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
Vvi1g1431 . . . . Adu03g04528 . . . . Aev03g2007 . Ahy13g4468 . Aip03g04954 . . . Amo13g5532 . . Arst3g05987 . . . . . Bva06g01747 Bva05g00036 . . . . . . . Dod04g0605 . . . . . . Gma08g00960 Gma18g00073 . . . . . . . . . . . . . . . . . . Lasa7g03941 . . . . . . . . . . Lja4g1058 . Mal7g4179 Mepo2g03858 . Mesa13g01288 . . . Mtr3g2813 Mtr8g2792 Phac2g02729 . Phco4g02029 . . . Psa5g2221 . Pste3g02733 . . . . . Pumo6g01240 . Pvu2g1797 . Rops2g01359 . Seca12g05699 . . . . . Sto3g1936 . Tpr2g4681 Tpr3g1313 Trre7g04519 . Tsu07g02723 Tsu02g01206 Vian1g02678 . Vifa2g02461 . Vimu11g01854 . Viun3g02267 . Vivi5g05576 . . .
Vvi1g1432 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1433 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1434 . . . . Adu10g00689 . . . . . . . . . . . . . . . Arst10g00881 . . . . . . Bva05g00038 . . . . . . . . . . . . . . . Gma18g00071 . . . . . . . . . . . . . . . . . . Lasa5g02615 . . . . . . . . . . . . . Mepo3g06225 . . . . . Mtr3g2812 . . . Phco2g02969 . . . Psa5g2225 . Pste7g02393 . . . . . Pumo1g00445 . Pvu1g2691 . Rops11g03724 . Seca6g01703 . Spst1g01899 . . . . . Tpr2g4680 . Trre5g03099 . Tsu07g02720 . Vian2g03176 . Vifa2g02458 . Vimu6g01519 . Viun1g03450 . . . . .
Vvi1g1435 . . . . Adu03g02840 . . . . Aev03g2009 . Ahy13g4471 . Aip03g04957 . . . . . . Arst3g03759 . . . . . Bva06g01746 Bva05g00039 . . . . . . . Dod04g0608 . . . . . . . Gma18g00070 . . . . . . . . . . . . . . . . Lapu3g03555 . Lasa7g04678 . . . . . . . . . . Lja4g1056 . Mal7g4888 Mepo2g04575 . . . . . Mtr3g2810 Mtr8g3420 . . Phco4g03252 . . . Psa5g2228 . Pste3g01136 . . Pte3g00157 . . Pumo6g00531 . Pvu2g2948 . Rops2g00600 . Seca12g06438 . Spst3g01135 . . . . . Tpr2g4679 Tpr3g0681 Trre7g05388 . Tsu07g02719 Tsu02g00502 Vian1g03796 . Vifa2g03427 . Vimu11g04362 . Viun3g00621 . Vivi5g05789 . . .
Vvi1g1436 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva05g00040 . . . . . . . . . . . . . . Gma08g00963 . . . . . . . . . . . . . . . . . . . Lasa7g03942 . . . . . . . . . . Lja4g1054 . Mal7g4189 . . Mesa13g01286 . . . Mtr3g2809 Mtr8g2796 Phac2g02723 . Phco4g02026 . . . Psa5g2229 . Pste3g02742 . . . . . Pumo6g01237 . Pvu2g1793 . Rops2g01358 . Seca12g05702 . . . . . Sto3g2664 . Tpr2g4678 Tpr3g1311 Trre7g04522 . Tsu07g02718 Tsu02g01203 Vian1g02675 . Vifa2g02456 . Vimu11g01855 . Viun3g02264 . Vivi5g05575 . . .
Vvi1g1437 . . . . . . . . . Aev03g2498 . Ahy13g4472 . Aip03g04958 . . . . . . . . . . . . . Bva05g00041 . . . . . . . Dod04g2022 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja4g1053 . Mal7g4193 . . . . . . . Mtr8g2797 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr3g1310 . . . . . . . . . . . . . . . .
Vvi1g1438 . . . . Adu03g04532 Adu08g02817 . . . . . . . Aip03g04959 . . . Amo13g5530 . . Arst3g05990 Arst8g03875 . Bach2g02253 . . Bva06g01745 Bva05g00042 . . . . . . . . . . . . . . Gma08g00964 . . . . . . . . . . . . . . . . . Lapu3g02343 . Lasa7g03944 . . . . . . . . . . Lja4g1052 . Mal7g4194 Mepo2g03861 . Mesa13g01283 . . . Mtr3g2808 Mtr8g2798 Phac2g02721 . Phco4g02024 Phco7g01974 . . Psa5g2230 . Pste3g02745 Pste2g00391 . . . Pte1g02006 Pumo6g01236 Pumo10g01889 Pvu2g1792 Pvu9g1722 Rops2g01355 . Seca12g05705 Seca12g01741 . Spst9g02110 . . Sto3g2662 . Tpr2g4677 Tpr3g1309 Trre7g04524 . Tsu07g02714 Tsu02g01202 Vian1g02674 . Vifa2g02454 . Vimu11g01857 . Viun3g02263 Viun9g01473 Vivi5g05572 . . .
