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
Vvi1g0051 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car02g00817 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0052 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0054 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car02g00815 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g3069 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0055 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0056 . . . . . Adu04g02886 Aed11g0440 . . Aev03g0375 . Ahy13g3891 . Aip03g04327 . . . Amo13g4906 Apr7g1420 Apr3g1517 Arst3g05203 Arst4g03813 . Bach8g02597 . . Bva08g01572 Bva11g00921 Car06g01850 . Cca06g00568 . . . . Dod04g1150 . . . . Gma02g01052 Gma01g00531 . . Gso2g0969 Gso2g0969 . . Lal6g0804 Lal22g0705 Lal18g0914 . Lal16g0805 Lal15g0779 Lan11g0808 Lan11g0808 Lan11g0808 . Lan11g0808 Lan11g0808 Lapu3g02288 Lapu1g01292 . . . . . . . . . . Lja2g1227 Lja4g3510 Mal6g2057 . Mepo2g02954 Mepo3g00244 Mesa13g02098 Mesa25g04543 . . Mtr5g1741 . Phac2g01719 . Phco4g01927 Phco3g02899 . . Psa2g2914 . Pste3g04001 Pste5g00714 . . Pte7g00841 Pte4g00646 . . Pvu2g1062 Pvu8g0356 . . . . Spst3g02346 . Ssu2g1513 . Sto11g0877 Sto6g2959 Tpr2g2063 . Trre7g02025 Trre13g00274 Tsu05g02018 . . . . . . . . . . Vivi6g00385 . .
Vvi1g0057 . . . . . . . . . . . . . . . . . . . Apr3g1516 . . . . . . . Bva11g00922 . . . . . . . . . . . . . . . . . . . . . . . Lal23g0826 Lal16g0807 Lal15g0780 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco4g01948 . . . . . . . . . . . . . Pvu2g1735 . . . . . Spst3g02365 . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0058 . . . . . . Aed11g0439 . . Aev03g0376 . Ahy13g3890 . Aip03g04326 . . . Amo13g4905 Apr7g1421 . . . Bach4g01347 . . . Bva08g01571 Bva11g00923 Car02g00813 . Cca06g00570 . . . . Dod04g1149 . . . . Gma02g01051 Gma01g00525 . . Gso2g0968 Gso2g0968 . . Lal6g0805 Lal22g0706 Lal18g0913 Lal23g0825 Lal16g0808 Lal15g0781 Lan11g0809 Lan11g0809 Lan11g0809 Lan11g0809 Lan11g0809 Lan11g0809 . . . . . . . . . . . . Lja2g1226 Lja4g3509 Mal6g2056 . . . . . . . Mtr5g1738 . . . Phco4g01947 . . . Psa2g2909 . Pste3g04002 . . . . . Pumo8g00961 . Pvu2g1734 . Rops1g01164 . Seca10g01810 . Spst3g02363 . Ssu2g1514 . Sto11g0879 . Tpr2g2062 . . . Tsu05g02017 . Vian10g01542 . Vifa1g05514 . . . Viun2g00857 . . . . .
Vvi1g0059 . . . . . . Aed11g0438 . . . . Ahy13g3887 . Aip03g04323 . . . Amo13g4895 Apr7g1422 . Arst3g05199 . . . . . Bva08g01569 . . . Cca06g00571 . . . . Dod04g1146 . . . . Gma02g01050 Gma01g00524 . . Gso2g0967 Gso2g0967 . . Lal6g0806 Lal22g0708 . . . . Lan11g0810 Lan11g0810 . . . . . . Lasa7g02819 Lasa2g00032 . . . . . . . . Lja2g1225 . Mal6g2053 . Mepo2g02933 . . . . . Mtr5g1736 . . . . Phco3g02838 . . Psa2g2907 . . Pste5g00758 . Pte12g01094 . . . . Pvu2g1067 Pvu8g0406 . . . . . . Ssu2g1515 . . Sto6g2963 Tpr2g2060 . . . . . . . . . . . . . Vivi5g03638 . . .
