547 Lal21g0602 . . . . . . . . . . . . . . . . . . . . . Lja1g4703 . . . . . . . . . . . Phac9g01268 . Phco7g01525 . . . Psa5g1666 . . . . . . . . . Pvu9g0403 . . . . . . . . . . . . . . . . . . . . . . . . . Vivi3g02676 . . .
Vvi16g1253 . . . . . . . . . . . . . . . . . . Apr1g0591 . . . . . . . Bva12g01872 Bva06g03053 . . . . . . . . . . . . . . . . . . . . Lal17g0631 . . . . . Lan15g0584 . . . . . . . . . . . . . . . . . Lja1g4704 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g1373 . . . . . . . . . . . . . . . . . .
Vvi16g1254 Acco10g2602 . Accr4g00179 . . . . . . . . . . . Alju08g0181 . . . Apr1g0593 . . . . . Bisa09g0848 . Bva12g01873 Bva06g03052 . . . . Dere04g1294 . . . Enph1g1868 . Glsi08g0891 . . . . . . . . . Lal17g0630 Lal4g0545 Lal21g0601 . . . Lan15g0585 Lan15g0585 Lan15g0585 . . . Lapu9g01269 . . . Lele01g0142 Lele02g0147 Lele03g0152 Lele04g0145 . . . . Lja1g4705 . . . Mepo3g06698 . Mesa9g04223 . Mibi05g0150 . . . Phac9g01270 . Phco7g01523 . . . Psa5g1667 . . . . . . . . . Pvu9g0401 . . . . . . . . . Sto9g2673 Sto5g1372 . . Trre5g04120 . . . . . . . . . . . Vivi3g02679 . . .
Vvi16g1255 . . . . Adu10g01551 . . . . . . . . . . . . . Apr1g0594 . Arst10g02008 . . . . . Bva12g01874 . . . . . . . . . . . . . . . . . . . . . Lal17g0628 Lal4g0544 . . . . Lan15g0587 Lan15g0587 . . . . Lapu9g01270 . Lasa5g03150 . . . . . . . . . Lja1g4706 . . . Mepo3g06653 . Mesa9g04207 . . . . . . . Phco7g01521 . . . Psa5g1669 . Pste2g03539 . . . . . Pumo10g01491 . Pvu9g0460 . Rops10g02193 . Seca4g02713 . Spst9g01559 . . . . Sto5g1371 . . Trre5g04064 . . . . . Vifa2g02962 . Vimu10g02004 . Viun9g02028 . Vivi3g02683 . . .
Vvi16g1256 . . . . Adu10g01549 . . . . . . . . . . . . . Apr1g0595 . Arst10g02005 . . . . . Bva12g01875 Bva06g03051 . . . . . . . . . . . . . . . . . . . . Lal17g0627 Lal4g0543 . . . . Lan15g0593 Lan15g0593 . . . . Lapu9g01272 . Lasa5g03148 . . . . . . . . . Lja1g4712 . . . Mepo3g06651 . . . . . . . Phac9g01274 . Phco7g01520 . . . Psa5g1672 . Pste2g03538 . . . . . Pumo10g01489 . Pvu9g0461 . . . . . Spst9g01558 . . . . Sto5g1369 . . . . . . Vian4g01281 . Vifa2g02961 . Vimu10g02007 . Viun9g02029 . Vivi3g02684 . . .
Vvi16g1257 . . . . . . . . . . . . . . . . . . Apr1g0596 . . . . . . . Bva12g01876 Bva06g03050 . . . . . . . . . . . . . . . . . . . . Lal17g0626 Lal4g0542 . . . . Lan15g0594 Lan15g0594 . . . . . . . . . . . . . . . . Lja1g4713 . . . . . . . . . . . . . . . . . Psa5g1675 . . . . . . . . . . . . . . . . . . . Sto9g2674 Sto5g1368 . . . . . . . . . . . . . . . . . .
