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
Vvi1g1581 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1582 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva05g00105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto3g2525 . . . . . . . . . . . . . . . . . . .
Vvi1g1583 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal3g3086 . . . . . . . Mtr7g2281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr6g1050 . . . Tsu07g02885 . . . . . . . . . . . . .
Vvi1g1584 Acco04g2335 . Accr8g00421 . Adu03g02932 . . . . . . . . . Alju06g2299 . . . . . Arst3g03865 Arst3g03865 . Bach2g02319 Bisa08g1657 . Bva06g01677 . . . . . Dere03g0520 . . . Enph6g0434 . Glsi02g0479 . . . . . . . . . . . . . . . . . . . . . Lapu3g03506 Lapu9g00910 Lasa7g04626 Lasa5g03494 Lele21g1625 . Lele23g0386 . . . . . . Lja4g0504 . . Mepo2g04522 Mepo3g06939 Mesa13g00600 Mesa9g04472 Mibi09g0469 . . Mtr8g3376 Phac2g04233 . Phco4g03195 Phco7g01899 Prci4g2607 . . Psa7g0905 Pste3g01333 Pste2g00217 . Pte3g00114 Pte3g00114 . Pumo6g00579 Pumo10g01814 Pvu2g2890 Pvu9g1660 Rops2g00678 Rops10g00875 Seca12g06380 Seca4g01807 Spst3g01211 Spst9g01784 . . . . . Tpr3g0729 . Trre5g04757 . Tsu02g00556 Vian1g03748 . Vifa2g03356 Vifa2g03356 Vimu11g04295 . Viun3g00702 Viun9g01599 Vivi5g05724 Vivi3g02262 . .
Vvi1g1585 . . . . Adu03g02934 . . . . . . . . . . . . . . . Arst3g03866 Arst3g03866 . Bach2g02320 . . Bva06g01676 Bva05g00106 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g03504 Lapu9g01119 Lasa7g04625 . . . . . . . . . . Lja4g0505 . Mal7g4837 Mepo2g04521 . . . . . . Mtr8g3375 . . . Phco7g01900 . . . Psa7g0908 . Pste2g00211 Pte2g02523 Pte3g00113 Pte3g00113 . Pumo6g00580 Pumo10g01813 Pvu2g2889 Pvu9g1659 Rops2g00679 Rops10g00876 Seca12g06379 Seca4g01809 Spst3g01212 Spst9g01786 . . . Sto4g0210 . Tpr3g0730 Trre7g05310 . . Tsu02g00557 Vian1g03747 . Vifa6g03387 . Vimu11g04293 Vimu10g01870 Viun3g00708 Viun9g01602 Vivi5g05723 . . .
Vvi1g1586 Acco04g2332 . Accr8g00427 . Adu03g02935 . . . . . . . . . Alju06g2294 . . . Apr4g2778 . . . . . Bisa08g1660 . . Bva05g00107 . . . . Dere03g0518 . . . Enph6g0432 . Glsi02g0476 . . . Gma08g03326 . . . . . . . Lal18g0661 . . . . . . . . . Lapu3g03503 . Lasa7g04623 . Lele21g1623 . Lele23g0389 . . . . . . Lja4g0506 . Mal7g4835 Mepo2g04519 . Mesa13g00604 . Mibi09g0471 . . Mtr8g3373 Phac2g04230 . Phco4g03194 . Prci4g2597 . . Psa7g0909 Pste3g01341 . . Pte3g00112 . . Pumo6g00582 . Pvu2g2888 . . . . . Spst3g01213 . . . Sto3g2529 . . Tpr3g0735 Trre7g05308 . . Tsu02g00559 Vian1g03746 . Vifa6g03385 . Vimu11g04291 . . . Vivi5g05721 . . .
Vvi1g1587 . . . . . . . . . . . . . . . . . . Apr4g2777 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal18g0659 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto3g2530 . . . . . . . . . . . . . . . . . . .
