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
Vvi18g1276 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g01890 Bva10g00944 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0118 . . . . . . . . . . . . . . . . . . .
Vvi18g1277 Acco10g1310 . Accr4g01452 . Adu08g00170 . . Aed9g0210 . Aev07g0673 Ahy17g2245 Ahy16g0047 Aip07g02404 Aip06g00040 Alju08g1503 . Amo17g2114 . . Apr5g1668 Arst8g00204 . Bach12g00074 . Bisa09g2073 . Bva06g01889 Bva10g00945 . Car05g03280 . Cca07g00254 . . Dod08g2293 Dod08g2293 Enph1g1040 . Glsi08g2057 . Gma04g00218 Gma06g00199 Gma14g02150 Gma17g02476 Gso4g0202 Gso4g0202 Gso4g0202 Gso4g0202 . . . . . . . . . . . . Lapu9g02305 . Lasa5g04554 . Lele01g1175 Lele02g1442 Lele03g1190 Lele04g1424 . . . . Lja1g3487 . . Mal2g0467 Mepo3g07838 . Mesa9g05515 . Mibi05g1393 . . Mtr3g4282 . . Phco7g00269 . Prci8g0732 . . . . . Pte3g01431 Pte1g02676 . . . . Pvu9g0185 . . . . . Spst9g00265 . . . Sto5g0117 Sto9g3715 . Tpr7g0220 Trre5g05699 . . Tsu07g00246 . . . . Vimu10g03505 . . . Vivi3g00634 . . Vra5g1667
Vvi18g1278 . . . . . . . . . Aev07g0672 . Ahy16g0046 . Aip06g00039 . . . . Apr9g0651 . . . . . . . Bva06g01888 . Car04g03598 . Cca05g00388 Cca07g00253 . . . Dod08g2296 . . . . . Gma06g00197 Gma16g01167 . . . . . Lal4g0060 . . . . . Lan14g0958 . . . . . . . . . . . . . . . . . Lja1g3486 Lja5g3336 Mal1g6115 . . . . . . . Mtr1g0734 . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0115 . Tpr1g3889 . . . Tsu01g00180 . . . . . . . . . . . Vra6g2018 Vra5g1668
Vvi18g1279 . . . . . . . . Aev08g0186 Aev07g0671 Ahy17g2242 Ahy16g0044 Aip07g02400 Aip06g00038 . . Amo17g2111 . Apr9g0652 Apr5g1669 . . . . . . . Bva10g00946 Car04g03600 Car05g03281 Cca05g00389 . . . Dod08g2298 Dod08g2298 . . . . Gma04g00215 . Gma14g02151 Gma17g02477 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g3485 . . Mal2g0466 . . . . . . . Mtr3g4283 . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g3716 . Tpr7g0219 . . . Tsu07g00245 . . . . . . . . . . Vra6g2017 .
Vvi18g1280 . . . . . . . . . . . . . . . . . . Apr9g0653 Apr5g1670 . . . . . . Bva06g01887 . Car04g03601 . Cca05g00390 . . . . . . . . . . . Gma16g01164 Gma17g02478 . . . . . Lal17g0055 . . . . . . . . . . . . . . . . . . . . . . . Lja5g3337 Mal1g6118 . . . . . . . Mtr1g0735 . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0114 . Tpr1g3890 . . . Tsu01g00179 . . . . . . . . . . . Vra6g2016 .
Vvi18g1281 . . . . . . Aed11g0032 . Aev08g0183 Aev07g0669 Ahy17g2239 Ahy16g0043 Aip07g02397 Aip06g00037 . . . . Apr9g0654 Apr5g1671 . . . . . . . Bva10g00947 . . Cca05g00395 . . . Dod08g2299 Dod08g2299 . . . . Gma04g00214 . Gma14g02153 Gma17g02479 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g3484 . Mal1g6120 Mal2g0464 . . . . . . Mtr1g0736 Mtr3g4285 . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g0043 . . Sto9g3717 Tpr1g3892 Tpr7g0218 . . . Tsu07g00244 . . . . . . . . . . Vra6g2014 .
