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
Vvi1g0031 . . . . . Adu04g02914 Aed11g0459 . Aev05g1866 . Ahy15g1830 . Aip05g01928 . . . Amo15g0647 . Apr7g1401 . . Arst4g03855 . Bach8g02580 . . Bva08g01594 Bva11g00909 Car02g00844 . Cca06g00546 . . . . . . . . . Gma02g01076 Gma01g00556 . . Gso2g0984 Gso2g0984 . . Lal6g0787 Lal22g0697 . . . . Lan11g0791 Lan11g0791 . . . . . Lapu1g01273 . Lasa3g00269 . . . . . . . . Lja2g1250 . . . . Mepo3g00285 . Mesa25g04500 . . . . . . . Phco3g02922 . . Psa2g2963 . . Pste5g00664 . . Pte7g00824 Pte4g00615 . Pumo5g00736 . Pvu8g0336 . Rops8g00563 . Seca10g02584 . Spst1g01426 Ssu2g1488 . Sto11g0858 Sto6g2942 . . . Trre13g00293 . . . Vian2g00316 . Vifa1g05618 . Vimu6g00987 . Viun5g00467 . . . .
Vvi1g0032 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cca09g01648 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g2155 . . . . . . . . . . . . . . . . . . . Vra7g1009
Vvi1g0033 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva11g00911 Car02g00842 . . . . . . . . . . . . . . . . . . . . . Lal18g0919 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0034 . . . . Adu06g00901 . . . . . . . . . . . . . Apr7g1403 . Arst6g01196 . . . . . Bva08g01591 Bva11g00912 Car02g00841 . . . . . . . . . . . Gma02g01073 . . . Gso2g0982 . . . Lal6g0790 . . . . . Lan11g0795 . . . . . . . . . . . . . . . . . Lja2g1248 . . . . . . . . . . . Phac1g01863 . . . . . Psa2g2953 . . . . . . . Pumo5g02582 . Pvu1g1401 Pvu8g0346 . . . . . . . . Sto11g0861 Sto6g2944 . . . . . . . . . . . . . . . . . .
Vvi1g0035 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0036 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva08g01587 . Car02g00840 . . . . . . . . . . . Gma02g01072 . . . Gso2g0981 . . . . Lal22g0700 . . . . . . . . . . . . . Lasa2g03866 . . . . . . . . Lja2g1247 . . . . . . . . . . . . . . . . . Psa2g2952 . . . . . Pte14g00041 . . . . Pvu3g0435 . . . . . Spst2g01662 . . . Sto6g2945 . . . . . . . . . . . Vimu7g00201 . . . . . .
Vvi1g0037 . . . . . . Aed11g0453 . . . . . . . . . . . Apr7g1405 . . . . . . Bisa01g2779 Bva08g01586 . Car02g00838 . Cca06g00551 . . Dere13g1472 . . . Enph14g1323 . Glsi09g1350 Gma02g01068 . . . Gso2g0979 . . . Lal6g0792 . . . . . Lan11g0796 . . . . . . Lapu2g01311 . Lasa2g03868 . . . . Lele53g0745 Lele54g0738 Lele55g0746 Lele56g0695 Lja2g1246 . Mal6g2411 . . Mepo5g02067 . Mesa17g02261 . . Mtr5g1777 . . . . Phco8g02989 . Prci5g1341 . . . Pste1g01903 . . . Pte12g01049 . . . Pvu3g0436 . . . Seca10g01836 . Spst2g01664 . . Sto11g0863 . Tpr2g2081 . . Trre9g02907 Tsu05g02048 . . Vian10g01525 . . . Vimu7g00200 . Viun2g00832 . . . .
Vvi1g0038 . . . . . Adu05g01928 . . . . Ahy15g1748 . Aip05g02037 . . . . . Apr7g1406 . . . . . . . Bva08g01585 . Car02g00837 . . . . . Dod02g1748 . . . . . Gma02g01067 Gma01g00546 . . . . . . Lal6g0793 . . . . . Lan11g0797 . . . . . . Lapu2g01310 . Lasa2g03870 . . . . . . . . Lja2g1245 . . . . Mepo5g02053 . Mesa17g02240 . . Mtr5g1770 . . . . Phco8g02988 . . Psa2g2941 . . Pste1g01900 . . . Pte12g01050 . . . Pvu3g0437 . . . . . Spst2g01665 . . . Sto6g2946 Tpr2g2080 . . Trre9g02905 Tsu05g02047 . . . . . . Vimu7g00199 . . . . . .
