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
Vvi4g1534 . Acco04g2189 . Accr8g00573 . Adu03g03020 Aed5g2134 . Aev03g2918 . Ahy13g3053 . Aip03g03450 . . Alju06g2148 Amo13g3718 . . . . Arst3g03986 . . . Bisa08g2432 . . . . Cca09g02270 . . Dere03g0393 Dod04g2543 . . Enph6g0334 . Glsi02g0366 . . . . . . . . . . . . . . . . . . . . . . . Lasa7g04538 . . . . Lele21g1526 Lele22g1513 Lele23g0486 Lele24g1475 . Lja4g0591 . Mal7g4747 . Mepo2g04424 . Mesa13g00699 . Mibi09g0596 . Mtr8g3289 . Phac2g04100 . Phco4g03107 . Prci4g2417 . . . Pste3g01554 . . . . . Pumo6g00663 . Pvu2g2809 . Rops2g00774 . Seca12g06296 . Spst3g01295 Ssu5g2870 . Sto3g3212 . . Tpr3g0813 . Trre7g05215 . Tsu02g00644 . Vian1g03673 . Vifa6g03258 . Vimu11g04197 . Viun3g00835 . Vivi5g04481 . .
Vvi4g1535 . . . . . . . . . . . . . . . . . . Apr1g0431 . . . . . . . . . . . Cca09g02277 . . . . . . . . . . . . . . . . . . . Lal17g0752 . . . . . . . . . . . . . . . . . . . . . Lja1g4486 . Mal2g1490 Mal7g4755 . . . . . . Mtr3g3370 Mtr8g3297 . . . . . . Psa5g1421 . . . . . . . . . . . . . . . . . . . . Sto4g0274 Tpr3g3170 Tpr3g0802 . . Tsu07g01292 Tsu02g00632 . . . . . . . . . . . .
Vvi4g1536 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1537 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1538 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1539 . . . . . . . . . . . . . . . . . . Apr1g0427 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal21g0671 . Lal17g0753 . . . . . . . . . . . . . . . . . . . . . Lja1g4482 . Mal2g1487 . . . . . . . Mtr3g3373 . . . . . . . Psa5g1417 . . . . . . . . . . . . . . . . . . . . Sto4g0268 Tpr3g3176 . . . Tsu07g01288 . . . . . . . . . . . . .
Vvi4g1540 . . . . . . . . . . . . . . . . . . Apr1g0426 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal4g0638 . . . . . . . . . . . . . . . . . . . . . . Lja1g4481 . Mal2g1478 . . . . . . . Mtr3g3375 . . . . . . . Psa5g1415 . . . . . . . . . Pvu9g1601 . . . . . Spst9g01880 . . . . Sto4g0267 Tpr3g3180 . . . Tsu07g01285 . . . . . Vimu10g01827 . . . . . . .
Vvi4g1541 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1542 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1543 . . . . Adu08g02577 Adu03g03012 Aed5g2143 . . . Ahy13g3048 . Aip03g03447 . . . Amo13g3713 . . . Arst8g03559 Arst3g03974 . . . . Bva05g01540 . . . Cca09g02281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g03446 . . . . . . . . . . . Lja4g0581 . . . . . . . . . . . . . Phco4g03115 . . . . . Pste3g01532 . . . . . Pumo6g00655 Pvu9g1605 Pvu2g2817 . Rops2g00765 . Seca12g06304 Spst9g01874 Spst3g01289 Ssu5g2877 . . . . . . . . . . Vian1g03680 . Vifa2g03230 Vimu10g01834 Vimu11g04205 . Viun3g00818 . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi4g1534 Chr4 23072459 23108432 -