Vvi18g1282 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g03443 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa5g0036 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1283 . . . . . . . . . . . . . . . . . . . Apr5g1672 . . . . . . . . . Car05g03282 . Cca07g00250 . . . . . . . . Gma04g00213 . . . Gso4g0200 . . . . Lal17g0054 . . . . . . . . . . . . Lasa5g04561 . . . . . . . . . . . . Mal2g0463 Mepo3g07835 . Mesa9g05518 . . . . Mtr3g4286 . . Phco7g00264 . . . . . . . . Pte1g02674 . . . . Pvu9g0189 . Rops10g02486 . Seca4g00389 . . . . . Sto5g0112 . . Tpr7g0216 Trre5g05702 . . Tsu07g00243 Vian4g02410 . Vifa2g04527 . . . Viun9g03696 . Vivi3g00639 . . .
Vvi18g1284 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma16g01161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0111 . . . . . . . . . . . . . . . . . . .
Vvi18g1285 . . . . . . . Aed9g0206 Aev08g0182 . Ahy17g2238 . Aip07g02396 . . . Amo17g2107 . . Apr5g1674 . . . . . . Bva06g01884 Bva10g00948 . Car05g03283 . Cca07g00249 . . . . . . . . Gma04g00210 Gma06g00195 . . . . . . . . Lal21g0107 . . . . . . . . . . . . . . . . . . . . . Lja1g3483 . . Mal2g0460 . . . . . . . Mtr3g4291 . . . . . . . Psa5g0263 . . . . . . . . . . . . . . . . . . . Sto9g3718 . Tpr7g0209 . . . Tsu07g00242 . . . . . . . . . . . Vra5g1672
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Ahy Ahy17g2245 Chr17 108974704 108978882 -
Aip Aip07g02404 Chr07 101173601 101177764 -
Amo Amo17g2114 Chr17 109694498 109698660 -
Dod Dod08g2293 Chr08 50971860 50978235 +
Vvi Vvi18g1276 Chr18 12783608 12784580 +
Bva Bva06g01890 Chr06 12907197 12908825 -
Bva Bva10g00944 Chr10 7048747 7051181 +
Sto Sto5g0118 Chr5 683354 684307 -
Vvi Vvi18g1277 Chr18 12787292 12809711 +
Acco Acco10g1310 Chr10 26959571 26964535 +
Accr Accr4g01452 Chr4 14633947 14638059 -
Adu Adu08g00170 Chr08 2621927 2625925 +
Aed Aed9g0210 Chr9 1489551 1494036 -
Aev Aev07g0673 Chr07 4264195 4269541 -
Ahy Ahy17g2245 Chr17 108974704 108978882 -
Ahy Ahy16g0047 Chr16 426205 431576 -
Aip Aip07g02404 Chr07 101173601 101177764 -
Aip Aip06g00040 Chr06 324107 329288 -
Alju Alju08g1503 Chr08 11735409 11740410 -
Amo Amo17g2114 Chr17 109694498 109698660 -
Apr Apr5g1668 Chr5 20266992 20272802 +
Arst Arst8g00204 Chr8 2634150 2638114 +
Bach Bach12g00074 Chr12 545530 549887 -
Bisa Bisa09g2073 Chr09 33156048 33162632 +
Bva Bva06g01889 Chr06 12899165 12903745 -
Bva Bva10g00945 Chr10 7052931 7057670 +
Car Car05g03280 Chr05 77524479 77529914 +
