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
Vvi18g1526 . . . . Adu09g03085 . . . Aev09g2116 . Ahy19g2785 . Aip09g03250 . . . . . . . Arst9g04141 . . . . . . . Car04g01106 . . . . . Dod06g0912 . . . . . Gma10g02131 Gma20g01582 . . Gso10g1994 Gso10g1994 . . . . . . . . . . . . . . Lapu7g01935 . Lasa6g03946 . . . . . . . . . Lja5g0739 . Mal1g2181 . Mepo4g04133 . Mesa1g04495 . . . Mtr1g3630 . Phac7g01255 . Phco6g02334 . . . Psa6g4363 . Pste4g02548 . . . . . Pumo3g01150 . Pvu7g0847 . Rops6g02576 . Seca8g07250 . Spst10g00828 . . . . . Tpr1g0869 . Trre1g05225 . Tsu01g04283 . Vian3g00737 . Vifa3g02761 . Vimu3g02898 . Viun7g03084 . Vivi1g04551 . . .
Vvi18g1527 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal13g0076 . . . . . Lan20g0092 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g1827 . . . . . . . . . . . . . . . . . . .
Vvi18g1528 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1529 . . . . . . . . Aev09g2060 . Ahy19g2715 . Aip09g03177 . . . Amo19g3444 . . Apr6g1319 . . Bach1g00239 . . . . . Car04g01108 . . . . . Dod06g0969 . . . . . Gma10g02132 Gma20g01581 Gma16g01474 . Gso10g1995 Gso10g1995 Gso10g1995 . . . . Lal1g0875 Lal2g0994 . . . . . . . . . Lasa1g02689 . . . . . . . . . Lja5g0738 Lja2g2792 Mal1g2180 . . . . . . . Mtr1g3631 . . . . . . . Psa6g4365 . Pste9g00981 . . Pte9g00448 . . Pumo6g02347 . Pvu4g0977 . Rops5g01116 . Seca10g03585 . Spst4g03398 . . . Sto10g1835 . Tpr1g0868 . Trre11g01049 . Tsu01g04284 . . . Vifa1g04657 . Vimu8g02676 . Viun4g01813 . Vivi2g05277 . . .
Vvi18g1530 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1531 . . . . . . . . . . . . . . . . . . . Apr6g1318 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal2g0993 . . . . . . . . . . . . . . . . . . . Lja5g0737 Lja2g2791 . . . . . . . . . . . . . . . . Psa6g4372 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1532 . . . . . . . . Aev09g2118 . Ahy19g2789 . Aip09g03253 . . . . . . . . . . . . . . . . . . . . . Dod06g0909 . . . . . . . . . . . . . . . . . Lal2g0992 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g4380 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1533 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1534 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1535 . . . . Adu05g03516 . . . Aev09g2119 . Ahy19g2790 . Aip09g03254 . . . Amo19g3560 . . Apr6g1316 Arst5g04511 . . . . . . . Car04g01110 . . . . . Dod06g0906 . . . . . Gma10g02135 Gma20g01580 Gma16g01476 . Gso10g1998 Gso10g1998 Gso10g1998 . . . . Lal1g0874 Lal2g0987 Lal9g0875 . . . . . . . . . . . . . . . . . . Lja5g0736 Lja2g2787 Mal1g2177 . . . Mesa22g01440 . . . Mtr1g3635 . . . . . . . . . Pste9g00985 . Pte16g00365 Pte9g00446 . . Pumo6g02351 . Pvu4g0981 . Rops5g01112 . Seca10g03598 . Spst4g03396 . . . Sto10g1880 . Tpr1g0865 . Trre11g01037 . Tsu01g04288 . Vian8g00704 . Vifa1g04680 . Vimu8g02672 . Viun4g01817 . Vivi2g05270 . . .
