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
Vvi19g0550 . . . . . Adu07g00359 Aed3g2478 . Aev07g0268 . Ahy17g0464 . Aip07g00403 . . . . . . Apr9g1713 . Arst7g00535 . . . Bisa05g2179 Bva12g02774 . Car02g02016 . Cca05g01909 . . . Dod08g0324 . . . . Glsi10g2118 . . Gma02g02718 Gma14g00221 . . . . Lal18g1551 . . . . . Lan2g1292 . . . . . . . . Lasa2g02199 . . . . . . . . . . . Mal8g0498 . . . Mesa17g04320 . . . Mtr5g3255 . Phac8g03544 . Phco3g00286 . . . . . Pste8g00502 . . . Pte4g00084 . Pumo9g01925 . Pvu8g2741 . Rops9g00385 . Seca8g00376 . Spst8g00844 Ssu6g3431 . . Sto5g1973 . Tpr4g3264 . Trre9g04902 . Tsu05g03799 . Vian7g01226 . Vifa1g03207 . Vimu1g00470 . Viun8g02772 . Vivi7g02784 Vra6g0269 .
Vvi19g0551 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva12g02773 . . . . . . . . . . . . . . Gma18g00904 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g1972 . . . . . . . . . . . . . . . . . .
Vvi19g0552 . . . . . . . Aed4g2528 . Aev01g1832 . Ahy11g0157 . Aip01g00146 . . . Amo11g0019 Apr2g0136 . Arst1g00886 . Bach12g01483 . . . . . . . . Cca09g01049 . . . Dod05g0283 . . . . Gma08g02938 . . . Gso8g2594 . . . . . . Lal3g0951 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco11g02078 . . . . . Pste7g01211 . . . . . Pumo1g00943 . Pvu6g0405 . Rops11g02904 . Seca6g03080 . Spst6g02233 . . Ssu9g0888 . . . . . . . . Vian6g00131 . . . Vimu2g02907 . Viun6g00702 . . . . .
Vvi19g0553 . . . . . Adu07g00357 Aed3g2481 . Aev07g0267 . Ahy17g0463 Ahy11g0156 Aip07g00401 Aip01g00145 . . . . Apr2g0137 Apr9g1714 . Arst7g00534 . Bach3g00825 . . Bva12g02772 . Car02g02018 . Cca05g01911 . . . Dod08g0322 Dod05g0282 . . . . . Gma18g00902 Gma02g02720 Gma14g00219 . . . . . Lal22g0089 . . . . . . . . . . . . . Lasa2g02200 . . . . . . . . . . . Mal8g0497 . . . Mesa17g04321 . . . Mtr5g3256 . Phac8g03546 . . . . . . . Pste8g00500 . . . . . Pumo9g01924 . Pvu8g2743 . Rops9g00384 . Seca8g00375 . . Ssu6g3432 . . . . Tpr4g3261 . Trre9g04903 . Tsu05g03801 . Vian7g01225 . Vifa1g03212 . Vimu1g00468 . Viun8g02774 . Vivi7g02782 Vra6g0268 .
Vvi19g0554 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0555 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0556 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0557 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0558 . . . . Adu01g00129 . . Aed4g2525 . Aev01g1834 . Ahy11g0154 . Aip01g00143 . . . Amo11g0021 Apr2g0139 . Arst1g00894 . Bach12g01480 . . . Bva12g02770 . . Car05g00954 . Cca09g01052 . . . Dod05g0280 . . . . Gma08g02941 Gma18g00900 . . Gso8g2597 Gso8g2597 . . . . . . . Lal11g1054 . . . . . . . . Lasa5g00968 . . . . . . . . . . . . . Mepo3g04518 . Mesa9g01593 . . . . . . . Phco11g02072 . . . . . Pste7g01217 . . . . . Pumo1g00940 . Pvu6g0411 . Rops11g02900 . . . Spst6g02240 . . Ssu9g0892 . Sto5g1949 . . Trre5g01420 . . . Vian6g00126 . Vifa2g00880 . Vimu2g02902 . Viun6g00706 . Vivi3g05785 . . .