Cca Cca07g00254 Chr07 3203620 3221005 -
Dod Dod08g2293 Chr08 50971860 50978235 +
Dod Dod08g2293 Chr08 50971860 50978235 +
Enph Enph1g1040 Chr1 36605209 36610779 -
Glsi Glsi08g2057 Chr08 14413959 14418020 +
Gma Gma04g00218 Chr04 1854589 1860275 -
Gma Gma06g00199 Chr06 1747261 1755928 -
Gma Gma14g02150 Chr14 52639855 52642006 +
Gma Gma17g02476 Chr17 42793688 42802300 +
Gso Gso4g0202 Chr4 1823824 1829542 -
Gso Gso4g0202 Chr4 1823824 1829542 -
Gso Gso4g0202 Chr4 1823824 1829542 -
Gso Gso4g0202 Chr4 1823824 1829542 -
Lapu Lapu9g02305 Chr9 37671423 37679361 +
Lasa Lasa5g04554 Chr5 673292155 673298946 -
Lele Lele01g1175 Chr01 6999030 7003466 -
Lele Lele02g1442 Chr02 18691502 18695355 -
Lele Lele03g1190 Chr03 6973599 6978072 -
Lele Lele04g1424 Chr04 19551137 19554556 -
Lja Lja1g3487 Chr1 43471068 43476505 -
Mal Mal2g0467 Chr2 5371313 5375990 -
Mepo Mepo3g07838 Chr3 91463835 91469198 -
Mesa Mesa9g05515 Chr9 90539582 90544454 +
Mibi Mibi05g1393 Chr05 16579365 16585243 -
Mtr Mtr3g4282 Chr3 56681354 56686814 +
Phco Phco7g00269 Chr7 1879518 1886471 -
Prci Prci8g0732 Chr8 4697866 4707213 -
Pte Pte3g01431 Chr3 12541914 12548135 -
Pte Pte1g02676 Chr1 46915591 46919457 -
Pvu Pvu9g0185 Chr9 3198738 3206425 +
Spst Spst9g00265 Chr9 2506702 2515004 -
Sto Sto5g0117 Chr5 676440 681313 -
Sto Sto9g3715 Chr9 35443187 35447453 +
Tpr Tpr7g0220 Chr7 1807876 1814038 -
Trre Trre5g05699 Chr5 57055099 57060627 +
Tsu Tsu07g00246 Chr07 1898672 1905365 -
Vimu Vimu10g03505 Chr10 44680432 44685807 +
Vivi Vivi3g00634 Chr3 10618355 10624347 -
Vra Vra5g1667 Chr5 23041794 23047090 +
Vvi Vvi18g1278 Chr18 12821158 12822813 +
Aev Aev07g0672 Chr07 4254947 4259424 -
Ahy Ahy16g0046 Chr16 409516 421639 -
Aip Aip06g00039 Chr06 289309 319326 -
Apr Apr9g0651 Chr9 10572416 10579449 +
Bva Bva06g01888 Chr06 12895071 12897485 -
Car Car04g03598 Chr04 65236789 65239807 +
Cca Cca05g00388 Chr05 8478213 8483413 +
Cca Cca07g00253 Chr07 3186740 3193674 -
Dod Dod08g2296 Chr08 51008269 51013779 +
Gma Gma06g00197 Chr06 1717334 1727970 -
Gma Gma16g01167 Chr16 28907520 28909867 -
Lal Lal4g0060 Chr4 340790 344156 -
Lan Lan14g0958 Chr14 15953654 15956972 +
Lja Lja1g3486 Chr1 43464580 43468563 -
Lja Lja5g3336 Chr5 64802783 64808999 -
Mal Mal1g6115 Chr1 140099211 140101550 +
Mtr Mtr1g0734 Chr1 8318062 8322440 +
Sto Sto5g0115 Chr5 659941 663794 -
Tpr Tpr1g3889 Chr1 43028469 43030601 +
Tsu Tsu01g00180 Chr01 1409216 1415000 -
Vra Vra6g2018 Chr6 36780986 36783617 -
Vra Vra5g1668 Chr5 23054463 23058077 +