   
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Select Species Gene Chromosome Start End Strand
Aev Aev09g2060 Chr09 23796984 23803695 +
Ahy Ahy19g2715 Chr19 148429400 148436003 +
Aip Aip09g03177 Chr09 137114791 137121178 +
Amo Amo19g3444 Chr19 147817283 147823932 +
Dod Dod06g0969 Chr06 12329237 12336589 -
Vvi Vvi18g1526 Chr18 19262862 19274847 -
Adu Adu09g03085 Chr09 118683838 118692013 +
Aev Aev09g2116 Chr09 24211318 24214929 -
Ahy Ahy19g2785 Chr19 149568499 149573169 -
Aip Aip09g03250 Chr09 138328436 138334157 -
Arst Arst9g04141 Chr9 116571473 116575989 +
Car Car04g01106 Chr04 11171717 11176462 -
Dod Dod06g0912 Chr06 11567693 11569228 +
Gma Gma10g02131 Chr10 48798989 48805209 -
Gma Gma20g01582 Chr20 42919648 42929511 +
Gso Gso10g1994 Chr10 46926008 46931863 -
Gso Gso10g1994 Chr10 46926008 46931863 -
Lapu Lapu7g01935 Chr7 35338321 35346150 -
Lasa Lasa6g03946 Chr6 605711433 605716130 -
Lja Lja5g0739 Chr5 6801805 6808652 +
Mal Mal1g2181 Chr1 28768317 28774124 +
Mepo Mepo4g04133 Chr4 51088552 51094629 -
Mesa Mesa1g04495 Chr1 70724733 70730376 -
Mtr Mtr1g3630 Chr1 47924134 47930333 -
Phac Phac7g01255 Chr7 8378041 8386048 +
Phco Phco6g02334 Chr6 44514420 44520946 -
Psa Psa6g4363 Chr6 383388178 383393152 -
Pste Pste4g02548 Chr4 17955504 17961703 -
Pumo Pumo3g01150 Chr3 18672326 18679040 +
Pvu Pvu7g0847 Chr7 8120097 8128028 +
Rops Rops6g02576 Chr6 46386281 46397872 -
Seca Seca8g07250 Chr8 168865165 168878838 -
Spst Spst10g00828 Chr10 8721448 8727244 -
Tpr Tpr1g0869 Chr1 7384596 7395759 +
Trre Trre1g05225 Chr1 58241545 58245796 -
Tsu Tsu01g04283 Chr01 50600038 50605794 -
Vian Vian3g00737 Chr3 7734313 7740860 +
Vifa Vifa3g02761 Chr3 765677009 765682383 -
Vimu Vimu3g02898 Chr3 43078448 43084827 -
Viun Viun7g03084 Chr7 33538932 33546099 -
Vivi Vivi1g04551 Chr1 97336256 97340066 +
Vvi Vvi18g1527 Chr18 19281686 19290355 -
Lal Lal13g0076 Chr13 502366 507722 +
Lan Lan20g0092 Chr20 537542 542930 +
Sto Sto10g1827 Chr10 27988727 27991792 -
Vvi Vvi18g1528 Chr18 19321938 19323255 -
Vvi Vvi18g1529 Chr18 19328978 19350107 +
Aev Aev09g2060 Chr09 23796984 23803695 +
Ahy Ahy19g2715 Chr19 148429400 148436003 +
Aip Aip09g03177 Chr09 137114791 137121178 +
Amo Amo19g3444 Chr19 147817283 147823932 +
Apr Apr6g1319 Chr6 18737955 18755471 -
Bach Bach1g00239 Chr1 2821192 2829042 +
Car Car04g01108 Chr04 11180954 11185184 +
Dod Dod06g0969 Chr06 12329237 12336589 -
Gma Gma10g02132 Chr10 48812174 48816559 +
Gma Gma20g01581 Chr20 42906743 42911757 -
Gma Gma16g01474 Chr16 33974762 33985390 +
Gso Gso10g1995 Chr10 46938463 46943480 +
Gso Gso10g1995 Chr10 46938463 46943480 +
Gso Gso10g1995 Chr10 46938463 46943480 +
Lal Lal1g0875 Chr1 6170332 6177503 -
Lal Lal2g0994 Chr2 6792193 6797998 -
Lasa Lasa1g02689 Chr1 517224611 517233388 +
Lja Lja5g0738 Chr5 6793020 6798216 -
Lja Lja2g2792 Chr2 42918116 42927128 -
Mal Mal1g2180 Chr1 28758664 28762369 -
Mtr Mtr1g3631 Chr1 47937750 47942164 +
Psa Psa6g4365 Chr6 383456477 383459761 +