Vvi1g0060 . . . . . . . . . Aev03g0377 . Ahy13g3886 . Aip03g04322 . . . Amo13g4894 . Apr3g1513 . . . . . . . Bva11g00925 Car06g01853 . . . . . . Dod04g1144 . . . . . . . . . . . . . . . . Lal16g0811 . . . . . . . . . . . . . . . . . . . . Lja4g3508 . . . . . . . . . . . . Phco4g01945 . . . . . Pste3g04003 . . . . . . . Pvu2g1733 . . . . . Spst3g02361 . . . Sto11g0882 . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi1g0051 Chr1 573751 579203 -
Car Car02g00817 Chr02 11705139 11709688 +
Vvi Vvi1g0052 Chr1 586502 589715 +
Vvi Vvi1g0053 Chr1 590563 592779 +
Vvi Vvi1g0054 Chr1 593761 595392 -
Car Car02g00815 Chr02 11697334 11699456 +
Psa Psa7g3069 Chr7 223762807 223765506 -
Vvi Vvi1g0055 Chr1 599284 602644 +
Vvi Vvi1g0056 Chr1 606078 607520 +
Adu Adu04g02886 Chr04 116965860 116967344 -
Aed Aed11g0440 Chr11 3838039 3840594 -
Aev Aev03g0375 Chr03 2771365 2772807 +
Ahy Ahy13g3891 Chr13 138376626 138379018 -
Aip Aip03g04327 Chr03 127725818 127727392 -
Amo Amo13g4906 Chr13 148016668 148018436 -
Apr Apr7g1420 Chr7 21302296 21305032 +
Apr Apr3g1517 Chr3 29959320 29961499 -
Arst Arst3g05203 Chr3 127352723 127354911 -
Arst Arst4g03813 Chr4 116944117 116946901 -
Bach Bach8g02597 Chr8 32404713 32405415 +
Bva Bva08g01572 Chr08 8262068 8264682 -
Bva Bva11g00921 Chr11 11357609 11360202 +
Car Car06g01850 Chr06 18383844 18386824 +
Cca Cca06g00568 Chr06 16741208 16744128 +
Dod Dod04g1150 Chr04 32134632 32137327 -
Gma Gma02g01052 Chr02 11449474 11451946 -
Gma Gma01g00531 Chr01 7632786 7635482 -
Gso Gso2g0969 Chr2 11262859 11265614 -
Gso Gso2g0969 Chr2 11262859 11265614 -
Lal Lal6g0804 Chr6 5394165 5395610 +
Lal Lal22g0705 Chr22 5087507 5088949 +
Lal Lal18g0914 Chr18 11902228 11903673 -
Lal Lal16g0805 Chr16 5213268 5224219 +
Lal Lal15g0779 Chr15 5600644 5603084 +
Lan Lan11g0808 Chr11 7623167 7625656 +
Lan Lan11g0808 Chr11 7623167 7625656 +
Lan Lan11g0808 Chr11 7623167 7625656 +
Lan Lan11g0808 Chr11 7623167 7625656 +
Lan Lan11g0808 Chr11 7623167 7625656 +
Lapu Lapu3g02288 Chr3 44061081 44062526 -
Lapu Lapu1g01292 Chr1 25700557 25703452 +
Lja Lja2g1227 Chr2 11619135 11621714 -
Lja Lja4g3510 Chr4 66015385 66017411 -
Mal Mal6g2057 Chr6 47196666 47198114 -
Mepo Mepo2g02954 Chr2 39260276 39262669 -
Mepo Mepo3g00244 Chr3 3375747 3378733 -
Mesa Mesa13g02098 Chr13 24629463 24630987 +
Mesa Mesa25g04543 Chr25 82914913 82916355 +
Mtr Mtr5g1741 Chr5 19250544 19253199 -
Phac Phac2g01719 Chr2 18949949 18951544 -
Phco Phco4g01927 Chr4 38235842 38237287 +
Phco Phco3g02899 Chr3 55435786 55437228 -
Psa Psa2g2914 Chr2 336285498 336288221 +
Pste Pste3g04001 Chr3 33925098 33926543 +
Pste Pste5g00714 Chr5 4652201 4653643 +
Pte Pte7g00841 Chr7 32577334 32578776 -