Vvi19g0559 . . . . . . . . . Aev01g1836 Ahy17g0439 Ahy11g0152 Aip07g00368 Aip01g00141 . . . Amo11g0023 Apr2g0141 Apr9g1719 . . . . . . Bva12g02769 . Car02g02021 Car05g00957 Cca05g01913 Cca09g01054 . . . Dod05g0278 . . . . Gma08g02944 . Gma02g02722 Gma14g00217 Gso8g2600 . Gso8g2600 Gso8g2600 Lal18g1554 . . . . . Lan2g1295 . . . . . . . . . . . . . . . . . . Lja6g2399 . Mal8g0495 . . . . . . . Mtr5g3258 . . . . . . . . . . . . . . . . . . . . . . . . Ssu6g3434 . . Sto5g1944 . Tpr4g3258 . . . Tsu05g03803 . . . . . . . . . . Vra6g0266 Vra6g0266
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Ahy Ahy17g0439 Chr17 4264177 4267043 +
Aip Aip07g00368 Chr07 3225185 3227999 +
Vvi Vvi19g0550 Chr19 6172599 6176239 +
Adu Adu07g00359 Chr07 3415540 3417997 -
Aed Aed3g2478 Chr3 27338192 27341710 +
Aev Aev07g0268 Chr07 1511099 1513175 -
Ahy Ahy17g0464 Chr17 4482724 4485124 -
Aip Aip07g00403 Chr07 3436891 3439341 -
Apr Apr9g1713 Chr9 26311431 26314494 +
Arst Arst7g00535 Chr7 3566036 3568476 -
Bisa Bisa05g2179 Chr05 49160986 49166930 -
Bva Bva12g02774 Chr12 20123074 20125704 -
Car Car02g02016 Chr02 50650995 50654600 +
Cca Cca05g01909 Chr05 38931911 38934832 +
Dod Dod08g0324 Chr08 3529566 3532690 -
Glsi Glsi10g2118 Chr10 16252418 16257576 -
Gma Gma02g02718 Chr02 52896005 52899764 +
Gma Gma14g00221 Chr14 1880674 1883652 -
Lal Lal18g1551 Chr18 17232019 17234000 +
Lan Lan2g1292 Chr2 23847032 23849931 +
Lasa Lasa2g02199 Chr2 496227425 496229440 +
Mal Mal8g0498 Chr8 7463961 7467369 -
Mesa Mesa17g04320 Chr17 73650835 73653782 +
Mtr Mtr5g3255 Chr5 41391005 41394745 +
Phac Phac8g03544 Chr8 42780073 42783106 +
Phco Phco3g00286 Chr3 2042450 2045040 -
Pste Pste8g00502 Chr8 2607861 2613891 -
Pte Pte4g00084 Chr4 1402083 1403425 -
Pumo Pumo9g01925 Chr9 48535980 48539042 -
Pvu Pvu8g2741 Chr8 57683648 57686472 +
Rops Rops9g00385 Chr9 5201644 5204666 -
Seca Seca8g00376 Chr8 4270788 4273260 -
Spst Spst8g00844 Chr8 7572717 7575076 +
Ssu Ssu6g3431 Chr6 76952921 76955423 +
Sto Sto5g1973 Chr5 14758568 14762504 -
Tpr Tpr4g3264 Chr4 38663250 38666526 -
Trre Trre9g04902 Chr9 55371823 55374697 +
Tsu Tsu05g03799 Chr05 49203846 49206836 +
Vian Vian7g01226 Chr7 20469500 20473079 -
Vifa Vifa1g03207 Chr1 502223276 502225014 +
Vimu Vimu1g00470 Chr1 2842671 2846436 -
Viun Viun8g02772 Chr8 36259531 36262055 +
Vivi Vivi7g02784 Chr7 91966603 91968866 -
Vra Vra6g0269 Chr6 1991148 1993714 -
Vvi Vvi19g0551 Chr19 6178875 6179162 -
Bva Bva12g02773 Chr12 20121039 20122907 +
