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
Vvi2g0492 . . . . . . Aed11g1676 . Aev05g0928 . Ahy15g0924 . Aip05g00950 . . . . . Apr7g0636 . . . . . . . Bva08g00239 Bva11g02054 Car08g00254 . Cca06g01749 . . . Dod02g1041 . . . . . Gma01g02153 Gma11g00251 . . Gso1g1822 Gso1g1822 . . Lal15g0287 . . . . . Lan18g0881 . . . . . . . . . . . . . . . . . Lja2g0039 . Mal6g1653 . . . . . . . Mtr5g0344 . . . . . . . Psa2g4121 . . . . . . . . . . . . . . . . . Ssu2g2804 . . . Tpr2g3829 . . . Tsu05g00322 . . . . . . . . . . . Vra11g0325 .
Vvi2g0493 . . . Accr6g00918 . . . . . . . . . . . Alju05g1185 . . . Apr10g1425 . . . Bach6g00778 . Bisa06g1102 . . . . . . . Dere11g0940 . . . Enph10g0007 . Glsi07g0997 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lele38g0650 . . . . . . . . . . . Mibi04g1125 . . . Phac10g01009 . Phco1g00905 . Prci12g1398 . . . . . . . . . Pumo7g00980 . Pvu10g0910 . Rops4g01355 . . . Spst4g01719 . . . . . . . . . . . Vian9g00775 . . . Vimu9g00473 . Viun10g01709 . Vivi7g04608 . .
Vvi2g0494 . . . . . . . . . . . . . . . . . . . Apr10g1426 . . . Bach6g00779 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa4g01044 . . . . . . . . . . . . . Mepo1g03602 . Mesa29g04138 . . . . . Phac10g01005 . Phco1g00906 . . . . . Pste6g02313 . . Pte1g00731 . . Pumo7g00982 . Pvu10g0908 . Rops4g01354 . Seca4g11157 . Spst4g01718 . . . . . . . . . . . Vian9g00777 . Vifa4g00704 . Vimu9g00476 . Viun10g01708 . Vivi7g04610 . .
Vvi2g0495 . . . . Adu05g00956 . Aed11g1674 . . . . . . . . . . . Apr7g0637 . Arst5g01184 . Bach4g00202 . . . Bva08g00240 Bva11g02053 Car08g00255 . Cca06g01748 . . . . . . . . . Gma01g02152 Gma11g00254 . . Gso1g1820 Gso1g1820 . . . . . Lal15g1367 . . . . . . . . Lapu2g00307 . . . . . . . . . . . Lja2g0040 . . . . . . . . . . . . . Phco4g00371 . . . . . Pste1g00653 . . . . . Pumo8g02258 . Pvu2g1572 . Rops1g02125 . Seca10g00400 . Spst2g00361 . Ssu2g2801 . . . . . . . . . Vian10g00319 . . . Vimu7g02500 . Viun2g02506 . . . Vra11g0326 .
Vvi2g0496 . . . . . Adu01g01581 . Aed6g0466 . . . . . . . . . . . Apr10g1530 . Arst1g02091 . . . . Bva08g00241 . . . . Cca11g01685 . . . . . . . . . . . Gma17g01239 . . . . . . . . . . . . . . . . . Lapu3g01261 . . . . . . . . . . . Lja4g2465 . Mal5g3938 . . . . . . . Mtr4g3658 . . . Phco8g00687 . . . . . . . . . . . Pumo4g01585 . Pvu3g2206 . Rops2g04191 . . . Spst3g04386 . Ssu6g1540 Sto6g3308 . . Tpr5g2711 . . . Tsu04g02464 . Vian1g01334 . . . Vimu7g00474 . Viun3g04250 . Vivi1g02357 . Vra7g1453
Vvi2g0497 . . . . . . . Aed6g0468 Aev05g0926 . Ahy15g0925 . Aip05g00951 . . . . . . . . . . . . . . . . Car07g01182 . Cca11g01684 . . Dod02g1035 . . . . . . . Gma05g00487 Gma17g01240 . . . . . . . Lal15g1366 . . . . . . . . . . . . . . . . . . . . . . Mal6g1652 . . . . . . . Mtr5g0345 . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu6g1542 . . . . . . . . . . . . . . . . . . . Vra7g1452
Vvi2g0498 . . . . . . . . . . . . . . . . . . Apr7g0638 Apr10g1531 . . . . . . . . Car08g00256 . . . . . . . . . . . . Gma11g00255 Gma05g00488 Gma17g01241 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g0041 Lja4g2466 Mal6g1651 . . . . . . . Mtr5g0346 . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3309 . Tpr2g3828 . . . Tsu05g00323 . . . . . . . . . . . . .