Pte Pte4g00646 Chr4 37349164 37352162 +
Pvu Pvu2g1062 Chr2 20705149 20707329 +
Pvu Pvu8g0356 Chr8 2917490 2920530 +
Spst Spst3g02346 Chr3 67175881 67177326 +
Ssu Ssu2g1513 Chr2 62053306 62054748 +
Sto Sto11g0877 Chr11 9428561 9430003 +
Sto Sto6g2959 Chr6 36761494 36762939 +
Tpr Tpr2g2063 Chr2 24732520 24735173 -
Trre Trre7g02025 Chr7 16037525 16039054 -
Trre Trre13g00274 Chr13 2192294 2193736 +
Tsu Tsu05g02018 Chr05 23487011 23489585 -
Vivi Vivi6g00385 Chr6 9644414 9647507 -
Vvi Vvi1g0057 Chr1 611149 613303 +
Apr Apr3g1516 Chr3 29947577 29951088 -
Bva Bva11g00922 Chr11 11360924 11363983 +
Lal Lal23g0826 Chr23 10723403 10726920 -
Lal Lal16g0807 Chr16 5226016 5229403 +
Lal Lal15g0780 Chr15 5605017 5608420 +
Phco Phco4g01948 Chr4 38595324 38597247 -
Pvu Pvu2g1735 Chr2 31135414 31138907 -
Spst Spst3g02365 Chr3 67335140 67336856 -
Vvi Vvi1g0058 Chr1 616107 617675 +
Aed Aed11g0439 Chr11 3825258 3826808 -
Aev Aev03g0376 Chr03 2775708 2777261 +
Ahy Ahy13g3890 Chr13 138366539 138369244 -
Aip Aip03g04326 Chr03 127716878 127719312 -
Amo Amo13g4905 Chr13 148006621 148008307 -
Apr Apr7g1421 Chr7 21317794 21319317 +
Bach Bach4g01347 Chr4 9461163 9462683 -
Bva Bva08g01571 Chr08 8256505 8258816 -
Bva Bva11g00923 Chr11 11367925 11369445 +
Car Car02g00813 Chr02 11618224 11620446 -
Cca Cca06g00570 Chr06 16785159 16787004 +
Dod Dod04g1149 Chr04 32126101 32128238 -
Gma Gma02g01051 Chr02 11430791 11432296 -
Gma Gma01g00525 Chr01 7509003 7510682 -
Gso Gso2g0968 Chr2 11245928 11248620 -
Gso Gso2g0968 Chr2 11245928 11248620 -
Lal Lal6g0805 Chr6 5401219 5403531 +
Lal Lal22g0706 Chr22 5098931 5100433 +
Lal Lal18g0913 Chr18 11851582 11853454 -
Lal Lal23g0825 Chr23 10720177 10721550 -
Lal Lal16g0808 Chr16 5232494 5233756 +
Lal Lal15g0781 Chr15 5610805 5612909 +
Lan Lan11g0809 Chr11 7634422 7636908 +
Lan Lan11g0809 Chr11 7634422 7636908 +
Lan Lan11g0809 Chr11 7634422 7636908 +
Lan Lan11g0809 Chr11 7634422 7636908 +
Lan Lan11g0809 Chr11 7634422 7636908 +
Lan Lan11g0809 Chr11 7634422 7636908 +
Lja Lja2g1226 Chr2 11608301 11609857 -
Lja Lja4g3509 Chr4 66009865 66011831 -
Mal Mal6g2056 Chr6 47171792 47173351 -
Mtr Mtr5g1738 Chr5 19224850 19227174 -
Phco Phco4g01947 Chr4 38580846 38582336 -
Psa Psa2g2909 Chr2 335855530 335858369 +
Pste Pste3g04002 Chr3 33938065 33939951 +
Pumo Pumo8g00961 Chr8 35200250 35202502 +
Pvu Pvu2g1734 Chr2 31119036 31122808 -
Rops Rops1g01164 Chr1 27185998 27188599 -
Seca Seca10g01810 Chr10 19976396 19977868 -
Spst Spst3g02363 Chr3 67331264 67332742 -
Ssu Ssu2g1514 Chr2 62095037 62096554 +
Sto Sto11g0879 Chr11 9439240 9440890 -
Tpr Tpr2g2062 Chr2 24718929 24721079 -
Tsu Tsu05g02017 Chr05 23471805 23473367 -
Vian Vian10g01542 Chr10 26216023 26217516 +