Vvi1g1439 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1440 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi1g1431 Chr1 20661678 20663794 -
Adu Adu03g04528 Chr03 134639294 134640746 -
Aev Aev03g2007 Chr03 22873485 22874804 -
Ahy Ahy13g4468 Chr13 144809787 144813067 -
Aip Aip03g04954 Chr03 134155691 134157186 -
Amo Amo13g5532 Chr13 156825339 156828463 +
Arst Arst3g05987 Chr3 133402328 133404132 -
Bva Bva06g01747 Chr06 12141501 12145927 +
Bva Bva05g00036 Chr05 185967 190510 -
Dod Dod04g0605 Chr04 8724788 8726120 -
Gma Gma08g00960 Chr08 8102462 8104236 -
Gma Gma18g00073 Chr18 593885 595138 +
Lasa Lasa7g03941 Chr7 626544105 626545433 -
Lja Lja4g1058 Chr4 9104006 9105658 +
Mal Mal7g4179 Chr7 108645509 108646787 -
Mepo Mepo2g03858 Chr2 47802699 47805338 -
Mesa Mesa13g01288 Chr13 15289875 15291148 +
Mtr Mtr3g2813 Chr3 42122919 42126148 +
Mtr Mtr8g2792 Chr8 38602454 38605034 -
Phac Phac2g02729 Chr2 28860143 28864280 +
Phco Phco4g02029 Chr4 40374125 40376038 +
Psa Psa5g2221 Chr5 174112818 174114519 -
Pste Pste3g02733 Chr3 20143553 20145553 -
Pumo Pumo6g01240 Chr6 16458345 16460278 +
Pvu Pvu2g1797 Chr2 32464122 32466285 +
Rops Rops2g01359 Chr2 19481497 19485584 +
Seca Seca12g05699 Chr12 148607911 148610655 -
Sto Sto3g1936 Chr3 15722795 15728921 +
Tpr Tpr2g4681 Chr2 52122293 52126070 +
Tpr Tpr3g1313 Chr3 11625361 11628230 +
Trre Trre7g04519 Chr7 53181752 53182985 -
Tsu Tsu07g02723 Chr07 31857634 31859096 +
Tsu Tsu02g01206 Chr02 10162431 10163628 +
Vian Vian1g02678 Chr1 40086380 40088234 +
Vifa Vifa2g02461 Chr2 645010535 645011818 +
Vimu Vimu11g01854 Chr11 26046989 26047546 -
Viun Viun3g02267 Chr3 19844966 19848455 +
Vivi Vivi5g05576 Chr5 158990556 158992403 +
Vvi Vvi1g1432 Chr1 20663845 20664271 -
Vvi Vvi1g1433 Chr1 20679501 20679923 +
Vvi Vvi1g1434 Chr1 20691029 20694968 +
Adu Adu10g00689 Chr10 8270795 8273530 -
Arst Arst10g00881 Chr10 7919834 7922271 -
Bva Bva05g00038 Chr05 191652 192386 +
Gma Gma18g00071 Chr18 585928 589601 -
Lasa Lasa5g02615 Chr5 492819925 492822922 -
Mepo Mepo3g06225 Chr3 76414647 76417993 -
Mtr Mtr3g2812 Chr3 42110687 42114450 -
Phco Phco2g02969 Chr2 58540519 58543248 +
Psa Psa5g2225 Chr5 174350085 174353681 +
Pste Pste7g02393 Chr7 22687473 22690128 +
Pumo Pumo1g00445 Chr1 6123740 6127496 +
Pvu Pvu1g2691 Chr1 51580507 51583778 +
Rops Rops11g03724 Chr11 70882939 70883574 -
Seca Seca6g01703 Chr6 71594700 71595359 -
Spst Spst1g01899 Chr1 27146828 27149642 -
Tpr Tpr2g4680 Chr2 52098617 52102586 -
Trre Trre5g03099 Chr5 26170680 26173935 -
Tsu Tsu07g02720 Chr07 31832916 31836939 -
Vian Vian2g03176 Chr2 52242755 52245623 +
Vifa Vifa2g02458 Chr2 643788693 643791675 -
Vimu Vimu6g01519 Chr6 14326774 14329625 -
Viun Viun1g03450 Chr1 41451679 41454645 +
Vvi Vvi1g1435 Chr1 20701556 20701831 -
Adu Adu03g02840 Chr03 107118619 107122830 -
Aev Aev03g2009 Chr03 22893852 22894133 -