Vvi Vvi18g1279 Chr18 12823491 12840392 +
Aev Aev08g0186 Chr08 1033689 1036524 -
Aev Aev07g0671 Chr07 4229277 4246328 -
Ahy Ahy17g2242 Chr17 108891752 108895465 -
Ahy Ahy16g0044 Chr16 383388 393072 -
Aip Aip07g02400 Chr07 101102222 101105056 -
Aip Aip06g00038 Chr06 283931 286452 -
Amo Amo17g2111 Chr17 109612427 109616029 -
Apr Apr9g0652 Chr9 10597023 10600876 +
Apr Apr5g1669 Chr5 20278171 20281555 +
Bva Bva10g00946 Chr10 7061787 7064206 +
Car Car04g03600 Chr04 65328243 65330059 +
Car Car05g03281 Chr05 77537476 77543076 +
Cca Cca05g00389 Chr05 8488181 8495607 +
Dod Dod08g2298 Chr08 51034655 51041178 +
Dod Dod08g2298 Chr08 51034655 51041178 +
Gma Gma04g00215 Chr04 1824433 1828345 -
Gma Gma14g02151 Chr14 52651994 52661114 +
Gma Gma17g02477 Chr17 42810631 42815771 +
Lja Lja1g3485 Chr1 43452276 43457204 -
Mal Mal2g0466 Chr2 5355972 5360985 -
Mtr Mtr3g4283 Chr3 56694827 56700249 +
Sto Sto9g3716 Chr9 35454109 35458001 +
Tpr Tpr7g0219 Chr7 1794961 1798040 -
Tsu Tsu07g00245 Chr07 1890826 1894517 -
Vra Vra6g2017 Chr6 36775092 36778393 -
Vvi Vvi18g1280 Chr18 12859184 12861492 +
Apr Apr9g0653 Chr9 10601829 10605256 +
Apr Apr5g1670 Chr5 20291835 20295071 +
Bva Bva06g01887 Chr06 12888069 12890769 -
Car Car04g03601 Chr04 65356262 65375720 +
Cca Cca05g00390 Chr05 8525935 8530837 +
Gma Gma16g01164 Chr16 28879961 28881933 -
Gma Gma17g02478 Chr17 42824382 42829475 +
Lal Lal17g0055 Chr17 323590 325401 -
Lja Lja5g3337 Chr5 64823405 64848621 +
Mal Mal1g6118 Chr1 140145190 140148164 +
Mtr Mtr1g0735 Chr1 8336879 8338903 +
Sto Sto5g0114 Chr5 651505 655089 -
Tpr Tpr1g3890 Chr1 43035302 43041440 +
Tsu Tsu01g00179 Chr01 1379282 1383285 -
Vra Vra6g2016 Chr6 36771579 36773580 -
Vvi Vvi18g1281 Chr18 12863066 12871404 +
Aed Aed11g0032 Chr11 204769 206145 -
Aev Aev08g0183 Chr08 1024312 1026070 -
Aev Aev07g0669 Chr07 4225557 4227883 -
Ahy Ahy17g2239 Chr17 108310511 108314690 -
Ahy Ahy16g0043 Chr16 379571 381449 -
Aip Aip07g02397 Chr07 100584541 100588036 -
Aip Aip06g00037 Chr06 281060 282600 -
Apr Apr9g0654 Chr9 10661570 10666970 +
Apr Apr5g1671 Chr5 20301702 20304367 +
Bva Bva10g00947 Chr10 7068325 7069855 +
Cca Cca05g00395 Chr05 8695260 8696848 +
Dod Dod08g2299 Chr08 51054351 51057313 +
Dod Dod08g2299 Chr08 51054351 51057313 +
Gma Gma04g00214 Chr04 1819136 1821089 -
Gma Gma14g02153 Chr14 52686967 52691875 +
Gma Gma17g02479 Chr17 42847944 42852721 +
Lja Lja1g3484 Chr1 43438781 43443168 -
Mal Mal1g6120 Chr1 140162558 140167738 +