Pste Pste9g00981 Chr9 6319543 6323203 +
Pte Pte9g00448 Chr9 5411289 5416202 -
Pumo Pumo6g02347 Chr6 46350591 46362031 +
Pvu Pvu4g0977 Chr4 24291189 24302068 +
Rops Rops5g01116 Chr5 22991350 23023727 -
Seca Seca10g03585 Chr10 67179482 67187680 +
Spst Spst4g03398 Chr4 74231343 74251529 -
Sto Sto10g1835 Chr10 28100054 28103384 +
Tpr Tpr1g0868 Chr1 7377538 7381877 -
Trre Trre11g01049 Chr11 9581189 9589109 -
Tsu Tsu01g04284 Chr01 50610142 50614235 +
Vifa Vifa1g04657 Chr1 728503670 728512140 +
Vimu Vimu8g02676 Chr8 37391267 37399105 -
Viun Viun4g01813 Chr4 32264118 32273205 +
Vivi Vivi2g05277 Chr2 176783787 176791816 -
Vvi Vvi18g1530 Chr18 19351756 19352852 +
Vvi Vvi18g1531 Chr18 19358276 19358836 +
Apr Apr6g1318 Chr6 18734400 18734933 -
Lal Lal2g0993 Chr2 6790422 6790934 -
Lja Lja5g0737 Chr5 6785345 6785875 -
Lja Lja2g2791 Chr2 42901155 42901679 -
Psa Psa6g4372 Chr6 383601850 383602374 +
Vvi Vvi18g1532 Chr18 19370366 19370914 +
Aev Aev09g2118 Chr09 24226667 24227203 +
Ahy Ahy19g2789 Chr19 149706965 149707750 +
Aip Aip09g03253 Chr09 138456046 138456921 +
Dod Dod06g0909 Chr06 11545594 11546335 -
Lal Lal2g0992 Chr2 6778198 6778704 -
Psa Psa6g4380 Chr6 384367775 384368754 -
Vvi Vvi18g1533 Chr18 19372185 19379984 -
Vvi Vvi18g1534 Chr18 19403165 19405899 +
Vvi Vvi18g1535 Chr18 19427229 19429012 -
Adu Adu05g03516 Chr05 107731767 107734263 -
Aev Aev09g2119 Chr09 24232158 24234059 -
Ahy Ahy19g2790 Chr19 149732086 149733856 -
Aip Aip09g03254 Chr09 138478117 138480252 -
Amo Amo19g3560 Chr19 149844816 149846419 -
Apr Apr6g1316 Chr6 18709066 18710936 +
Arst Arst5g04511 Chr5 106409944 106412406 -
Car Car04g01110 Chr04 11201189 11203469 -
Dod Dod06g0906 Chr06 11518316 11520841 +
Gma Gma10g02135 Chr10 48834682 48836248 -
Gma Gma20g01580 Chr20 42887819 42889147 +
Gma Gma16g01476 Chr16 34013840 34016131 -
Gso Gso10g1998 Chr10 46960478 46962268 -
Gso Gso10g1998 Chr10 46960478 46962268 -
Gso Gso10g1998 Chr10 46960478 46962268 -
Lal Lal1g0874 Chr1 6159177 6161914 +
Lal Lal2g0987 Chr2 6750842 6753276 +
Lal Lal9g0875 Chr9 6563347 6566327 +
Lja Lja5g0736 Chr5 6771171 6773656 +
Lja Lja2g2787 Chr2 42633563 42635788 +
Mal Mal1g2177 Chr1 28736458 28738344 +
Mesa Mesa22g01440 Chr22 29161966 29164157 +
Mtr Mtr1g3635 Chr1 47974650 47977484 -
Pste Pste9g00985 Chr9 6348727 6351425 -
Pte Pte16g00365 Chr16 4921655 4923770 +
Pte Pte9g00446 Chr9 5386577 5389150 -
Pumo Pumo6g02351 Chr6 46399486 46402475 -
Pvu Pvu4g0981 Chr4 24438791 24441164 -
Rops Rops5g01112 Chr5 22858528 22860838 +
Seca Seca10g03598 Chr10 67512391 67514152 -
Spst Spst4g03396 Chr4 74210416 74212380 +
Sto Sto10g1880 Chr10 28454513 28456515 -
Tpr Tpr1g0865 Chr1 7364169 7367092 +
Trre Trre11g01037 Chr11 9506586 9509133 +
Tsu Tsu01g04288 Chr01 50654190 50656254 -
Vian Vian8g00704 Chr8 13797086 13798709 -
Vifa Vifa1g04680 Chr1 731251981 731253381 -
Vimu Vimu8g02672 Chr8 37350451 37352382 +
Viun Viun4g01817 Chr4 32337551 32340312 -
Vivi Vivi2g05270 Chr2 176371251 176373192 +