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
Vvi4g0584 . . . . . . . . . Aev08g0558 . Ahy20g2063 . Aip10g02418 . . . Amo20g2653 . . . . . . . . . . . . . . . . . Dod09g1853 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g0661 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0585 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma17g02066 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g0660 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0586 . . . . . . . . . Aev08g0559 . Ahy20g2062 . Aip10g02415 . . . Amo20g2646 . . . . . . . . . . . . . . . . . Dod09g1852 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g0659 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0587 . . . . . . . . . Aev08g0560 . Ahy20g2060 . Aip10g02413 . . . Amo20g2645 . . . Arst6g03737 . Bach3g01994 . . . . . . . . . . . Dod09g1851 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa5g04006 . . . . . . . . . . . . . Mepo4g00592 . Mesa1g00628 . . . . . . . Phco2g00546 . . . . . Pste8g00124 . . Pte3g01162 . . Pumo9g00589 . Pvu1g0476 . Rops9g01940 . Seca4g01050 . Spst8g01506 . . . . . . . . . . . Vian7g00465 . . . Vimu1g02661 . Viun8g00708 . Vivi3g01438 . .
Vvi4g0588 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0590 Acco10g1959 . Accr4g00831 . Adu10g01828 . . . . Aev08g0561 . Ahy20g2059 . Aip10g02412 Alju08g0837 . . Amo20g2642 . . Arst10g02330 . Bach12g00465 . Bisa09g1149 . . Bva06g02352 Car05g02926 . . . Dere04g0515 . . Dod09g1850 Enph1g1353 . Glsi08g1636 . . . Gma04g00584 Gma06g00570 . . . . . . Lal17g0214 . . . . . . . . . Lapu9g01926 . Lasa5g04007 . Lele01g0671 . Lele03g0667 . . . . . . . Mal2g0931 . Mepo3g07395 . Mesa9g04992 . Mibi05g0763 . Mtr3g3872 . . . Phco7g00713 . Prci8g0025 . . . Pste2g01634 . Pte3g01160 . . . Pumo10g00133 . Pvu9g0917 . Rops10g01364 . Seca4g01047 . Spst9g00735 . . . . . . . Trre5g05131 . Tsu07g00695 . Vian4g02018 . Vifa2g03945 . Vimu10g03007 . Viun9g03134 . Vivi3g01437 . . .
Vvi4g0591 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0593 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco7g02482 . . . . Psa6g0658 Pste2g00908 . . . . . . . Pvu9g2144 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi4g0584 Chr4 5630158 5631018 +
Aev Aev08g0558 Chr08 3186625 3187425 +
Ahy Ahy20g2063 Chr20 116399453 116400640 -
Aip Aip10g02418 Chr10 109120374 109121557 -
Amo Amo20g2653 Chr20 123027592 123028839 -
Dod Dod09g1853 Chr09 40134642 40135734 -
Psa Psa6g0661 Chr6 22450901 22451716 -
Vvi Vvi4g0585 Chr4 5637197 5639581 -
Gma Gma17g02066 Chr17 37664614 37680760 +
Psa Psa6g0660 Chr6 22428776 22431215 +
Vvi Vvi4g0586 Chr4 5653155 5655668 +
Aev Aev08g0559 Chr08 3195083 3196601 +
Ahy Ahy20g2062 Chr20 116264560 116266547 -
Aip Aip10g02415 Chr10 108982148 108984248 -
Amo Amo20g2646 Chr20 122829425 122831454 -
Dod Dod09g1852 Chr09 40120345 40122877 -
Psa Psa6g0659 Chr6 22393349 22396912 -
Vvi Vvi4g0587 Chr4 5662685 5663800 -
Aev Aev08g0560 Chr08 3201002 3202072 -
Ahy Ahy20g2060 Chr20 116245433 116246865 +
Aip Aip10g02413 Chr10 108962906 108964259 +
Amo Amo20g2645 Chr20 122810562 122812855 +