Vvi1g1588 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva05g00108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1589 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1590 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi1g1581 Chr1 22586463 22593857 -
Vvi Vvi1g1582 Chr1 22596675 22602000 +
Bva Bva05g00105 Chr05 528714 533616 +
Sto Sto3g2525 Chr3 29347148 29353255 +
Vvi Vvi1g1583 Chr1 22603254 22607524 +
Mal Mal3g3086 Chr3 105896129 105899063 +
Mtr Mtr7g2281 Chr7 39208701 39211408 +
Tpr Tpr6g1050 Chr6 9883682 9886514 +
Tsu Tsu07g02885 Chr07 34084860 34087271 +
Vvi Vvi1g1584 Chr1 22609492 22613488 -
Acco Acco04g2335 Chr04 39598348 39600787 +
Accr Accr8g00421 Chr8 6492942 6495952 -
Adu Adu03g02932 Chr03 110844008 110848255 -
Alju Alju06g2299 Chr06 49363597 49369931 +
Arst Arst3g03865 Chr3 109549572 109553787 -
Arst Arst3g03865 Chr3 109549572 109553787 -
Bach Bach2g02319 Chr2 29716536 29718534 -
Bisa Bisa08g1657 Chr08 38701432 38703498 -
Bva Bva06g01677 Chr06 11774895 11777807 +
Dere Dere03g0520 Chr03 9052745 9054697 +
Enph Enph6g0434 Chr6 7671790 7674799 +
Glsi Glsi02g0479 Chr02 3056212 3058069 +
Lapu Lapu3g03506 Chr3 58391918 58403346 +
Lapu Lapu9g00910 Chr9 13642925 13646063 +
Lasa Lasa7g04626 Chr7 673420590 673424575 +
Lasa Lasa5g03494 Chr5 567171001 567172251 +
Lele Lele21g1625 Chr21 24212816 24215142 +
Lele Lele23g0386 Chr23 2799494 2803174 -
Lja Lja4g0504 Chr4 4114096 4120442 -
Mepo Mepo2g04522 Chr2 53650756 53654236 +
Mepo Mepo3g06939 Chr3 83007577 83010027 +
Mesa Mesa13g00600 Chr13 7140322 7179526 -
Mesa Mesa9g04472 Chr9 78087667 78090025 +
Mibi Mibi09g0469 Chr09 6117763 6119894 -
Mtr Mtr8g3376 Chr8 44244090 44250446 +
Phac Phac2g04233 Chr2 40954161 40961729 +
Phco Phco4g03195 Chr4 52652720 52660044 +
Phco Phco7g01899 Chr7 22717713 22719966 -
Prci Prci4g2607 Chr4 38314966 38318362 +
Psa Psa7g0905 Chr7 68711349 68714140 -
Pste Pste3g01333 Chr3 8313741 8324720 -
Pste Pste2g00217 Chr2 1196064 1198659 +
Pte Pte3g00114 Chr3 1105097 1107559 +
Pte Pte3g00114 Chr3 1105097 1107559 +
Pumo Pumo6g00579 Chr6 7370071 7377018 -
Pumo Pumo10g01814 Chr10 23809748 23812678 +
Pvu Pvu2g2890 Chr2 44474845 44480756 +
Pvu Pvu9g1660 Chr9 23267271 23269904 +
Rops Rops2g00678 Chr2 9650967 9655565 -
Rops Rops10g00875 Chr10 19794198 19796316 -
Seca Seca12g06380 Chr12 155774002 155781830 +
Seca Seca4g01807 Chr4 29914961 29917574 -
Spst Spst3g01211 Chr3 15649146 15657845 -
Spst Spst9g01784 Chr9 20162075 20169056 -
Tpr Tpr3g0729 Chr3 7011297 7016012 -
Trre Trre5g04757 Chr5 49417017 49419637 -
Tsu Tsu02g00556 Chr02 4705322 4710177 -
Vian Vian1g03748 Chr1 60348474 60352701 +
Vifa Vifa2g03356 Chr2 964143309 964144870 +
Vifa Vifa2g03356 Chr2 964143309 964144870 +
Vimu Vimu11g04295 Chr11 64310469 64314127 +