Vifa Vifa1g05514 Chr1 856049356 856050813 -
Viun Viun2g00857 Chr2 19224576 19226877 +
Vvi Vvi1g0059 Chr1 630941 633424 -
Aed Aed11g0438 Chr11 3808611 3811492 +
Ahy Ahy13g3887 Chr13 138316184 138320645 +
Aip Aip03g04323 Chr03 127670823 127675181 +
Amo Amo13g4895 Chr13 147883881 147888158 +
Apr Apr7g1422 Chr7 21331486 21339592 -
Arst Arst3g05199 Chr3 127307004 127311028 +
Bva Bva08g01569 Chr08 8241839 8248501 +
Cca Cca06g00571 Chr06 16799551 16807250 -
Dod Dod04g1146 Chr04 32075650 32080782 +
Gma Gma02g01050 Chr02 11412483 11419700 +
Gma Gma01g00524 Chr01 7492056 7499932 +
Gso Gso2g0967 Chr2 11227738 11235005 +
Gso Gso2g0967 Chr2 11227738 11235005 +
Lal Lal6g0806 Chr6 5410457 5417649 -
Lal Lal22g0708 Chr22 5108242 5112303 -
Lan Lan11g0810 Chr11 7645524 7653070 -
Lan Lan11g0810 Chr11 7645524 7653070 -
Lasa Lasa7g02819 Chr7 551525907 551529173 -
Lasa Lasa2g00032 Chr2 2359264 2363477 -
Lja Lja2g1225 Chr2 11595662 11601161 +
Mal Mal6g2053 Chr6 47068143 47072861 +
Mepo Mepo2g02933 Chr2 39108146 39111652 -
Mtr Mtr5g1736 Chr5 19194159 19205564 +
Phco Phco3g02838 Chr3 54814970 54820165 +
Psa Psa2g2907 Chr2 335666076 335671610 +
Pste Pste5g00758 Chr5 4842135 4846949 +
Pte Pte12g01094 Chr12 28041895 28050374 +
Pvu Pvu2g1067 Chr2 20868782 20871665 +
Pvu Pvu8g0406 Chr8 3354570 3359078 -
Ssu Ssu2g1515 Chr2 62135893 62139128 -
Sto Sto6g2963 Chr6 36792246 36795486 -
Tpr Tpr2g2060 Chr2 24682587 24690100 +
Vivi Vivi5g03638 Chr5 129568193 129573394 -
Vvi Vvi1g0060 Chr1 649077 654363 -
Aev Aev03g0377 Chr03 2781713 2786794 -
Ahy Ahy13g3886 Chr13 138301098 138306864 +
Aip Aip03g04322 Chr03 127660395 127665549 +
Amo Amo13g4894 Chr13 147874789 147880576 +
Apr Apr3g1513 Chr3 29913549 29923987 +
Bva Bva11g00925 Chr11 11378441 11384708 -
Car Car06g01853 Chr06 18409373 18416350 -
Dod Dod04g1144 Chr04 32043601 32051527 +
Lal Lal16g0811 Chr16 5244765 5252159 -
Lja Lja4g3508 Chr4 65971871 65978146 +
Phco Phco4g01945 Chr4 38554744 38563650 +
Pste Pste3g04003 Chr3 33950254 33960105 -
Pvu Pvu2g1733 Chr2 31098506 31107502 +
Spst Spst3g02361 Chr3 67304968 67317441 +
Sto Sto11g0882 Chr11 9453493 9460056 -
Phac Phac2g01719 Chr2 18949949 18951544 -
Adu Adu04g02886 Chr04 116965860 116967344 -
Arst Arst4g03813 Chr4 116944117 116946901 -
Bach Bach8g02597 Chr8 32404713 32405415 +
Lapu Lapu1g01292 Chr1 25700557 25703452 +
Mepo Mepo3g00244 Chr3 3375747 3378733 -
Mesa Mesa25g04543 Chr25 82914913 82916355 +
Phco Phco3g02899 Chr3 55435786 55437228 -
Pste Pste5g00714 Chr5 4652201 4653643 +
Pte Pte7g00841 Chr7 32577334 32578776 -
Pte Pte4g00646 Chr4 37349164 37352162 +
Pvu Pvu8g0356 Chr8 2917490 2920530 +
Trre Trre13g00274 Chr13 2192294 2193736 +
Vivi Vivi6g00385 Chr6 9644414 9647507 -