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
Vvi4g1404 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1405 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1406 . Acco04g2092 . Accr8g00649 Adu10g01727 Adu03g03095 Aed5g2092 . Aev03g2879 Aev08g0615 Ahy13g3104 Ahy20g1960 Aip03g03520 Aip10g02303 . Alju06g2072 . Amo20g2489 Apr1g0490 . Arst3g04061 Arst3g04061 . Bach2g00045 . Bisa08g2497 . . . . Cca09g02227 . . Dere03g0330 Dod04g2500 Dod09g1775 . Enph6g0286 . Glsi02g0310 . . . . . . . . Lal21g0650 Lal4g0610 Lal17g0707 . . . . . . . . . Lapu9g01164 Lapu3g03403 Lasa5g03292 . . . . . Lele21g1474 Lele22g1463 Lele23g0538 Lele24g1415 Lja1g4546 Lja4g0634 Mal2g1559 . Mepo3g06786 . Mesa9g04303 . . Mibi09g0650 Mtr3g3308 . . . Phco7g01680 Phco4g03045 . . Psa5g1506 . Pste2g03681 Pste3g01669 Pte3g00050 Pte1g02121 Pte2g02614 Pte3g00050 Pumo10g01625 Pumo6g00709 Pvu9g1517 Pvu2g2764 Rops10g02328 Rops2g00818 Seca4g02018 . Spst9g01691 Spst3g01351 Ssu5g2823 . Sto3g3151 Sto4g0327 Tpr3g3106 . Trre5g04244 . Tsu07g01362 . . Vian1g03630 Vifa2g03128 Vifa2g03128 Vimu10g01802 Vimu11g04136 Viun9g01844 Viun3g00895 Vivi3g02512 . . .
Vvi4g1407 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1408 . . . . Adu10g01728 . . . . Aev08g0614 . Ahy20g1961 . Aip10g02304 . . . . Apr1g0489 . Arst10g02218 . . . . . Bva05g01598 . . . . . . . . Dod09g1776 . . . . . . . . . . . . . . Lal17g0708 . . . . . . . . . Lapu9g01163 . Lasa5g03294 . . . . . . . . . Lja1g4545 . Mal2g1558 . Mepo3g06789 . Mesa9g04306 . . . Mtr3g3309 . . . Phco7g01681 . . . . . Pste2g03682 . Pte3g00051 . . . Pumo10g01626 . Pvu9g1518 . . . Seca4g02013 . Spst9g01693 . . . Sto3g3153 . Tpr3g3107 . Trre5g04246 . Tsu07g01361 . . . Vifa2g03132 . Vimu10g01801 . Viun9g01842 . Vivi3g02510 . . .
Vvi4g1409 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1410 . . . . Adu10g01729 . . . Aev03g2880 Aev08g0612 Ahy13g3102 Ahy20g1962 Aip03g03513 Aip10g02305 . Alju03g0700 . Amo20g2490 Apr1g0487 . Arst3g04059 . . . . Bisa07g0502 Bva05g01597 . . . Cca09g02229 . . Dere02g2432 Dod04g2502 Dod09g1777 . . . Glsi11g2743 . . . . . . . . Lal21g0651 Lal4g0612 Lal17g0709 . . . Lan3g0725 Lan3g0725 Lan3g0725 . . . Lapu9g01162 . . . . . . . . . . . Lja1g4542 Lja4g0633 Mal2g1551 Mal7g4694 Mepo3g06790 . . . . . Mtr3g3313 Mtr8g3240 . . Phco7g01683 Phco4g02347 . Prci3g0483 . . Pste2g03683 . . . . Pte19g00746 Pumo10g01627 . Pvu9g1519 Pvu2g2105 Rops10g02333 . . . . . Ssu5g2824 . Sto3g3154 Sto4g0326 . Tpr3g0858 . . . Tsu02g00699 Vian4g01109 . . . Vimu10g01800 Vimu11g01352 Viun9g01838 . Vivi3g02509 . . .