Vvi1g0039 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0040 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g2934 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi1g0031 Chr1 434039 439421 +
Adu Adu04g02914 Chr04 117336808 117339733 -
Aed Aed11g0459 Chr11 4014229 4020734 +
Aev Aev05g1866 Chr05 16616662 16620254 -
Ahy Ahy15g1830 Chr15 68360161 68364796 +
Aip Aip05g01928 Chr05 60066563 60071144 -
Amo Amo15g0647 Chr15 42489483 42493534 -
Apr Apr7g1401 Chr7 21156149 21160783 +
Arst Arst4g03855 Chr4 117315152 117317966 -
Bach Bach8g02580 Chr8 32104858 32107527 +
Bva Bva08g01594 Chr08 8391481 8395084 -
Bva Bva11g00909 Chr11 11292199 11296003 +
Car Car02g00844 Chr02 12392862 12396504 -
Cca Cca06g00546 Chr06 16402203 16406076 -
Gma Gma02g01076 Chr02 11661438 11666508 +
Gma Gma01g00556 Chr01 8271729 8276791 +
Gso Gso2g0984 Chr2 11474322 11479568 +
Gso Gso2g0984 Chr2 11474322 11479568 +
Lal Lal6g0787 Chr6 5305470 5309113 +
Lal Lal22g0697 Chr22 5027863 5032814 +
Lan Lan11g0791 Chr11 7485524 7488683 +
Lan Lan11g0791 Chr11 7485524 7488683 +
Lapu Lapu1g01273 Chr1 25532727 25536324 +
Lasa Lasa3g00269 Chr3 17281754 17284477 -
Lja Lja2g1250 Chr2 11808998 11813587 -
Mepo Mepo3g00285 Chr3 3871398 3876221 -
Mesa Mesa25g04500 Chr25 82049212 82052650 +
Phco Phco3g02922 Chr3 55633408 55636671 -
Psa Psa2g2963 Chr2 338399476 338402943 -
Pste Pste5g00664 Chr5 4301258 4305387 +
Pte Pte7g00824 Chr7 32158719 32161053 +
Pte Pte4g00615 Chr4 37009337 37011532 +
Pumo Pumo5g00736 Chr5 14923176 14926395 +
Pvu Pvu8g0336 Chr8 2721694 2725030 +
Rops Rops8g00563 Chr8 11571607 11575303 +
Seca Seca10g02584 Chr10 32326720 32330318 +
Spst Spst1g01426 Chr1 17702499 17707883 -
Ssu Ssu2g1488 Chr2 61668311 61671823 -
Sto Sto11g0858 Chr11 9270609 9272941 +
Sto Sto6g2942 Chr6 36628768 36633385 +
Trre Trre13g00293 Chr13 2319267 2323113 -
Vian Vian2g00316 Chr2 3566110 3568512 +
Vifa Vifa1g05618 Chr1 869953753 869956322 -
Vimu Vimu6g00987 Chr6 10647622 10648118 -
Viun Viun5g00467 Chr5 2756332 2759156 +
Vvi Vvi1g0032 Chr1 442128 445496 -
Cca Cca09g01648 Chr09 40336667 40338669 -
Ssu Ssu5g2155 Chr5 62065824 62066202 -
Vra Vra7g1009 Chr7 24361045 24362678 +
Vvi Vvi1g0033 Chr1 448552 450338 -
Bva Bva11g00911 Chr11 11301405 11302106 -
Car Car02g00842 Chr02 12355430 12358097 +
Lal Lal18g0919 Chr18 12011145 12012620 +
Vvi Vvi1g0034 Chr1 454749 457824 +
Adu Adu06g00901 Chr06 11027177 11031181 +
Apr Apr7g1403 Chr7 21177766 21182252 +
Arst Arst6g01196 Chr6 11057516 11061539 +
Bva Bva08g01591 Chr08 8366101 8370149 -
Bva Bva11g00912 Chr11 11304876 11306507 +