Vvi2g0499 . . . . . . Aed11g1673 . . . Ahy15g0926 . Aip05g00955 . . . . . . . . . . . . . . . . . Cca06g01747 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr5g0347 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu2g2800 . . . . . . . . . . . . . . . . . . . Vra11g0327 .
Vvi2g0500 . . . . . . . . . . . . . . . . . . Apr7g0639 . . . . . . . . . Car08g00257 . . . . . . . . . . . Gma01g02151 Gma11g00256 . . Gso1g1819 Gso1g1819 . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g0042 Lja4g2467 Mal6g1649 . . . . . . . Mtr5g0348 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr2g3826 . . . Tsu05g00324 . . . . . . . . . . . . .
Vvi2g0501 . . . . . . Aed11g1671 . Aev05g0924 . Ahy15g0936 . Aip05g00962 . . . . . . . . . . . . . . . Car08g00258 . Cca06g01746 . . . . . . . . . Gma01g02150 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g0043 . . . . . . . . . Mtr5g0349 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu2g2799 . . . . . . . . . . . . . . . . . . . Vra11g0328 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0492 Chr2 4282539 4283777 +
Aed Aed11g1676 Chr11 20510595 20512081 -
Aev Aev05g0928 Chr05 6535448 6537057 -
Ahy Ahy15g0924 Chr15 13644763 13646336 +
Aip Aip05g00950 Chr05 13199688 13201241 +
Apr Apr7g0636 Chr7 13067964 13070468 +
Bva Bva08g00239 Chr08 1151972 1153295 +
Bva Bva11g02054 Chr11 17232778 17234149 -
Car Car08g00254 Chr08 2059120 2060548 +
Cca Cca06g01749 Chr06 32779245 32781094 -
Dod Dod02g1041 Chr02 13037239 13040425 -
Gma Gma01g02153 Chr01 56840269 56842095 -
Gma Gma11g00251 Chr11 2011997 2013133 +
Gso Gso1g1822 Chr1 55016060 55018139 -
Gso Gso1g1822 Chr1 55016060 55018139 -
Lal Lal15g0287 Chr15 1935578 1937236 -
Lan Lan18g0881 Chr18 14128050 14145940 +
Lja Lja2g0039 Chr2 332895 336107 +
Mal Mal6g1653 Chr6 30546367 30548932 -
Mtr Mtr5g0344 Chr5 3212562 3215158 +
Psa Psa2g4121 Chr2 419687379 419690200 -
Ssu Ssu2g2804 Chr2 88934099 88936988 -
Tpr Tpr2g3829 Chr2 41073246 41075468 -
Tsu Tsu05g00322 Chr05 2408084 2412029 +
Vra Vra11g0325 Chr11 2341527 2342917 +
Vvi Vvi2g0493 Chr2 4287706 4290381 +
Accr Accr6g00918 Chr6 20221925 20222428 -
Alju Alju05g1185 Chr05 37824453 37843024 +
Apr Apr10g1425 Chr10 26582539 26584871 -
Bach Bach6g00778 Chr6 5760725 5761776 -
Bisa Bisa06g1102 Chr06 39313130 39314403 +
Dere Dere11g0940 Chr11 17907668 17908971 +
Enph Enph10g0007 Chr10 621575 626308 +
Glsi Glsi07g0997 Chr07 11591083 11591592 +
Lele Lele38g0650 Chr38 6314154 6324346 -
Mibi Mibi04g1125 Chr04 24405771 24408026 -
Phac Phac10g01009 Chr10 31031115 31033543 +
Phco Phco1g00905 Chr1 8971862 8974259 -
Prci Prci12g1398 Chr12 29753828 29754362 +
Pumo Pumo7g00980 Chr7 18008074 18014401 -
Pvu Pvu10g0910 Chr10 32614556 32617168 +
Rops Rops4g01355 Chr4 35229908 35232636 +
Spst Spst4g01719 Chr4 57120863 57123119 +
Vian Vian9g00775 Chr9 10665410 10667120 -