Vvi4g1411 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1412 . . . . . . . . . . . . . . . . . . Apr3g2041 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Alju Alju03g0700 Chr03 30417690 30424449 +
Bisa Bisa07g0502 Chr07 12703871 12708765 -
Dere Dere02g2432 Chr02 26084420 26091298 +
Glsi Glsi11g2743 Chr11 20521678 20530954 +
Phco Phco4g02347 Chr4 44605418 44607512 -
Prci Prci3g0483 Chr3 6267154 6270673 +
Pte Pte19g00746 Chr19 5948842 5949791 -
Pvu Pvu2g2105 Chr2 36468883 36471341 -
Vimu Vimu11g01352 Chr11 15024684 15025150 +
Vvi Vvi4g1404 Chr4 20960509 20962850 -
Vvi Vvi4g1405 Chr4 20963960 20964181 +
Vvi Vvi4g1406 Chr4 20976206 20978154 +
Acco Acco04g2092 Chr04 36763837 36765863 +
Accr Accr8g00649 Chr8 10201551 10203579 -
Adu Adu10g01727 Chr10 79540444 79544388 +
Adu Adu03g03095 Chr03 115387457 115397064 -
Aed Aed5g2092 Chr5 23309110 23313004 +
Aev Aev03g2879 Chr03 28212860 28214728 +
Aev Aev08g0615 Chr08 3528812 3530911 -
Ahy Ahy13g3104 Chr13 125007420 125009790 -
Ahy Ahy20g1960 Chr20 109924524 109928061 +
Aip Aip03g03520 Chr03 114967374 114969865 -
Aip Aip10g02303 Chr10 103129109 103133103 +
Alju Alju06g2072 Chr06 46682050 46684080 +
Amo Amo20g2489 Chr20 116102330 116106234 +
Apr Apr1g0490 Chr1 5986372 5989976 -
Arst Arst3g04061 Chr3 114101410 114103803 -
Arst Arst3g04061 Chr3 114101410 114103803 -
Bach Bach2g00045 Chr2 552959 555424 -
Bisa Bisa08g2497 Chr08 58845469 58847442 -
Cca Cca09g02227 Chr09 47471556 47474111 +
Dere Dere03g0330 Chr03 6958091 6960387 +
Dod Dod04g2500 Chr04 48830022 48833170 +
Dod Dod09g1775 Chr09 39400167 39403871 +
Enph Enph6g0286 Chr6 6238332 6242471 +
Glsi Glsi02g0310 Chr02 2008663 2010648 +
Lal Lal21g0650 Chr21 4970222 4973481 -
Lal Lal4g0610 Chr4 4473640 4476967 -
Lal Lal17g0707 Chr17 4996202 5000646 -
Lapu Lapu9g01164 Chr9 25178271 25183428 -
Lapu Lapu3g03403 Chr3 57275749 57278225 +
Lasa Lasa5g03292 Chr5 551057142 551058981 +
Lele Lele21g1474 Chr21 23117785 23119722 +
Lele Lele22g1463 Chr22 20448178 20450152 +
Lele Lele23g0538 Chr23 3940120 3942080 -
Lele Lele24g1415 Chr24 20159534 20162336 +
Lja Lja1g4546 Chr1 59388209 59391264 -
Lja Lja4g0634 Chr4 5229309 5233173 -
Mal Mal2g1559 Chr2 18769713 18771611 -
Mepo Mepo3g06786 Chr3 81616050 81619058 +
Mesa Mesa9g04303 Chr9 76105134 76107020 +
Mibi Mibi09g0650 Chr09 8425800 8427796 -
Mtr Mtr3g3308 Chr3 47038573 47041397 +
Phco Phco7g01680 Chr7 16601839 16603704 +
Phco Phco4g03045 Chr4 51475445 51477308 +