Vvi16g1258 Acco10g2600 . Accr4g00182 . . . . . . . . . . . . . . . Apr1g0599 . Arst10g01990 . Bach12g01041 . Bisa09g0850 . Bva12g01877 Bva06g03049 . . . . Dere04g1290 . . . Enph1g1866 . Glsi08g0896 . . . . . . . . . . . Lal21g0599 . . . . . . . . . Lapu9g01274 . Lasa5g03145 . Lele01g0144 Lele02g0149 Lele03g0154 Lele04g0146 . . . . Lja1g4715 . . . Mepo3g06646 . Mesa9g04201 . Mibi05g0153 . . . Phac9g01279 . Phco7g01517 . Prci15g0224 . Psa5g1677 . Pste2g03533 . . . . . . . Pvu9g0464 . . . . . Spst9g01555 . . . Sto9g2675 . . . Trre5g04049 . . . . . . . Vimu10g02014 . . . Vivi3g02688 . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi16g1249 Chr16 21120452 21126501 +
Apr Apr1g0588 Chr1 7135368 7140608 +
Lal Lal4g0548 Chr4 3975462 3980522 -
Lja Lja1g4701 Chr1 62158708 62162753 +
Vvi Vvi16g1250 Chr16 21131306 21132993 +
Acco Acco10g2606 Chr10 36898614 36900382 -
Accr Accr4g00175 Chr4 1778808 1780645 +
Alju Alju08g0176 Chr08 1345399 1347182 +
Apr Apr1g0589 Chr1 7147131 7149398 +
Bisa Bisa09g0842 Chr09 12150345 12152362 +
Bva Bva12g01868 Chr12 15097772 15099991 +
Bva Bva06g03057 Chr06 18925920 18928102 -
Dere Dere04g1298 Chr04 14742753 14744817 -
Enph Enph1g1871 Chr1 43565848 43569014 -
Glsi Glsi08g0887 Chr08 6591147 6593062 +
Lele Lele01g0139 Chr01 817452 822737 +
Lele Lele02g0144 Chr02 808256 814718 +
Lele Lele03g0148 Chr03 789112 794585 +
Lele Lele04g0141 Chr04 808154 809980 +
Lja Lja1g4702 Chr1 62164146 62165995 +
Mibi Mibi05g0147 Chr05 1581349 1583442 +
Phco Phco7g01527 Chr7 14490662 14492885 -
Prci Prci15g0218 Chr15 1483655 1485923 +
Pvu Pvu9g0405 Chr9 7971648 7974288 -
Sto Sto9g2669 Chr9 28838121 28840044 +
Sto Sto5g1375 Chr5 9408112 9409936 -
Vivi Vivi3g02674 Chr3 44750913 44752794 +
Vvi Vvi16g1251 Chr16 21140127 21142455 +
Bva Bva12g01869 Chr12 15101506 15103519 +
Bva Bva06g03056 Chr06 18921812 18923630 -
Sto Sto9g2671 Chr9 28843252 28844701 +
Vvi Vvi16g1252 Chr16 21145032 21150589 +
Apr Apr1g0590 Chr1 7162988 7168452 +
Bva Bva12g01871 Chr12 15106935 15112389 +
Bva Bva06g03054 Chr06 18914418 18918895 -
Lal Lal4g0547 Chr4 3967511 3973090 -
Lal Lal21g0602 Chr21 4528552 4534120 -
Lja Lja1g4703 Chr1 62178361 62184821 +
Phac Phac9g01268 Chr9 9965333 9970556 +
Phco Phco7g01525 Chr7 14436632 14441891 -
Psa Psa5g1666 Chr5 130243303 130250031 +
Pvu Pvu9g0403 Chr9 7939680 7944837 -
Vivi Vivi3g02676 Chr3 44757604 44763474 +
Vvi Vvi16g1253 Chr16 21152035 21155296 +
Apr Apr1g0591 Chr1 7170671 7172013 +
Bva Bva12g01872 Chr12 15113342 15114878 +
Bva Bva06g03053 Chr06 18911724 18913391 -
Lal Lal17g0631 Chr17 4475014 4477879 -
Lan Lan15g0584 Chr15 13254547 13256610 +
Lja Lja1g4704 Chr1 62190246 62192500 +
Sto Sto5g1373 Chr5 9388033 9389627 -
Vvi Vvi16g1254 Chr16 21156433 21158249 -
Acco Acco10g2602 Chr10 36882324 36884812 +
Accr Accr4g00179 Chr4 1793715 1795560 -
Alju Alju08g0181 Chr08 1373870 1376383 -
Apr Apr1g0593 Chr1 7176539 7179155 -