Arst Arst6g03737 Chr6 105528293 105529886 +
Bach Bach3g01994 Chr3 27698871 27699911 +
Dod Dod09g1851 Chr09 40107566 40109233 +
Lasa Lasa5g04006 Chr5 618755664 618756713 -
Mepo Mepo4g00592 Chr4 8140533 8141123 -
Mesa Mesa1g00628 Chr1 8097023 8097613 -
Phco Phco2g00546 Chr2 5196099 5197094 -
Pste Pste8g00124 Chr8 723625 724638 +
Pte Pte3g01162 Chr3 9930318 9931370 +
Pumo Pumo9g00589 Chr9 9884329 9886387 -
Pvu Pvu1g0476 Chr1 5038861 5040854 -
Rops Rops9g01940 Chr9 35638076 35639412 +
Seca Seca4g01050 Chr4 16920658 16921722 +
Spst Spst8g01506 Chr8 15812647 15813663 -
Vian Vian7g00465 Chr7 11822126 11823136 +
Vimu Vimu1g02661 Chr1 38503319 38506226 +
Viun Viun8g00708 Chr8 5749150 5750783 -
Vivi Vivi3g01438 Chr3 23400905 23402875 +
Vvi Vvi4g0588 Chr4 5676577 5681200 -
Vvi Vvi4g0589 Chr4 5682710 5684278 -
Vvi Vvi4g0590 Chr4 5696955 5697876 -
Acco Acco10g1959 Chr10 32359077 32360438 -
Accr Accr4g00831 Chr4 7810400 7811085 +
Adu Adu10g01828 Chr10 83826272 83829356 +
Aev Aev08g0561 Chr08 3213676 3214625 -
Ahy Ahy20g2059 Chr20 116176080 116177327 +
Aip Aip10g02412 Chr10 108896836 108899834 +
Alju Alju08g0837 Chr08 6302245 6305179 +
Amo Amo20g2642 Chr20 122740447 122741498 +
Arst Arst10g02330 Chr10 82729925 82747368 +
Bach Bach12g00465 Chr12 3167033 3167696 -
Bisa Bisa09g1149 Chr09 16726721 16727418 -
Bva Bva06g02352 Chr06 15199167 15200321 -
Car Car05g02926 Chr05 74240333 74241373 -
Dere Dere04g0515 Chr04 5218760 5219445 -
Dod Dod09g1850 Chr09 40089511 40090836 +
Enph Enph1g1353 Chr1 39170490 39171622 -
Glsi Glsi08g1636 Chr08 11623600 11624585 +
Gma Gma04g00584 Chr04 5309988 5311265 -
Gma Gma06g00570 Chr06 5109791 5111114 -
Lal Lal17g0214 Chr17 1319435 1320887 -
Lapu Lapu9g01926 Chr9 34094437 34095222 +
Lasa Lasa5g04007 Chr5 619152444 619153186 -
Lele Lele01g0671 Chr01 3900297 3902967 +
Lele Lele03g0667 Chr03 3909898 3912621 +
Mal Mal2g0931 Chr2 10800071 10800865 +
Mepo Mepo3g07395 Chr3 87357230 87358288 -
Mesa Mesa9g04992 Chr9 84351335 84352134 -
Mibi Mibi05g0763 Chr05 7122833 7123503 +
Mtr Mtr3g3872 Chr3 52556005 52557166 -
Phco Phco7g00713 Chr7 5483610 5484641 -
Prci Prci8g0025 Chr8 120154 121362 +
Pste Pste2g01634 Chr2 17117995 17118992 -
Pte Pte3g01160 Chr3 9921821 9922549 +
Pumo Pumo10g00133 Chr10 1997794 1998971 +
Pvu Pvu9g0917 Chr9 13898357 13899669 -
Rops Rops10g01364 Chr10 26467665 26468631 -
Seca Seca4g01047 Chr4 16794032 16794865 +
Spst Spst9g00735 Chr9 6313303 6314063 -
Trre Trre5g05131 Chr5 52678621 52679390 -
Tsu Tsu07g00695 Chr07 5582029 5583230 +
Vian Vian4g02018 Chr4 36837057 36837756 +
Vifa Vifa2g03945 Chr2 1158321975 1158322686 -
Vimu Vimu10g03007 Chr10 40981733 40982431 +
Viun Viun9g03134 Chr9 38771527 38772613 +
Vivi Vivi3g01437 Chr3 23330993 23332213 +
Vvi Vvi4g0591 Chr4 5708942 5710171 -
Vvi Vvi4g0592 Chr4 5713208 5717621 +
Vvi Vvi4g0593 Chr4 5719989 5720313 -
Phco Phco7g02482 Chr7 43605018 43605495 +
Psa Psa6g0658 Chr6 22351489 22353573 +
Pste Pste2g00908 Chr2 9736939 9737492 +
Pvu Pvu9g2144 Chr9 30731789 30732397 +
Phco Phco7g02482 Chr7 43605018 43605495 +
Pste Pste2g00908 Chr2 9736939 9737492 +
Pvu Pvu9g2144 Chr9 30731789 30732397 +