Mal Mal2g0464 Chr2 5233402 5240612 -
Mtr Mtr1g0736 Chr1 8352518 8357466 +
Mtr Mtr3g4285 Chr3 56715340 56718563 +
Ssu Ssu5g0043 Chr5 714025 746812 -
Sto Sto9g3717 Chr9 35467477 35472539 +
Tpr Tpr1g3892 Chr1 43050785 43056251 +
Tpr Tpr7g0218 Chr7 1786738 1790335 -
Tsu Tsu07g00244 Chr07 1876271 1880502 -
Vra Vra6g2014 Chr6 36759739 36761199 -
Vvi Vvi18g1282 Chr18 12887635 12890053 -
Car Car05g03443 Chr05 78924798 78927134 -
Psa Psa5g0036 Chr5 2066578 2069162 -
Vvi Vvi18g1283 Chr18 12893775 12898329 +
Apr Apr5g1672 Chr5 20305221 20307356 +
Car Car05g03282 Chr05 77556397 77559143 +
Cca Cca07g00250 Chr07 3168691 3170846 -
Gma Gma04g00213 Chr04 1814811 1817248 -
Gso Gso4g0200 Chr4 1785137 1787717 -
Lal Lal17g0054 Chr17 319356 322948 -
Lasa Lasa5g04561 Chr5 674317485 674319443 +
Mal Mal2g0463 Chr2 5228162 5231542 -
Mepo Mepo3g07835 Chr3 91435617 91438744 -
Mesa Mesa9g05518 Chr9 90586966 90588827 +
Mtr Mtr3g4286 Chr3 56725039 56727822 +
Phco Phco7g00264 Chr7 1839685 1841569 -
Pte Pte1g02674 Chr1 46902941 46906371 -
Pvu Pvu9g0189 Chr9 3355958 3357899 +
Rops Rops10g02486 Chr10 43411865 43414365 +
Seca Seca4g00389 Chr4 6359900 6363183 -
Sto Sto5g0112 Chr5 647065 649551 -
Tpr Tpr7g0216 Chr7 1778413 1783821 -
Trre Trre5g05702 Chr5 57092329 57095053 +
Tsu Tsu07g00243 Chr07 1865222 1868082 -
Vian Vian4g02410 Chr4 40762393 40764282 +
Vifa Vifa2g04527 Chr2 1331872017 1331874291 +
Viun Viun9g03696 Chr9 42172457 42174512 +
Vivi Vivi3g00639 Chr3 10796509 10799366 +
Vvi Vvi18g1284 Chr18 12901041 12904645 +
Gma Gma16g01161 Chr16 28844160 28845799 -
Sto Sto5g0111 Chr5 644401 645028 -
Vvi Vvi18g1285 Chr18 12908878 12912467 -
Aed Aed9g0206 Chr9 1454497 1457746 +
Aev Aev08g0182 Chr08 1019505 1023301 +
Ahy Ahy17g2238 Chr17 108303431 108310583 +
Aip Aip07g02396 Chr07 100578777 100584329 +
Amo Amo17g2107 Chr17 108978939 108986735 +
Apr Apr5g1674 Chr5 20316862 20321925 -
Bva Bva06g01884 Chr06 12876509 12879667 +
Bva Bva10g00948 Chr10 7070302 7073635 -
Car Car05g03283 Chr05 77571616 77575869 -
Cca Cca07g00249 Chr07 3161779 3166971 +
Gma Gma04g00210 Chr04 1783405 1787422 +
Gma Gma06g00195 Chr06 1699307 1706281 +
Lal Lal21g0107 Chr21 730181 737190 +
Lja Lja1g3483 Chr1 43428777 43438520 +
Mal Mal2g0460 Chr2 5209642 5214124 +
Mtr Mtr3g4291 Chr3 56851304 56855607 -
Psa Psa5g0263 Chr5 19470356 19473561 -
Sto Sto9g3718 Chr9 35476028 35478583 -
Tpr Tpr7g0209 Chr7 1734404 1737938 +
Tsu Tsu07g00242 Chr07 1811636 1864838 +
Vra Vra5g1672 Chr5 23079980 23083432 -