Bisa Bisa09g0848 Chr09 12227692 12230503 -
Bva Bva12g01873 Chr12 15115145 15117311 -
Bva Bva06g03052 Chr06 18909685 18911522 +
Dere Dere04g1294 Chr04 14716753 14718916 +
Enph Enph1g1868 Chr1 43544127 43546290 +
Glsi Glsi08g0891 Chr08 6608968 6610824 -
Lal Lal17g0630 Chr17 4472279 4477852 +
Lal Lal4g0545 Chr4 3963474 3966179 +
Lal Lal21g0601 Chr21 4521517 4526826 +
Lan Lan15g0585 Chr15 13257377 13260066 -
Lan Lan15g0585 Chr15 13257377 13260066 -
Lan Lan15g0585 Chr15 13257377 13260066 -
Lapu Lapu9g01269 Chr9 26668845 26671065 -
Lele Lele01g0142 Chr01 833403 837174 -
Lele Lele02g0147 Chr02 826780 827186 -
Lele Lele03g0152 Chr03 808149 809999 -
Lele Lele04g0145 Chr04 821346 822031 -
Lja Lja1g4705 Chr1 62199302 62202137 -
Mepo Mepo3g06698 Chr3 80757492 80759222 +
Mesa Mesa9g04223 Chr9 75028063 75029445 +
Mibi Mibi05g0150 Chr05 1609950 1613879 -
Phac Phac9g01270 Chr9 9973841 9975801 -
Phco Phco7g01523 Chr7 14431190 14432604 +
Psa Psa5g1667 Chr5 130378267 130381241 -
Pvu Pvu9g0401 Chr9 7934549 7936274 +
Sto Sto9g2673 Chr9 28857939 28859645 -
Sto Sto5g1372 Chr5 9385171 9385683 +
Trre Trre5g04120 Chr5 42888083 42890869 +
Vivi Vivi3g02679 Chr3 44772181 44773903 -
Vvi Vvi16g1255 Chr16 21159330 21160238 -
Adu Adu10g01551 Chr10 68414074 68415575 +
Apr Apr1g0594 Chr1 7180342 7181374 -
Arst Arst10g02008 Chr10 67548144 67549573 +
Bva Bva12g01874 Chr12 15118043 15119529 -
Lal Lal17g0628 Chr17 4465499 4468010 +
Lal Lal4g0544 Chr4 3959914 3961844 +
Lan Lan15g0587 Chr15 13266229 13267978 -
Lan Lan15g0587 Chr15 13266229 13267978 -
Lapu Lapu9g01270 Chr9 26675641 26676415 -
Lasa Lasa5g03150 Chr5 538634247 538635209 +
Lja Lja1g4706 Chr1 62237235 62238067 -
Mepo Mepo3g06653 Chr3 80411391 80412502 +
Mesa Mesa9g04207 Chr9 74891107 74891916 +
Phco Phco7g01521 Chr7 14415496 14416325 +
Psa Psa5g1669 Chr5 130392041 130394472 -
Pste Pste2g03539 Chr2 37054476 37055406 +
Pumo Pumo10g01491 Chr10 19838814 19840358 +
Pvu Pvu9g0460 Chr9 8584162 8584959 -
Rops Rops10g02193 Chr10 39431681 39432839 +
Seca Seca4g02713 Chr4 46691998 46692981 +
Spst Spst9g01559 Chr9 15865748 15866549 +
Sto Sto5g1371 Chr5 9380071 9380816 +
Trre Trre5g04064 Chr5 42307967 42309267 +
Vifa Vifa2g02962 Chr2 847134448 847135481 +
Vimu Vimu10g02004 Chr10 29290402 29291212 -
Viun Viun9g02028 Chr9 30128716 30134073 -
Vivi Vivi3g02683 Chr3 44831437 44834689 -
Vvi Vvi16g1256 Chr16 21165542 21177943 +
Adu Adu10g01549 Chr10 68324336 68330907 -
Apr Apr1g0595 Chr1 7191647 7195007 +
Arst Arst10g02005 Chr10 67458394 67464740 -
Bva Bva12g01875 Chr12 15121537 15124074 +
Bva Bva06g03051 Chr06 18905636 18908282 -
Lal Lal17g0627 Chr17 4454344 4457729 -
Lal Lal4g0543 Chr4 3953502 3957397 -
Lan Lan15g0593 Chr15 13386629 13392804 +
Lan Lan15g0593 Chr15 13386629 13392804 +
Lapu Lapu9g01272 Chr9 26689611 26693552 +
Lasa Lasa5g03148 Chr5 538581605 538583827 -
Lja Lja1g4712 Chr1 63032029 63036304 +
Mepo Mepo3g06651 Chr3 80391052 80395474 -
