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
Vvi1g0881 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0882 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car02g00624 . . . . . . . . . . . . . . . . . . . . . . Lal23g1039 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g4364 . . . . . . . . . . . . . . . . . .
Vvi1g0883 . . . . . Adu03g03805 . . . . . . . . . . . . . . . . . . . . . Bva11g01100 . Car07g02003 . . . . . . . . . . . . Gma08g02741 Gma18g01205 . . . . . . . . . . . . . . . . . . . Lasa4g01702 . . . . . . . . . Lja4g2845 . . . Mepo1g02691 . . . . . Mtr8g1916 . Phac3g00792 . Phco8g02833 . . . Psa4g2936 . Pste7g00757 . . . . . . . Pvu3g0567 . . . . . Spst3g02516 . . . Sto6g4369 . Tpr7g1938 . Trre15g02101 . . . . . . . Vimu11g02568 . . . . . .
Vvi1g0884 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva08g01358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal6g1712 . . . . . . . Mtr5g1455 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tsu05g01567 . . . . . . . . . . . . .
Vvi1g0885 . . . . . Adu03g03808 . . . . . . . . . . . . . Apr3g0831 . . . . . . . . . Car07g02006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja4g2848 . . . . . . . . . . . . . . . . . Psa4g2938 . Pste7g00758 . . . . . . . Pvu3g0569 . . . . . . . . . Sto6g4370 . . . . . . . . . . . Vimu11g02562 . . . . . .
Vvi1g0886 . . . . . . . . Aev05g1323 . Ahy15g1494 . Aip05g01568 . . . . . . . . . . . . . . Bva11g01098 . . . . . . Dod02g1504 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g1026 . Mal6g1714 . . . . . . . Mtr5g1456 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g4371 . . . . . . . . . . . . . . . . . .
Vvi1g0887 . . . . Adu05g01548 . . . . Aev03g0518 . Ahy13g3733 . Aip03g04176 . . . Amo13g4716 . . Arst5g01986 . Bach4g01328 . . . Bva08g01359 . . . . . . . . Dod04g0018 . . . . . Gma01g00326 Gma08g02742 Gma18g01204 . . . . . . . . . Lal15g0505 . . . . . . . . Lasa2g00399 . . . . . . . . . . . Mal6g1715 . Mepo5g01956 . . . . . Mtr5g1457 . . . Phco4g01504 . . . . Psa4g2945 Pste1g00085 . Pte14g00212 . . . Pumo8g01180 . Pvu2g0774 . Rops1g00911 . . . Spst3g02514 . . . . Sto6g4372 Tpr2g1793 . . . . . Vian10g01133 . Vifa1g04792 . Vimu7g03777 . Viun2g01151 . . . . .
Vvi1g0888 . . . . . Adu03g03809 . . . . . . . . . . . . . Apr3g0832 . . . . . . Bva08g01360 Bva11g01096 . Car07g02007 . . . . . . . . . . . . . Gma18g01202 . . . . . . . . Lal16g0561 . . . . . . . . . . . . . . . . . . . . . . Mal5g2930 . Mepo1g02694 . . . . . Mtr8g1915 . Phac3g01050 . Phco8g02830 . . . . . . . . . . . . . Pvu3g0570 . . . . . Spst3g02512 . . . . . . . Trre15g02108 . . . . . . . Vimu11g02559 . . . . . .
Vvi1g0889 . Acco13g0642 . Accr12g00584 . . . . . . . . . . . Alju13g1545 . . Apr7g1598 . . Arst3g04986 . Bach2g02098 . Bisa02g1338 Bva08g01361 . . . . . . Dere14g0537 . . . Enph5g0511 . Glsi13g1259 . . . . . . . . . . . . Lal16g0562 . . . . . . . . Lapu9g00754 . Lasa5g02235 . . . . Lele17g1015 Lele18g0523 Lele19g0541 Lele20g0910 . . Mal6g1716 . . Mepo3g05874 . Mesa9g03341 . Mibi13g0633 Mtr5g1458 . . Phac6g00496 . Phco7g02165 . . Psa2g2526 . . Pste2g00153 . . Pte3g00264 Pte1g01937 . Pumo10g02072 . Pvu9g1872 . Rops10g00628 . Seca4g03123 . Spst9g02256 . . . Sto6g4373 . . . Trre5g02646 . . . Vian4g00825 . . . Vimu10g01169 . Viun9g01159 . Vivi3g03869 . .