Viun Viun3g00702 Chr3 4358932 4371929 -
Viun Viun9g01599 Chr9 23795691 23798222 -
Vivi Vivi5g05724 Chr5 160721325 160725670 +
Vivi Vivi3g02262 Chr3 37276801 37278919 -
Vvi Vvi1g1585 Chr1 22621795 22625826 +
Adu Adu03g02934 Chr03 110907944 110910814 +
Arst Arst3g03866 Chr3 109613391 109616200 +
Arst Arst3g03866 Chr3 109613391 109616200 +
Bach Bach2g02320 Chr2 29721109 29724553 +
Bva Bva06g01676 Chr06 11770662 11774015 -
Bva Bva05g00106 Chr05 534259 537136 +
Lapu Lapu3g03504 Chr3 58373469 58377306 -
Lapu Lapu9g01119 Chr9 24230701 24240690 -
Lasa Lasa7g04625 Chr7 673263523 673265414 -
Lja Lja4g0505 Chr4 4125040 4128163 +
Mal Mal7g4837 Chr7 116823994 116827640 -
Mepo Mepo2g04521 Chr2 53644018 53647426 -
Mtr Mtr8g3375 Chr8 44236653 44239786 -
Phco Phco7g01900 Chr7 22915332 22919016 +
Psa Psa7g0908 Chr7 68859736 68863197 +
Pste Pste2g00211 Chr2 1137265 1141859 -
Pte Pte2g02523 Chr2 44393514 44396646 +
Pte Pte3g00113 Chr3 1098032 1100988 -
Pte Pte3g00113 Chr3 1098032 1100988 -
Pumo Pumo6g00580 Chr6 7392485 7395797 +
Pumo Pumo10g01813 Chr10 23793766 23797579 -
Pvu Pvu2g2889 Chr2 44460846 44464200 -
Pvu Pvu9g1659 Chr9 23249724 23254293 -
Rops Rops2g00679 Chr2 9681673 9685173 +
Rops Rops10g00876 Chr10 19809982 19814678 +
Seca Seca12g06379 Chr12 155754018 155758070 -
Seca Seca4g01809 Chr4 29962072 29965939 +
Spst Spst3g01212 Chr3 15674458 15677652 +
Spst Spst9g01786 Chr9 20228850 20232222 +
Sto Sto4g0210 Chr4 1587706 1590711 +
Tpr Tpr3g0730 Chr3 7020360 7024094 +
Trre Trre7g05310 Chr7 59340343 59343391 -
Tsu Tsu02g00557 Chr02 4723703 4726526 +
Vian Vian1g03747 Chr1 60325938 60328833 -
Vifa Vifa6g03387 Chr6 1112280837 1112282651 -
Vimu Vimu11g04293 Chr11 64281515 64284426 -
Vimu Vimu10g01870 Chr10 26835034 26836936 -
Viun Viun3g00708 Chr3 4374314 4377823 +
Viun Viun9g01602 Chr9 23859092 23863674 +
Vivi Vivi5g05723 Chr5 160704765 160706919 -
Vvi Vvi1g1586 Chr1 22629058 22633539 +
Acco Acco04g2332 Chr04 39555673 39559294 -
Accr Accr8g00427 Chr8 6657165 6660451 +
Adu Adu03g02935 Chr03 110917087 110918471 +
Alju Alju06g2294 Chr06 49309164 49313731 -
Apr Apr4g2778 Chr4 36316874 36320865 +
Bisa Bisa08g1660 Chr08 38765138 38769390 +
Bva Bva05g00107 Chr05 538536 542101 +
Dere Dere03g0518 Chr03 9026342 9029329 -
Enph Enph6g0432 Chr6 7645072 7645323 -
Glsi Glsi02g0476 Chr02 3038851 3042759 -
Gma Gma08g03326 Chr08 50060692 50065322 -
Lal Lal18g0661 Chr18 5697049 5702213 +
Lapu Lapu3g03503 Chr3 58367003 58370789 -
Lasa Lasa7g04623 Chr7 673216842 673218572 -
Lele Lele21g1623 Chr21 24199056 24199531 -
Lele Lele23g0389 Chr23 2820298 2822067 +
Lja Lja4g0506 Chr4 4129880 4132638 +
Mal Mal7g4835 Chr7 116806378 116809292 -
Mepo Mepo2g04519 Chr2 53628724 53633102 -
Mesa Mesa13g00604 Chr13 7209961 7212396 +
Mibi Mibi09g0471 Chr09 6164056 6166824 +