Psa Psa5g1506 Chr5 115721597 115724268 -
Pste Pste2g03681 Chr2 40173335 40176596 +
Pste Pste3g01669 Chr3 10533243 10535267 -
Pte Pte3g00050 Chr3 671890 675208 +
Pte Pte1g02121 Chr1 42389289 42390646 -
Pte Pte2g02614 Chr2 45179850 45181899 -
Pte Pte3g00050 Chr3 671890 675208 +
Pumo Pumo10g01625 Chr10 21361086 21362862 +
Pumo Pumo6g00709 Chr6 8892790 8895679 -
Pvu Pvu9g1517 Chr9 21492168 21495174 +
Pvu Pvu2g2764 Chr2 43384681 43386969 +
Rops Rops10g02328 Chr10 41119835 41122453 +
Rops Rops2g00818 Chr2 11732033 11734589 -
Seca Seca4g02018 Chr4 34440135 34441110 -
Spst Spst9g01691 Chr9 17298266 17300150 +
Spst Spst3g01351 Chr3 16931033 16932422 -
Ssu Ssu5g2823 Chr5 74317809 74319271 +
Sto Sto3g3151 Chr3 36384886 36386674 +
Sto Sto4g0327 Chr4 2557606 2559562 -
Tpr Tpr3g3106 Chr3 34180798 34183780 +
Trre Trre5g04244 Chr5 44403434 44405433 +
Tsu Tsu07g01362 Chr07 11992590 11995712 -
Vian Vian1g03630 Chr1 59034934 59036800 +
Vifa Vifa2g03128 Chr2 899359725 899361608 +
Vifa Vifa2g03128 Chr2 899359725 899361608 +
Vimu Vimu10g01802 Chr10 25469120 25470995 -
Vimu Vimu11g04136 Chr11 63007834 63009967 +
Viun Viun9g01844 Chr9 28047386 28050568 -
Viun Viun3g00895 Chr3 5514229 5516232 -
Vivi Vivi3g02512 Chr3 42079656 42082505 -
Vvi Vvi4g1407 Chr4 20985266 20986192 +
Vvi Vvi4g1408 Chr4 20988399 20996526 -
Adu Adu10g01728 Chr10 79546257 79550165 -
Aev Aev08g0614 Chr08 3521042 3525189 +
Ahy Ahy20g1961 Chr20 109929984 109934854 -
Aip Aip10g02304 Chr10 103134789 103141667 -
Apr Apr1g0489 Chr1 5969035 5980307 +
Arst Arst10g02218 Chr10 78465487 78470342 -
Bva Bva05g01598 Chr05 13006917 13011312 +
Dod Dod09g1776 Chr09 39412440 39416961 -
Lal Lal17g0708 Chr17 5005168 5012160 -
Lapu Lapu9g01163 Chr9 25173029 25178220 +
Lasa Lasa5g03294 Chr5 551234288 551238494 -
Lja Lja1g4545 Chr1 59377112 59382756 +
Mal Mal2g1558 Chr2 18760540 18764801 +
Mepo Mepo3g06789 Chr3 81635547 81640737 -
Mesa Mesa9g04306 Chr9 76120656 76125561 -
Mtr Mtr3g3309 Chr3 47053761 47059033 -
Phco Phco7g01681 Chr7 16617059 16620335 -
Pste Pste2g03682 Chr2 40223409 40232195 -
Pte Pte3g00051 Chr3 677580 684115 -
Pumo Pumo10g01626 Chr10 21367413 21377325 -
Pvu Pvu9g1518 Chr9 21504669 21508342 -
Seca Seca4g02013 Chr4 34404439 34404651 +
Spst Spst9g01693 Chr9 17342712 17345644 -
Sto Sto3g3153 Chr3 36395897 36398927 -
Tpr Tpr3g3107 Chr3 34188293 34193629 -
Trre Trre5g04246 Chr5 44416400 44420877 -
Tsu Tsu07g01361 Chr07 11980923 11988058 +
Vifa Vifa2g03132 Chr2 899879695 899880096 -