Ahy Ahy13g4471 Chr13 144829678 144830152 -
Aip Aip03g04957 Chr03 134166795 134167435 -
Arst Arst3g03759 Chr3 105846282 105850031 -
Bva Bva06g01746 Chr06 12133658 12139062 +
Bva Bva05g00039 Chr05 195668 198128 -
Dod Dod04g0608 Chr04 8755560 8755841 -
Gma Gma18g00070 Chr18 581012 585034 +
Lapu Lapu3g03555 Chr3 58997843 59004167 +
Lasa Lasa7g04678 Chr7 679302880 679308266 +
Lja Lja4g1056 Chr4 9087568 9088888 +
Mal Mal7g4888 Chr7 117479774 117484784 +
Mepo Mepo2g04575 Chr2 54197544 54202980 +
Mtr Mtr3g2810 Chr3 42083704 42085457 +
Mtr Mtr8g3420 Chr8 44783251 44789245 +
Phco Phco4g03252 Chr4 53168820 53174931 +
Psa Psa5g2228 Chr5 174384395 174386548 -
Pste Pste3g01136 Chr3 7259899 7267929 -
Pte Pte3g00157 Chr3 1534877 1538824 +
Pumo Pumo6g00531 Chr6 6642388 6648092 -
Pvu Pvu2g2948 Chr2 45016388 45023149 +
Rops Rops2g00600 Chr2 8556050 8562451 -
Seca Seca12g06438 Chr12 156456523 156462408 +
Spst Spst3g01135 Chr3 14673534 14679623 -
Tpr Tpr2g4679 Chr2 52093920 52095834 +
Tpr Tpr3g0681 Chr3 6566485 6572663 -
Trre Trre7g05388 Chr7 59947817 59952766 +
Tsu Tsu07g02719 Chr07 31824788 31826930 +
Tsu Tsu02g00502 Chr02 4202799 4209616 -
Vian Vian1g03796 Chr1 61010074 61016315 +
Vifa Vifa2g03427 Chr2 990224886 990231758 +
Vimu Vimu11g04362 Chr11 64936322 64943648 +
Viun Viun3g00621 Chr3 3812150 3819220 -
Vivi Vivi5g05789 Chr5 161782294 161788686 +
Vvi Vvi1g1436 Chr1 20704030 20712389 -
Bva Bva05g00040 Chr05 198105 202134 -
Gma Gma08g00963 Chr08 8117705 8120931 -
Lasa Lasa7g03942 Chr7 626675988 626679489 -
Lja Lja4g1054 Chr4 9064847 9068134 +
Mal Mal7g4189 Chr7 108776007 108779309 -
Mesa Mesa13g01286 Chr13 15218223 15222245 +
Mtr Mtr3g2809 Chr3 42077930 42080101 +
Mtr Mtr8g2796 Chr8 38635393 38639930 -
Phac Phac2g02723 Chr2 28824000 28827732 +
Phco Phco4g02026 Chr4 40320562 40323714 +
Psa Psa5g2229 Chr5 174405700 174408120 -
Pste Pste3g02742 Chr3 20229778 20232774 -
Pumo Pumo6g01237 Chr6 16426774 16433381 +
Pvu Pvu2g1793 Chr2 32426672 32429993 +
Rops Rops2g01358 Chr2 19447302 19457738 +
Seca Seca12g05702 Chr12 148641080 148644369 -
Sto Sto3g2664 Chr3 31104486 31111879 +
Tpr Tpr2g4678 Chr2 52090331 52092317 +
Tpr Tpr3g1311 Chr3 11606793 11610005 +
Trre Trre7g04522 Chr7 53223003 53225939 -
Tsu Tsu07g02718 Chr07 31816005 31818092 +
Tsu Tsu02g01203 Chr02 10124971 10137541 +
Vian Vian1g02675 Chr1 40008876 40012001 +
Vifa Vifa2g02456 Chr2 643641279 643642429 +
Vimu Vimu11g01855 Chr11 26175983 26181907 -
Viun Viun3g02264 Chr3 19743704 19746858 +
Vivi Vivi5g05575 Chr5 158972710 158975259 +
Vvi Vvi1g1437 Chr1 20714886 20726477 -
Aev Aev03g2498 Chr03 25938805 25946170 -
Ahy Ahy13g4472 Chr13 144838571 144846895 -
Aip Aip03g04958 Chr03 134175635 134183898 -
Bva Bva05g00041 Chr05 203298 210429 -
Dod Dod04g2022 Chr04 43670300 43676986 -
Lja Lja4g1053 Chr4 9051148 9060140 +
Mal Mal7g4193 Chr7 108808706 108815154 -
Mtr Mtr8g2797 Chr8 38642067 38649352 -