Acco Acco04g2189 Chr04 37809568 37817975 -
Accr Accr8g00573 Chr8 9030825 9036156 +
Adu Adu03g03020 Chr03 113595491 113599543 +
Aed Aed5g2134 Chr5 23587449 23591875 -
Aev Aev03g2918 Chr03 28515577 28525196 -
Ahy Ahy13g3053 Chr13 122787538 122791606 +
Aip Aip03g03450 Chr03 112901789 112905838 +
Alju Alju06g2148 Chr06 47500450 47509280 -
Amo Amo13g3718 Chr13 125726242 125730564 +
Arst Arst3g03986 Chr3 112300517 112304607 +
Bisa Bisa08g2432 Chr08 57931451 57936781 +
Cca Cca09g02270 Chr09 47919999 47927258 -
Dere Dere03g0393 Chr03 7610850 7618035 -
Dod Dod04g2543 Chr04 49263330 49268797 -
Enph Enph6g0334 Chr6 6665225 6671480 -
Glsi Glsi02g0366 Chr02 2337751 2342699 -
Lasa Lasa7g04538 Chr7 666563376 666568027 -
Lele Lele21g1526 Chr21 23485092 23490379 -
Lele Lele22g1513 Chr22 20818037 20826136 -
Lele Lele23g0486 Chr23 3559785 3570782 +
Lele Lele24g1475 Chr24 20595496 20603588 -
Lja Lja4g0591 Chr4 4905061 4906661 +
Mal Mal7g4747 Chr7 115776578 115779867 -
Mepo Mepo2g04424 Chr2 52762050 52766495 -
Mesa Mesa13g00699 Chr13 8289197 8294183 +
Mibi Mibi09g0596 Chr09 7788064 7797716 +
Mtr Mtr8g3289 Chr8 43377428 43382786 -
Phac Phac2g04100 Chr2 40219658 40226498 -
Phco Phco4g03107 Chr4 51975276 51981771 -
Prci Prci4g2417 Chr4 36900140 36903856 -
Pste Pste3g01554 Chr3 9673369 9677005 +
Pumo Pumo6g00663 Chr6 8340440 8346988 +
Pvu Pvu2g2809 Chr2 43796422 43802594 -
Rops Rops2g00774 Chr2 11056090 11061884 +
Seca Seca12g06296 Chr12 154845818 154848903 -
Spst Spst3g01295 Chr3 16365142 16371055 +
Ssu Ssu5g2870 Chr5 75088310 75099310 -
Sto Sto3g3212 Chr3 36889705 36894208 -
Tpr Tpr3g0813 Chr3 7663223 7667735 +
Trre Trre7g05215 Chr7 58653513 58657424 -
Tsu Tsu02g00644 Chr02 5458936 5463526 +
Vian Vian1g03673 Chr1 59530771 59539013 -
Vifa Vifa6g03258 Chr6 1074776267 1074782469 -
Vimu Vimu11g04197 Chr11 63511003 63520510 -
Viun Viun3g00835 Chr3 5126675 5132454 +
Vivi Vivi5g04481 Chr5 142765384 142771746 -
Vvi Vvi4g1535 Chr4 23110760 23112150 -
Apr Apr1g0431 Chr1 5330886 5335698 +
Cca Cca09g02277 Chr09 48003770 48005681 -
Lal Lal17g0752 Chr17 5380928 5385434 -
Lja Lja1g4486 Chr1 58430843 58433795 +
Mal Mal2g1490 Chr2 17852322 17854952 +
Mal Mal7g4755 Chr7 115845650 115848103 -
Mtr Mtr3g3370 Chr3 47574429 47577285 -
Mtr Mtr8g3297 Chr8 43436366 43438456 -
Psa Psa5g1421 Chr5 110317186 110320297 -
Sto Sto4g0274 Chr4 2076893 2077336 +
Tpr Tpr3g3170 Chr3 34926230 34930962 +
Tpr Tpr3g0802 Chr3 7591394 7593928 +
Tsu Tsu07g01292 Chr07 11316341 11320299 +
Tsu Tsu02g00632 Chr02 5335042 5336978 -
Vvi Vvi4g1536 Chr4 23119212 23120549 +