Vvi1g0890 . . . . . Adu04g02737 Aed11g0230 . . . . . . . . . . . . . . . . . . . Bva08g01363 . . . Cca06g00782 . . . . . . . . . Gma02g00273 . . . Gso2g0257 . . . . . . . . . . . . . . . . Lapu1g01377 . . . . . . . . . . . . . . . . . . . . . . . . . Phco3g02787 . . . . . . . . . . . . . Pvu8g0452 . . . . . . Ssu2g1735 . Sto11g1082 . . . . . . . . . . . . Vimu6g00814 . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi1g0881 Chr1 9410542 9423702 -
Vvi Vvi1g0882 Chr1 9424059 9437419 +
Car Car02g00624 Chr02 7971914 7977317 -
Lal Lal23g1039 Chr23 12163290 12170639 +
Sto Sto6g4364 Chr6 46217489 46223918 +
Vvi Vvi1g0883 Chr1 9449811 9452550 +
Adu Adu03g03805 Chr03 126739734 126742580 -
Bva Bva11g01100 Chr11 12315495 12318955 +
Car Car07g02003 Chr07 23505676 23508538 -
Gma Gma08g02741 Chr08 43011543 43014908 -
Gma Gma18g01205 Chr18 18930092 18934107 +
Lasa Lasa4g01702 Chr4 318502693 318504947 +
Lja Lja4g2845 Chr4 48498912 48501043 -
Mepo Mepo1g02691 Chr1 28502982 28507873 -
Mtr Mtr8g1916 Chr8 28940823 28945222 +
Phac Phac3g00792 Chr3 6785557 6789810 -
Phco Phco8g02833 Chr8 41730452 41733792 +
Psa Psa4g2936 Chr4 235375862 235378214 +
Pste Pste7g00757 Chr7 6898037 6901308 +
Pvu Pvu3g0567 Chr3 6960413 6964471 -
Spst Spst3g02516 Chr3 73060568 73063823 +
Sto Sto6g4369 Chr6 46242982 46245301 +
Tpr Tpr7g1938 Chr7 23074899 23077726 -
Trre Trre15g02101 Chr15 17094190 17097073 -
Vimu Vimu11g02568 Chr11 45381268 45385153 +
Vvi Vvi1g0884 Chr1 9454040 9455898 -
Bva Bva08g01358 Chr08 7119146 7121286 -
Mal Mal6g1712 Chr6 32577467 32581146 -
Mtr Mtr5g1455 Chr5 15271462 15275642 -
Tsu Tsu05g01567 Chr05 15224862 15228851 +
Vvi Vvi1g0885 Chr1 9458179 9476207 -
Adu Adu03g03808 Chr03 126767257 126773158 +
Apr Apr3g0831 Chr3 21740308 21749718 +
Car Car07g02006 Chr07 23659192 23666744 +
Lja Lja4g2848 Chr4 49126797 49139901 +
Psa Psa4g2938 Chr4 235388301 235395281 -
Pste Pste7g00758 Chr7 6908338 6916312 -
Pvu Pvu3g0569 Chr3 7010040 7017137 +
Sto Sto6g4370 Chr6 46246124 46254379 -
Vimu Vimu11g02562 Chr11 45283156 45288872 -
Vvi Vvi1g0886 Chr1 9477768 9494472 -
Aev Aev05g1323 Chr05 9415573 9418228 +
Ahy Ahy15g1494 Chr15 28301681 28305017 +
Aip Aip05g01568 Chr05 27136594 27143931 +
Bva Bva11g01098 Chr11 12295974 12298537 -
Dod Dod02g1504 Chr02 18183062 18183628 +
Lja Lja2g1026 Chr2 9650664 9653506 +
Mal Mal6g1714 Chr6 32606410 32609467 -
Mtr Mtr5g1456 Chr5 15277673 15281058 -
Sto Sto6g4371 Chr6 46255423 46257617 -
Vvi Vvi1g0887 Chr1 9503596 9505790 +
Adu Adu05g01548 Chr05 26876653 26881209 -
Aev Aev03g0518 Chr03 3794863 3798428 +
Ahy Ahy13g3733 Chr13 136252658 136257339 -
Aip Aip03g04176 Chr03 125724544 125727880 -
Amo Amo13g4716 Chr13 144989231 144993565 -
Arst Arst5g01986 Chr5 26957882 26962489 -
Bach Bach4g01328 Chr4 9325875 9328984 -
Bva Bva08g01359 Chr08 7130402 7134010 +
Dod Dod04g0018 Chr04 323575 328445 +
Gma Gma01g00326 Chr01 3799906 3802993 -
Gma Gma08g02742 Chr08 43023256 43028145 -
Gma Gma18g01204 Chr18 18852831 18858190 +
Lal Lal15g0505 Chr15 3495550 3500298 -
Lasa Lasa2g00399 Chr2 47934042 47937394 +
Mal Mal6g1715 Chr6 32637312 32641011 +
Mepo Mepo5g01956 Chr5 21702640 21707207 -
Mtr Mtr5g1457 Chr5 15288464 15292916 +
Phco Phco4g01504 Chr4 13685360 13691117 -
Psa Psa4g2945 Chr4 237009052 237011721 -
Pste Pste1g00085 Chr1 350184 354021 -
Pte Pte14g00212 Chr14 8116237 8119701 -