Vimu Vimu10g01801 Chr10 25450535 25453795 +
Viun Viun9g01842 Chr9 28032006 28035740 +
Vivi Vivi3g02510 Chr3 42064785 42070404 +
Vvi Vvi4g1409 Chr4 21004227 21005979 -
Vvi Vvi4g1410 Chr4 21012656 21016175 +
Adu Adu10g01729 Chr10 79640317 79644049 +
Aev Aev03g2880 Chr03 28222613 28228240 +
Aev Aev08g0612 Chr08 3514409 3517405 -
Ahy Ahy13g3102 Chr13 124897801 124900619 -
Ahy Ahy20g1962 Chr20 110018481 110022752 +
Aip Aip03g03513 Chr03 114868776 114871223 -
Aip Aip10g02305 Chr10 103218650 103222813 +
Alju Alju03g0700 Chr03 30417690 30424449 +
Amo Amo20g2490 Chr20 116270156 116275001 +
Apr Apr1g0487 Chr1 5947515 5951110 -
Arst Arst3g04059 Chr3 114043887 114046198 -
Bisa Bisa07g0502 Chr07 12703871 12708765 -
Bva Bva05g01597 Chr05 13003058 13004863 -
Cca Cca09g02229 Chr09 47501715 47508762 +
Dere Dere02g2432 Chr02 26084420 26091298 +
Dod Dod04g2502 Chr04 48845766 48850323 +
Dod Dod09g1777 Chr09 39420933 39424874 +
Glsi Glsi11g2743 Chr11 20521678 20530954 +
Lal Lal21g0651 Chr21 4987840 4991882 +
Lal Lal4g0612 Chr4 4498253 4502634 +
Lal Lal17g0709 Chr17 5016503 5019614 +
Lan Lan3g0725 Chr3 13279223 13283907 -
Lan Lan3g0725 Chr3 13279223 13283907 -
Lan Lan3g0725 Chr3 13279223 13283907 -
Lapu Lapu9g01162 Chr9 25154772 25161518 -
Lja Lja1g4542 Chr1 59320415 59325768 -
Lja Lja4g0633 Chr4 5206305 5220973 -
Mal Mal2g1551 Chr2 18557809 18561030 -
Mal Mal7g4694 Chr7 115158820 115163129 +
Mepo Mepo3g06790 Chr3 81649384 81651854 +
Mtr Mtr3g3313 Chr3 47082986 47086470 +
Mtr Mtr8g3240 Chr8 42923733 42928897 +
Phco Phco7g01683 Chr7 16639593 16644666 +
Phco Phco4g02347 Chr4 44605418 44607512 -
Prci Prci3g0483 Chr3 6267154 6270673 +
Pste Pste2g03683 Chr2 40239805 40246217 +
Pte Pte19g00746 Chr19 5948842 5949791 -
Pumo Pumo10g01627 Chr10 21378759 21385446 +
Pvu Pvu9g1519 Chr9 21517316 21520296 +
Pvu Pvu2g2105 Chr2 36468883 36471341 -
Rops Rops10g02333 Chr10 41161491 41163850 +
Ssu Ssu5g2824 Chr5 74339248 74342228 +
Sto Sto3g3154 Chr3 36414112 36417648 +
Sto Sto4g0326 Chr4 2528505 2531640 -
Tpr Tpr3g0858 Chr3 8068882 8073102 -
Tsu Tsu02g00699 Chr02 5879141 5882363 -
Vian Vian4g01109 Chr4 17930004 17936519 -
Vimu Vimu10g01800 Chr10 25435366 25436974 -
Vimu Vimu11g01352 Chr11 15024684 15025150 +
Viun Viun9g01838 Chr9 27991606 28003624 -
Vivi Vivi3g02509 Chr3 42038232 42044407 -
Vvi Vvi4g1411 Chr4 21017599 21018612 -
Vvi Vvi4g1412 Chr4 21051496 21053877 +
Apr Apr3g2041 Chr3 36398254 36405879 +
Vvi Vvi4g1413 Chr4 21074524 21075093 +