Vimu Vimu9g00473 Chr9 5651256 5652978 -
Viun Viun10g01709 Chr10 32172745 32176181 +
Vivi Vivi7g04608 Chr7 117821362 117823624 -
Vvi Vvi2g0494 Chr2 4296586 4298704 -
Apr Apr10g1426 Chr10 26588348 26593404 -
Bach Bach6g00779 Chr6 5765980 5767214 -
Lasa Lasa4g01044 Chr4 61993683 62019707 -
Mepo Mepo1g03602 Chr1 41875635 41877326 +
Mesa Mesa29g04138 Chr29 67730388 67731836 +
Phac Phac10g01005 Chr10 30974642 30978187 -
Phco Phco1g00906 Chr1 8981982 8987232 -
Pste Pste6g02313 Chr6 11192340 11215242 -
Pte Pte1g00731 Chr1 10185946 10189768 +
Pumo Pumo7g00982 Chr7 18022624 18024911 -
Pvu Pvu10g0908 Chr10 32493029 32495477 +
Rops Rops4g01354 Chr4 35215171 35218227 -
Seca Seca4g11157 Chr4 250015701 250023263 +
Spst Spst4g01718 Chr4 57114361 57117366 +
Vian Vian9g00777 Chr9 10690331 10691810 -
Vifa Vifa4g00704 Chr4 204763315 204764360 -
Vimu Vimu9g00476 Chr9 5669694 5673851 -
Viun Viun10g01708 Chr10 32160905 32166837 -
Vivi Vivi7g04610 Chr7 117846115 117847434 -
Vvi Vvi2g0495 Chr2 4309326 4311950 +
Adu Adu05g00956 Chr05 12220489 12224223 +
Aed Aed11g1674 Chr11 20500517 20502983 -
Apr Apr7g0637 Chr7 13072632 13076692 +
Arst Arst5g01184 Chr5 12264133 12267896 +
Bach Bach4g00202 Chr4 1334973 1338152 +
Bva Bva08g00240 Chr08 1158599 1161684 +
Bva Bva11g02053 Chr11 17228515 17232109 -
Car Car08g00255 Chr08 2061096 2064648 +
Cca Cca06g01748 Chr06 32766895 32771188 -
Gma Gma01g02152 Chr01 56823521 56827878 -
Gma Gma11g00254 Chr11 2019542 2024646 +
Gso Gso1g1820 Chr1 54999968 55004412 -
Gso Gso1g1820 Chr1 54999968 55004412 -
Lal Lal15g1367 Chr15 15798439 15803046 -
Lapu Lapu2g00307 Chr2 2520748 2523152 +
Lja Lja2g0040 Chr2 338648 343703 +
Phco Phco4g00371 Chr4 2430033 2433564 +
Pste Pste1g00653 Chr1 2067629 2068500 +
Pumo Pumo8g02258 Chr8 59708381 59712384 -
Pvu Pvu2g1572 Chr2 29349475 29353426 -
Rops Rops1g02125 Chr1 42500182 42504245 -
Seca Seca10g00400 Chr10 3498879 3499871 +
Spst Spst2g00361 Chr2 2835133 2836186 +
Ssu Ssu2g2801 Chr2 88910791 88914047 -
Vian Vian10g00319 Chr10 2910422 2913014 +
Vimu Vimu7g02500 Chr7 21344134 21346700 +
Viun Viun2g02506 Chr2 31418031 31422052 -
Vra Vra11g0326 Chr11 2344858 2349055 +
Vvi Vvi2g0496 Chr2 4323610 4327289 +
Adu Adu01g01581 Chr01 48437398 48439033 -
Aed Aed6g0466 Chr6 4054557 4060047 +
Apr Apr10g1530 Chr10 27753659 27755380 +
Arst Arst1g02091 Chr1 48933048 48934407 -
Bva Bva08g00241 Chr08 1162204 1163939 +
Cca Cca11g01685 Chr11 41137305 41139003 -
Gma Gma17g01239 Chr17 10938392 10939939 +
Lapu Lapu3g01261 Chr3 13651454 13654007 +
Lja Lja4g2465 Chr4 28820388 28822457 +
Mal Mal5g3938 Chr5 108873667 108874812 -
Mtr Mtr4g3658 Chr4 50363528 50367243 -
Phco Phco8g00687 Chr8 6916599 6917638 +
Pumo Pumo4g01585 Chr4 20085620 20087173 +
Pvu Pvu3g2206 Chr3 42951492 42952906 +
Rops Rops2g04191 Chr2 76305282 76306755 +
Spst Spst3g04386 Chr3 95489572 95490617 -