Tpr Tpr3g1310 Chr3 11598673 11605700 +
Vvi Vvi1g1438 Chr1 20746190 20749788 +
Adu Adu03g04532 Chr03 134679407 134682741 +
Adu Adu08g02817 Chr08 44753210 44755950 -
Aip Aip03g04959 Chr03 134198683 134199150 +
Amo Amo13g5530 Chr13 156775070 156778350 -
Arst Arst3g05990 Chr3 133442687 133445755 +
Arst Arst8g03875 Chr8 49156900 49159637 -
Bach Bach2g02253 Chr2 29224614 29227767 +
Bva Bva06g01745 Chr06 12130008 12133296 -
Bva Bva05g00042 Chr05 212762 215364 +
Gma Gma08g00964 Chr08 8124926 8128327 +
Lapu Lapu3g02343 Chr3 44823521 44827451 -
Lasa Lasa7g03944 Chr7 626956018 626961223 +
Lja Lja4g1052 Chr4 9045353 9048687 -
Mal Mal7g4194 Chr7 108823385 108828352 +
Mepo Mepo2g03861 Chr2 47846518 47851578 +
Mesa Mesa13g01283 Chr13 15185038 15190191 -
Mtr Mtr3g2808 Chr3 42072099 42075099 -
Mtr Mtr8g2798 Chr8 38660363 38664988 +
Phac Phac2g02721 Chr2 28813831 28816620 -
Phco Phco4g02024 Chr4 40285645 40288249 -
Phco Phco7g01974 Chr7 33475155 33478279 -
Psa Psa5g2230 Chr5 174424545 174427576 +
Pste Pste3g02745 Chr3 20253834 20256516 +
Pste Pste2g00391 Chr2 3384919 3387727 -
Pte Pte1g02006 Chr1 41230366 41232922 +
Pumo Pumo6g01236 Chr6 16423803 16426728 -
Pumo Pumo10g01889 Chr10 24922848 24925990 -
Pvu Pvu2g1792 Chr2 32400343 32403008 -
Pvu Pvu9g1722 Chr9 24348693 24352355 -
Rops Rops2g01355 Chr2 19400123 19404165 -
Seca Seca12g05705 Chr12 148671020 148676719 +
Seca Seca12g01741 Chr12 19233933 19237855 +
Spst Spst9g02110 Chr9 43390490 43393203 +
Sto Sto3g2662 Chr3 31095309 31100205 -
Tpr Tpr2g4677 Chr2 52085268 52088594 -
Tpr Tpr3g1309 Chr3 11591162 11595020 -
Trre Trre7g04524 Chr7 53242912 53247866 +
Tsu Tsu07g02714 Chr07 31770811 31773342 -
Tsu Tsu02g01202 Chr02 10112832 10117218 -
Vian Vian1g02674 Chr1 39999363 40001966 -
Vifa Vifa2g02454 Chr2 643193734 643195710 -
Vimu Vimu11g01857 Chr11 26190865 26194461 +
Viun Viun3g02263 Chr3 19718175 19720888 -
Viun Viun9g01473 Chr9 17579180 17582616 +
Vivi Vivi5g05572 Chr5 158940544 158944731 -
Vvi Vvi1g1439 Chr1 20751549 20753927 -
Vvi Vvi1g1440 Chr1 20767534 20771154 -
Bva Bva06g01747 Chr06 12141501 12145927 +
Arst Arst3g03759 Chr3 105846282 105850031 -
Mal Mal7g4888 Chr7 117479774 117484784 +
Mtr Mtr8g3420 Chr8 44783251 44789245 +
Pte Pte3g00157 Chr3 1534877 1538824 +
Tpr Tpr3g0681 Chr3 6566485 6572663 -
Tsu Tsu02g00502 Chr02 4202799 4209616 -
Vifa Vifa2g03427 Chr2 990224886 990231758 +
Adu Adu08g02817 Chr08 44753210 44755950 -
Arst Arst8g03875 Chr8 49156900 49159637 -
Bach Bach2g02253 Chr2 29224614 29227767 +
Phco Phco7g01974 Chr7 33475155 33478279 -
Pste Pste2g00391 Chr2 3384919 3387727 -
Pte Pte1g02006 Chr1 41230366 41232922 +
Pumo Pumo10g01889 Chr10 24922848 24925990 -
Pvu Pvu9g1722 Chr9 24348693 24352355 -
Seca Seca12g01741 Chr12 19233933 19237855 +
Seca Seca12g01741 Chr12 19233933 19237855 +
Spst Spst9g02110 Chr9 43390490 43393203 +
Viun Viun9g01473 Chr9 17579180 17582616 +