Pumo Pumo8g01180 Chr8 42916240 42919528 +
Pvu Pvu2g0774 Chr2 10835443 10842097 -
Rops Rops1g00911 Chr1 21936579 21940179 -
Spst Spst3g02514 Chr3 73047393 73050277 +
Sto Sto6g4372 Chr6 46266700 46270899 +
Tpr Tpr2g1793 Chr2 21214394 21219285 -
Vian Vian10g01133 Chr10 18257682 18260306 +
Vifa Vifa1g04792 Chr1 749925376 749928706 -
Vimu Vimu7g03777 Chr7 33362169 33366246 -
Viun Viun2g01151 Chr2 22439434 22443231 +
Vvi Vvi1g0888 Chr1 9510816 9518104 +
Adu Adu03g03809 Chr03 126774494 126777011 -
Apr Apr3g0832 Chr3 21749833 21751932 -
Bva Bva08g01360 Chr08 7139802 7144998 +
Bva Bva11g01096 Chr11 12289711 12291373 +
Car Car07g02007 Chr07 23676183 23678950 -
Gma Gma18g01202 Chr18 18661248 18663897 +
Lal Lal16g0561 Chr16 3610811 3615867 -
Mal Mal5g2930 Chr5 87199630 87203747 -
Mepo Mepo1g02694 Chr1 28530864 28533954 +
Mtr Mtr8g1915 Chr8 28929599 28932268 -
Phac Phac3g01050 Chr3 10169860 10196200 -
Phco Phco8g02830 Chr8 41681582 41683662 +
Pvu Pvu3g0570 Chr3 7018159 7020598 -
Spst Spst3g02512 Chr3 73019437 73020743 +
Trre Trre15g02108 Chr15 17139272 17146261 -
Vimu Vimu11g02559 Chr11 45272367 45274336 +
Vvi Vvi1g0889 Chr1 9518439 9519444 -
Acco Acco13g0642 Chr13 4702712 4703782 +
Accr Accr12g00584 Chr12 5514640 5515716 +
Alju Alju13g1545 Chr13 33727409 33728495 -
Apr Apr7g1598 Chr7 23160043 23161771 -
Arst Arst3g04986 Chr3 125503711 125505262 +
Bach Bach2g02098 Chr2 28222874 28224149 -
Bisa Bisa02g1338 Chr02 22838564 22839518 +
Bva Bva08g01361 Chr08 7144804 7146566 -
Dere Dere14g0537 Chr14 5508895 5509950 -
Enph Enph5g0511 Chr5 4187086 4189022 +
Glsi Glsi13g1259 Chr13 30052321 30057126 -
Lal Lal16g0562 Chr16 3610814 3615495 +
Lapu Lapu9g00754 Chr9 10234901 10236644 +
Lasa Lasa5g02235 Chr5 463991782 463992615 +
Lele Lele17g1015 Chr17 20870932 20871971 -
Lele Lele18g0523 Chr18 3090036 3091063 +
Lele Lele19g0541 Chr19 3136055 3138360 +
Lele Lele20g0910 Chr20 15438979 15439905 -
Mal Mal6g1716 Chr6 32678665 32680081 -
Mepo Mepo3g05874 Chr3 73060149 73061659 +
Mesa Mesa9g03341 Chr9 64246573 64247564 +
Mibi Mibi13g0633 Chr13 8280318 8281325 +
Mtr Mtr5g1458 Chr5 15317205 15319023 -
Phac Phac6g00496 Chr6 10001947 10005988 -
Phco Phco7g02165 Chr7 38426986 38428119 +
Psa Psa2g2526 Chr2 291814559 291816535 -
Pste Pste2g00153 Chr2 684059 685190 -
Pte Pte3g00264 Chr3 2240128 2242410 +
Pte Pte1g01937 Chr1 40580920 40582496 +
Pumo Pumo10g02072 Chr10 27908547 27910332 +
Pvu Pvu9g1872 Chr9 26682679 26684267 +
Rops Rops10g00628 Chr10 15466222 15467727 -
Seca Seca4g03123 Chr4 53575883 53577724 +
Spst Spst9g02256 Chr9 52472882 52474128 +
Sto Sto6g4373 Chr6 46279020 46279518 -
Trre Trre5g02646 Chr5 20766896 20768391 -
Vian Vian4g00825 Chr4 10859399 10860337 -
Vimu Vimu10g01169 Chr10 11377523 11378388 -
Viun Viun9g01159 Chr9 10047112 10048331 -
Vivi Vivi3g03869 Chr3 66604176 66605365 -
Vvi Vvi1g0890 Chr1 9525636 9529314 -
Adu Adu04g02737 Chr04 115113382 115117610 +
Aed Aed11g0230 Chr11 1898878 1903915 +
Bva Bva08g01363 Chr08 7158094 7162802 -
Cca Cca06g00782 Chr06 20668870 20673177 -
Gma Gma02g00273 Chr02 2886649 2893518 -
Gso Gso2g0257 Chr2 2792860 2797762 -
Lapu Lapu1g01377 Chr1 26569244 26572843 -
Phco Phco3g02787 Chr3 54247923 54262926 +
Pvu Pvu8g0452 Chr8 3852572 3855043 -
Ssu Ssu2g1735 Chr2 67489947 67494008 -
Sto Sto11g1082 Chr11 10961900 10965375 -
Vimu Vimu6g00814 Chr6 9070167 9070803 +
Pte Pte3g00264 Chr3 2240128 2242410 +