Ssu Ssu6g1540 Chr6 25306129 25307251 +
Sto Sto6g3308 Chr6 39300766 39303514 +
Tpr Tpr5g2711 Chr5 49285809 49288370 -
Tsu Tsu04g02464 Chr04 27812892 27814797 -
Vian Vian1g01334 Chr1 14475453 14476484 +
Vimu Vimu7g00474 Chr7 5025382 5026414 -
Viun Viun3g04250 Chr3 50197483 50198885 -
Vivi Vivi1g02357 Chr1 49824141 49825912 +
Vra Vra7g1453 Chr7 31805507 31806864 -
Vvi Vvi2g0497 Chr2 4329210 4331174 -
Aed Aed6g0468 Chr6 4062214 4064142 -
Aev Aev05g0926 Chr05 6525584 6528060 -
Ahy Ahy15g0925 Chr15 13648218 13652040 +
Aip Aip05g00951 Chr05 13204413 13211100 +
Car Car07g01182 Chr07 10608959 10611500 -
Cca Cca11g01684 Chr11 41131818 41134133 +
Dod Dod02g1035 Chr02 13009694 13012161 -
Gma Gma05g00487 Chr05 4624231 4626480 -
Gma Gma17g01240 Chr17 10943415 10945664 -
Lal Lal15g1366 Chr15 15786120 15788366 +
Mal Mal6g1652 Chr6 30540088 30542355 +
Mtr Mtr5g0345 Chr5 3217059 3219323 -
Ssu Ssu6g1542 Chr6 25309390 25310967 -
Vra Vra7g1452 Chr7 31800907 31803500 +
Vvi Vvi2g0498 Chr2 4332608 4334560 -
Apr Apr7g0638 Chr7 13109681 13111975 -
Apr Apr10g1531 Chr10 27756899 27759359 -
Car Car08g00256 Chr08 2065571 2067253 -
Gma Gma11g00255 Chr11 2026461 2028737 -
Gma Gma05g00488 Chr05 4642111 4644770 -
Gma Gma17g01241 Chr17 10949970 10952347 -
Lja Lja2g0041 Chr2 344835 347338 -
Lja Lja4g2466 Chr4 28822658 28825010 -
Mal Mal6g1651 Chr6 30529821 30532153 +
Mtr Mtr5g0346 Chr5 3223016 3225298 -
Sto Sto6g3309 Chr6 39304528 39311447 -
Tpr Tpr2g3828 Chr2 41065781 41072368 +
Tsu Tsu05g00323 Chr05 2412710 2414965 -
Vvi Vvi2g0499 Chr2 4337077 4339299 -
Aed Aed11g1673 Chr11 20497623 20499083 +
Ahy Ahy15g0926 Chr15 13652631 13655912 +
Aip Aip05g00955 Chr05 13238218 13246834 +
Cca Cca06g01747 Chr06 32761029 32763967 +
Mtr Mtr5g0347 Chr5 3230823 3233576 -
Ssu Ssu2g2800 Chr2 88905858 88908176 +
Vra Vra11g0327 Chr11 2350997 2353707 -
Vvi Vvi2g0500 Chr2 4341153 4343387 -
Apr Apr7g0639 Chr7 13122262 13124499 -
Car Car08g00257 Chr08 2069706 2071388 -
Gma Gma01g02151 Chr01 56819785 56822233 +
Gma Gma11g00256 Chr11 2030526 2032772 -
Gso Gso1g1819 Chr1 54990060 54992630 +
Gso Gso1g1819 Chr1 54990060 54992630 +
Lja Lja2g0042 Chr2 350097 352349 -
Lja Lja4g2467 Chr4 28829915 28832752 -
Mal Mal6g1649 Chr6 30522391 30524718 +
Mtr Mtr5g0348 Chr5 3235637 3238228 -
Tpr Tpr2g3826 Chr2 41060716 41063098 +
Tsu Tsu05g00324 Chr05 2416372 2418645 -
Vvi Vvi2g0501 Chr2 4354053 4355792 -
Aed Aed11g1671 Chr11 20493584 20495053 +
Aev Aev05g0924 Chr05 6518753 6521053 +
Ahy Ahy15g0936 Chr15 13952112 13954388 -
Aip Aip05g00962 Chr05 13471176 13473650 -
Car Car08g00258 Chr08 2075645 2078016 -
Cca Cca06g01746 Chr06 32754995 32757734 +
Gma Gma01g02150 Chr01 56813661 56815904 +
Lja Lja2g0043 Chr2 356320 358534 -
Mtr Mtr5g0349 Chr5 3241008 3243254 -
Ssu Ssu2g2799 Chr2 88894613 88901466 +
Vra Vra11g0328 Chr11 2357566 2359811 -
Apr Apr10g1426 Chr10 26588348 26593404 -