Car Car02g00841 Chr02 12342174 12347849 -
Gma Gma02g01073 Chr02 11626729 11632668 -
Gso Gso2g0982 Chr2 11437862 11445766 -
Lal Lal6g0790 Chr6 5319339 5325376 +
Lan Lan11g0795 Chr11 7519931 7525024 +
Lja Lja2g1248 Chr2 11796783 11801820 -
Phac Phac1g01863 Chr1 28397126 28400559 +
Psa Psa2g2953 Chr2 337726603 337728391 -
Pumo Pumo5g02582 Chr5 71249508 71253680 +
Pvu Pvu1g1401 Chr1 37948400 37952635 +
Pvu Pvu8g0346 Chr8 2834009 2836206 +
Sto Sto11g0861 Chr11 9305278 9311508 +
Sto Sto6g2944 Chr6 36646501 36649506 +
Vvi Vvi1g0035 Chr1 459188 463238 -
Vvi Vvi1g0036 Chr1 464665 473684 -
Bva Bva08g01587 Chr08 8345221 8352624 +
Car Car02g00840 Chr02 12335184 12342596 +
Gma Gma02g01072 Chr02 11620443 11626597 +
Gso Gso2g0981 Chr2 11431971 11438858 +
Lal Lal22g0700 Chr22 5043674 5050358 +
Lasa Lasa2g03866 Chr2 561453988 561457555 -
Lja Lja2g1247 Chr2 11792693 11797823 +
Psa Psa2g2952 Chr2 337725890 337726443 +
Pte Pte14g00041 Chr14 2452270 2457283 -
Pvu Pvu3g0435 Chr3 4720806 4727254 -
Spst Spst2g01662 Chr2 15610588 15610968 -
Sto Sto6g2945 Chr6 36654709 36655712 -
Vimu Vimu7g00201 Chr7 2484661 2491745 +
Vvi Vvi1g0037 Chr1 475801 481438 -
Aed Aed11g0453 Chr11 3961599 3963545 +
Apr Apr7g1405 Chr7 21192734 21195648 -
Bisa Bisa01g2779 Chr01 55498705 55500669 -
Bva Bva08g01586 Chr08 8342040 8344687 +
Car Car02g00838 Chr02 12318988 12320955 +
Cca Cca06g00551 Chr06 16507445 16510063 +
Dere Dere13g1472 Chr13 19877313 19879280 +
Enph Enph14g1323 Chr14 15027848 15041767 +
Glsi Glsi09g1350 Chr09 9933390 9935354 +
Gma Gma02g01068 Chr02 11600750 11602931 +
Gso Gso2g0979 Chr2 11410709 11413612 +
Lal Lal6g0792 Chr6 5328264 5330225 -
Lan Lan11g0796 Chr11 7527105 7529542 -
Lapu Lapu2g01311 Chr2 23964980 23973569 +
Lasa Lasa2g03868 Chr2 561483953 561484642 -
Lele Lele53g0745 Chr53 17451847 17453811 -
Lele Lele54g0738 Chr54 14302231 14306069 -
Lele Lele55g0746 Chr55 4993708 4995672 +
Lele Lele56g0695 Chr56 5199617 5202434 +
Lja Lja2g1246 Chr2 11787710 11790068 +
Mal Mal6g2411 Chr6 56526096 56528111 -
Mepo Mepo5g02067 Chr5 22918014 22920510 +
Mesa Mesa17g02261 Chr17 33492249 33494228 +
Mtr Mtr5g1777 Chr5 19626112 19631430 +
Phco Phco8g02989 Chr8 43889659 43891626 +
Prci Prci5g1341 Chr5 32666060 32669099 -
Pste Pste1g01903 Chr1 5901041 5903251 +
Pte Pte12g01049 Chr12 25507305 25510159 -
Pvu Pvu3g0436 Chr3 4729203 4733507 -
Seca Seca10g01836 Chr10 20315153 20320139 +
Spst Spst2g01664 Chr2 15622257 15624221 -
Sto Sto11g0863 Chr11 9328189 9330159 -
Tpr Tpr2g2081 Chr2 24902532 24909797 +
Trre Trre9g02907 Chr9 36893743 36896951 +