Vvi Vvi4g1537 Chr4 23134466 23135818 -
Vvi Vvi4g1538 Chr4 23141979 23143556 +
Vvi Vvi4g1539 Chr4 23153418 23156996 -
Apr Apr1g0427 Chr1 5278255 5281953 +
Lal Lal21g0671 Chr21 5215775 5219619 -
Lal Lal17g0753 Chr17 5396473 5399992 -
Lja Lja1g4482 Chr1 58322687 58326461 +
Mal Mal2g1487 Chr2 17779707 17782756 +
Mtr Mtr3g3373 Chr3 47616172 47619823 -
Psa Psa5g1417 Chr5 109609171 109612386 +
Sto Sto4g0268 Chr4 2030379 2034602 +
Tpr Tpr3g3176 Chr3 34978960 34982820 -
Tsu Tsu07g01288 Chr07 11276835 11280632 +
Vvi Vvi4g1540 Chr4 23171392 23225736 -
Apr Apr1g0426 Chr1 5239921 5270288 +
Lal Lal4g0638 Chr4 4748914 4771426 -
Lja Lja1g4481 Chr1 58288282 58310702 +
Mal Mal2g1478 Chr2 17661258 17675867 +
Mtr Mtr3g3375 Chr3 47653666 47668318 -
Psa Psa5g1415 Chr5 109488741 109516776 +
Pvu Pvu9g1601 Chr9 22492177 22499197 +
Spst Spst9g01880 Chr9 24865220 24880820 -
Sto Sto4g0267 Chr4 2010605 2023368 +
Tpr Tpr3g3180 Chr3 35020078 35037794 -
Tsu Tsu07g01285 Chr07 11198549 11209256 +
Vimu Vimu10g01827 Chr10 25852951 25863388 +
Vvi Vvi4g1541 Chr4 23227298 23228100 +
Vvi Vvi4g1542 Chr4 23261748 23272920 +
Vvi Vvi4g1543 Chr4 23278194 23287284 +
Adu Adu08g02577 Chr08 41843118 41848820 +
Adu Adu03g03012 Chr03 113278408 113281573 -
Aed Aed5g2143 Chr5 23644985 23650617 +
Ahy Ahy13g3048 Chr13 122620295 122623537 +
Aip Aip03g03447 Chr03 112752741 112755807 +
Amo Amo13g3713 Chr13 125563447 125566818 +
Arst Arst8g03559 Chr8 46215792 46221466 +
Arst Arst3g03974 Chr3 111983347 111986695 -
Bva Bva05g01540 Chr05 12719083 12724555 -
Cca Cca09g02281 Chr09 48031237 48040117 +
Lapu Lapu3g03446 Chr3 57727998 57736836 +
Lja Lja4g0581 Chr4 4850608 4854139 -
Phco Phco4g03115 Chr4 52015450 52025434 +
Pste Pste3g01532 Chr3 9543112 9548793 -
Pumo Pumo6g00655 Chr6 8220389 8226960 -
Pvu Pvu9g1605 Chr9 22568381 22575241 -
Pvu Pvu2g2817 Chr2 43841333 43849228 +
Rops Rops2g00765 Chr2 10849114 10861570 -
Seca Seca12g06304 Chr12 154939819 154944531 +
Spst Spst9g01874 Chr9 24709046 24720174 +
Spst Spst3g01289 Chr3 16314863 16320645 -
Ssu Ssu5g2877 Chr5 75233280 75240598 +
Vian Vian1g03680 Chr1 59602718 59608759 +
Vifa Vifa2g03230 Chr2 926573129 926575693 +
Vimu Vimu10g01834 Chr10 25939567 25949122 -
Vimu Vimu11g04205 Chr11 63567572 63577619 +
Viun Viun3g00818 Chr3 5058577 5066495 -
Mal Mal2g1490 Chr2 17852322 17854952 +
Mtr Mtr3g3370 Chr3 47574429 47577285 -
Psa Psa5g1421 Chr5 110317186 110320297 -
Tpr Tpr3g3170 Chr3 34926230 34930962 +
Tsu Tsu07g01292 Chr07 11316341 11320299 +
Mal Mal2g1487 Chr2 17779707 17782756 +
Mtr Mtr3g3373 Chr3 47616172 47619823 -
Psa Psa5g1417 Chr5 109609171 109612386 +
Tpr Tpr3g3176 Chr3 34978960 34982820 -
Tsu Tsu07g01288 Chr07 11276835 11280632 +