Phac Phac9g01274 Chr9 10007346 10011065 +
Phco Phco7g01520 Chr7 14401275 14402674 -
Psa Psa5g1672 Chr5 130586569 130589427 +
Pste Pste2g03538 Chr2 37038624 37041293 -
Pumo Pumo10g01489 Chr10 19805879 19809321 -
Pvu Pvu9g0461 Chr9 8600878 8602599 +
Spst Spst9g01558 Chr9 15848815 15851195 -
Sto Sto5g1369 Chr5 9369213 9372343 -
Vian Vian4g01281 Chr4 25905723 25907209 +
Vifa Vifa2g02961 Chr2 846528843 846531286 -
Vimu Vimu10g02007 Chr10 29385817 29387272 +
Viun Viun9g02029 Chr9 30139027 30140665 +
Vivi Vivi3g02684 Chr3 44862543 44865244 +
Vvi Vvi16g1257 Chr16 21183240 21186735 -
Apr Apr1g0596 Chr1 7195548 7202399 -
Bva Bva12g01876 Chr12 15124277 15127568 -
Bva Bva06g03050 Chr06 18897372 18902652 +
Lal Lal17g0626 Chr17 4449071 4454015 +
Lal Lal4g0542 Chr4 3948801 3954114 +
Lan Lan15g0594 Chr15 13393128 13398696 -
Lan Lan15g0594 Chr15 13393128 13398696 -
Lja Lja1g4713 Chr1 63036876 63049733 -
Psa Psa5g1675 Chr5 130603571 130606363 -
Sto Sto9g2674 Chr9 28860906 28865780 -
Sto Sto5g1368 Chr5 9365504 9368826 +
Vvi Vvi16g1258 Chr16 21201381 21202391 +
Acco Acco10g2600 Chr10 36859051 36861086 -
Accr Accr4g00182 Chr4 1815297 1816328 +
Apr Apr1g0599 Chr1 7246178 7248772 +
Arst Arst10g01990 Chr10 66157113 66158742 -
Bach Bach12g01041 Chr12 7324512 7325543 -
Bisa Bisa09g0850 Chr09 12322038 12324475 +
Bva Bva12g01877 Chr12 15133680 15134711 +
Bva Bva06g03049 Chr06 18892370 18893942 -
Dere Dere04g1290 Chr04 14660978 14662009 -
Enph Enph1g1866 Chr1 43531583 43536170 -
Glsi Glsi08g0896 Chr08 6663131 6666041 +
Lal Lal21g0599 Chr21 4506309 4510711 -
Lapu Lapu9g01274 Chr9 26744785 26745795 +
Lasa Lasa5g03145 Chr5 538252544 538253575 +
Lele Lele01g0144 Chr01 846922 847875 +
Lele Lele02g0149 Chr02 831525 833793 +
Lele Lele03g0154 Chr03 822306 824632 +
Lele Lele04g0146 Chr04 829354 831637 +
Lja Lja1g4715 Chr1 63095704 63097559 +
Mepo Mepo3g06646 Chr3 80347110 80348065 -
Mesa Mesa9g04201 Chr9 74820842 74821619 -
Mibi Mibi05g0153 Chr05 1634584 1636957 +
Phac Phac9g01279 Chr9 10107985 10115961 +
Phco Phco7g01517 Chr7 14327823 14331248 -
Prci Prci15g0224 Chr15 1525937 1529309 +
Psa Psa5g1677 Chr5 131019620 131023414 -
Pste Pste2g03533 Chr2 36914731 36915720 -
Pvu Pvu9g0464 Chr9 8685737 8687245 +
Spst Spst9g01555 Chr9 15785809 15786819 -
Sto Sto9g2675 Chr9 28877513 28878544 +
Trre Trre5g04049 Chr5 42025145 42026718 +
Vimu Vimu10g02014 Chr10 29544093 29547785 +
Vivi Vivi3g02688 Chr3 44992132 44993816 -
Acco Acco10g2600 Chr10 36859051 36861086 -
Accr Accr4g00182 Chr4 1815297 1816328 +
Bisa Bisa09g0850 Chr09 12322038 12324475 +
Dere Dere04g1290 Chr04 14660978 14662009 -
Enph Enph1g1866 Chr1 43531583 43536170 -
Glsi Glsi08g0896 Chr08 6663131 6666041 +
Lele Lele01g0144 Chr01 846922 847875 +
Lele Lele02g0149 Chr02 831525 833793 +
Lele Lele03g0154 Chr03 822306 824632 +
Lele Lele04g0146 Chr04 829354 831637 +
Mibi Mibi05g0153 Chr05 1634584 1636957 +
Prci Prci15g0224 Chr15 1525937 1529309 +