Tsu Tsu05g02048 Chr05 24235912 24237894 +
Vian Vian10g01525 Chr10 25956974 25958941 -
Vimu Vimu7g00200 Chr7 2466701 2468668 +
Viun Viun2g00832 Chr2 18998924 18999574 -
Vvi Vvi1g0038 Chr1 482097 494055 +
Adu Adu05g01928 Chr05 64559120 64564361 -
Ahy Ahy15g1748 Chr15 57065302 57071934 +
Aip Aip05g02037 Chr05 70382384 70387686 -
Apr Apr7g1406 Chr7 21198713 21204009 +
Bva Bva08g01585 Chr08 8337321 8341015 -
Car Car02g00837 Chr02 12295926 12302789 -
Dod Dod02g1748 Chr02 22013201 22018835 -
Gma Gma02g01067 Chr02 11583838 11587933 -
Gma Gma01g00546 Chr01 7943178 7949367 -
Lal Lal6g0793 Chr6 5330620 5335532 +
Lan Lan11g0797 Chr11 7530147 7535987 +
Lapu Lapu2g01310 Chr2 23949976 23957088 -
Lasa Lasa2g03870 Chr2 561488674 561492346 +
Lja Lja2g1245 Chr2 11781565 11787345 -
Mepo Mepo5g02053 Chr5 22804594 22811849 -
Mesa Mesa17g02240 Chr17 33094857 33101015 -
Mtr Mtr5g1770 Chr5 19549751 19556763 -
Phco Phco8g02988 Chr8 43878006 43883441 -
Psa Psa2g2941 Chr2 337287787 337289995 +
Pste Pste1g01900 Chr1 5885767 5891477 -
Pte Pte12g01050 Chr12 25569166 25573147 +
Pvu Pvu3g0437 Chr3 4737058 4742982 +
Spst Spst2g01665 Chr2 15626152 15630593 +
Sto Sto6g2946 Chr6 36658063 36665001 +
Tpr Tpr2g2080 Chr2 24896984 24902396 -
Trre Trre9g02905 Chr9 36871400 36875104 -
Tsu Tsu05g02047 Chr05 24187567 24191715 -
Vimu Vimu7g00199 Chr7 2448374 2457678 -
Vvi Vvi1g0039 Chr1 496535 498475 +
Vvi Vvi1g0040 Chr1 498867 500444 -
Psa Psa2g2934 Chr2 337128864 337130696 +
Vifa Vifa1g05618 Chr1 869953753 869956322 -
Adu Adu06g00901 Chr06 11027177 11031181 +
Arst Arst6g01196 Chr6 11057516 11061539 +
Phac Phac1g01863 Chr1 28397126 28400559 +
Pumo Pumo5g02582 Chr5 71249508 71253680 +
Pvu Pvu1g1401 Chr1 37948400 37952635 +
Adu Adu04g02914 Chr04 117336808 117339733 -
Arst Arst4g03855 Chr4 117315152 117317966 -
Bach Bach8g02580 Chr8 32104858 32107527 +
Lapu Lapu1g01273 Chr1 25532727 25536324 +
Lasa Lasa3g00269 Chr3 17281754 17284477 -
Mepo Mepo3g00285 Chr3 3871398 3876221 -
Mesa Mesa25g04500 Chr25 82049212 82052650 +
Phco Phco3g02922 Chr3 55633408 55636671 -
Pste Pste5g00664 Chr5 4301258 4305387 +
Pte Pte7g00824 Chr7 32158719 32161053 +
Pte Pte4g00615 Chr4 37009337 37011532 +
Pumo Pumo5g00736 Chr5 14923176 14926395 +
Pvu Pvu8g0336 Chr8 2721694 2725030 +
Rops Rops8g00563 Chr8 11571607 11575303 +
Seca Seca10g02584 Chr10 32326720 32330318 +
Spst Spst1g01426 Chr1 17702499 17707883 -
Trre Trre13g00293 Chr13 2319267 2323113 -
Vian Vian2g00316 Chr2 3566110 3568512 +
Vifa Vifa1g05618 Chr1 869953753 869956322 -
Vimu Vimu6g00987 Chr6 10647622 10648118 -
Viun Viun5g00467 Chr5 2756332 2759156 +