Mtr Mtr8g3373 Chr8 44220962 44224243 -
Phac Phac2g04230 Chr2 40932410 40935724 -
Phco Phco4g03194 Chr4 52627202 52637925 -
Prci Prci4g2597 Chr4 38258484 38262635 -
Psa Psa7g0909 Chr7 68886626 68888391 +
Pste Pste3g01341 Chr3 8368096 8372102 +
Pte Pte3g00112 Chr3 1094617 1096692 -
Pumo Pumo6g00582 Chr6 7401039 7404037 +
Pvu Pvu2g2888 Chr2 44455832 44458943 -
Spst Spst3g01213 Chr3 15680871 15682909 +
Sto Sto3g2529 Chr3 29396224 29399770 +
Tpr Tpr3g0735 Chr3 7068723 7071891 +
Trre Trre7g05308 Chr7 59321646 59324303 -
Tsu Tsu02g00559 Chr02 4734084 4737397 +
Vian Vian1g03746 Chr1 60320678 60323245 -
Vifa Vifa6g03385 Chr6 1110570186 1110591348 -
Vimu Vimu11g04291 Chr11 64275301 64277859 -
Vivi Vivi5g05721 Chr5 160682854 160684983 -
Vvi Vvi1g1587 Chr1 22635293 22637683 +
Apr Apr4g2777 Chr4 36311456 36315941 -
Lal Lal18g0659 Chr18 5645368 5655536 -
Sto Sto3g2530 Chr3 29427153 29430671 +
Vvi Vvi1g1588 Chr1 22640625 22643804 -
Bva Bva05g00108 Chr05 545393 548850 -
Vvi Vvi1g1589 Chr1 22647054 22649329 -
Vvi Vvi1g1590 Chr1 22666634 22667976 +
Arst Arst3g03866 Chr3 109613391 109616200 +
Bach Bach2g02320 Chr2 29721109 29724553 +
Lapu Lapu9g01119 Chr9 24230701 24240690 -
Lja Lja4g0505 Chr4 4125040 4128163 +
Mal Mal7g4837 Chr7 116823994 116827640 -
Mtr Mtr8g3375 Chr8 44236653 44239786 -
Phco Phco7g01900 Chr7 22915332 22919016 +
Pste Pste2g00211 Chr2 1137265 1141859 -
Pte Pte3g00113 Chr3 1098032 1100988 -
Pumo Pumo10g01813 Chr10 23793766 23797579 -
Pvu Pvu9g1659 Chr9 23249724 23254293 -
Rops Rops10g00876 Chr10 19809982 19814678 +
Seca Seca4g01809 Chr4 29962072 29965939 +
Spst Spst9g01786 Chr9 20228850 20232222 +
Tpr Tpr3g0730 Chr3 7020360 7024094 +
Tsu Tsu02g00557 Chr02 4723703 4726526 +
Vimu Vimu10g01870 Chr10 26835034 26836936 -
Viun Viun9g01602 Chr9 23859092 23863674 +
Arst Arst3g03865 Chr3 109549572 109553787 -
Bach Bach2g02319 Chr2 29716536 29718534 -
Lapu Lapu9g00910 Chr9 13642925 13646063 +
Lasa Lasa5g03494 Chr5 567171001 567172251 +
Lja Lja4g0504 Chr4 4114096 4120442 -
Mepo Mepo3g06939 Chr3 83007577 83010027 +
Mesa Mesa9g04472 Chr9 78087667 78090025 +
Mtr Mtr8g3376 Chr8 44244090 44250446 +
Phco Phco7g01899 Chr7 22717713 22719966 -
Psa Psa7g0905 Chr7 68711349 68714140 -
Pste Pste2g00217 Chr2 1196064 1198659 +
Pte Pte3g00114 Chr3 1105097 1107559 +
Pumo Pumo10g01814 Chr10 23809748 23812678 +
Pvu Pvu9g1660 Chr9 23267271 23269904 +
Rops Rops10g00875 Chr10 19794198 19796316 -
Seca Seca4g01807 Chr4 29914961 29917574 -
Spst Spst9g01784 Chr9 20162075 20169056 -
Tpr Tpr3g0729 Chr3 7011297 7016012 -
Trre Trre5g04757 Chr5 49417017 49419637 -
Tsu Tsu02g00556 Chr02 4705322 4710177 -
Vifa Vifa2g03356 Chr2 964143309 964144870 +
Viun Viun9g01599 Chr9 23795691 23798222 -
Vivi Vivi3g02262 Chr3 37276801 37278919 -