Gma Gma18g00904 Chr18 10635909 10639368 +
Sto Sto5g1972 Chr5 14752805 14755289 +
Vvi Vvi19g0552 Chr19 6182172 6184581 -
Aed Aed4g2528 Chr4 27210845 27212730 +
Aev Aev01g1832 Chr01 23319119 23321420 -
Ahy Ahy11g0157 Chr11 1612202 1614617 +
Aip Aip01g00146 Chr01 1495091 1497658 +
Amo Amo11g0019 Chr11 163229 165584 -
Apr Apr2g0136 Chr2 1982467 1984841 -
Arst Arst1g00886 Chr1 9001838 9004504 -
Bach Bach12g01483 Chr12 10494542 10496047 +
Cca Cca09g01049 Chr09 31070723 31074593 -
Dod Dod05g0283 Chr05 3573890 3576747 -
Gma Gma08g02938 Chr08 45827326 45831132 -
Gso Gso8g2594 Chr8 43557917 43561433 -
Lal Lal3g0951 Chr3 10161195 10163764 -
Phco Phco11g02078 Chr11 17223133 17225878 +
Pste Pste7g01211 Chr7 11222068 11226850 -
Pumo Pumo1g00943 Chr1 14550783 14554850 +
Pvu Pvu6g0405 Chr6 14843654 14846550 -
Rops Rops11g02904 Chr11 50753081 50755884 +
Seca Seca6g03080 Chr6 96893477 96897503 +
Spst Spst6g02233 Chr6 31003019 31004371 -
Ssu Ssu9g0888 Chr9 38209305 38213468 -
Vian Vian6g00131 Chr6 3514280 3517715 +
Vimu Vimu2g02907 Chr2 27524047 27527871 +
Viun Viun6g00702 Chr6 17018303 17022883 -
Vvi Vvi19g0553 Chr19 6186492 6186977 -
Adu Adu07g00357 Chr07 3411879 3414314 +
Aed Aed3g2481 Chr3 27342940 27344678 -
Aev Aev07g0267 Chr07 1508579 1509085 +
Ahy Ahy17g0463 Chr17 4478007 4480612 +
Ahy Ahy11g0156 Chr11 1608313 1610646 +
Aip Aip07g00401 Chr07 3432320 3434773 +
Aip Aip01g00145 Chr01 1491519 1493864 +
Apr Apr2g0137 Chr2 1998149 2000102 -
Apr Apr9g1714 Chr9 26317138 26319139 -
Arst Arst7g00534 Chr7 3562248 3564299 +
Bach Bach3g00825 Chr3 19147766 19148257 -
Bva Bva12g02772 Chr12 20116098 20118696 +
Car Car02g02018 Chr02 50657785 50658321 -
Cca Cca05g01911 Chr05 38948427 38948933 -
Dod Dod08g0322 Chr08 3527110 3527613 +
Dod Dod05g0282 Chr05 3566472 3568976 +
Gma Gma18g00902 Chr18 10612210 10614276 +
Gma Gma02g02720 Chr02 52902287 52902802 -
Gma Gma14g00219 Chr14 1876529 1877038 +
Lal Lal22g0089 Chr22 555065 555829 +
Lasa Lasa2g02200 Chr2 496247141 496247674 -
Mal Mal8g0497 Chr8 7459581 7460102 +
Mesa Mesa17g04321 Chr17 73657774 73658289 -
Mtr Mtr5g3256 Chr5 41398155 41400381 -
Phac Phac8g03546 Chr8 42785529 42788798 -
Pste Pste8g00500 Chr8 2602703 2604422 +
Pumo Pumo9g01924 Chr9 48526872 48530019 +
Pvu Pvu8g2743 Chr8 57689412 57691453 -
Rops Rops9g00384 Chr9 5186913 5189459 +
Seca Seca8g00375 Chr8 4265133 4265645 +
Ssu Ssu6g3432 Chr6 76959574 76960080 -
Tpr Tpr4g3261 Chr4 38638592 38641612 +
Trre Trre9g04903 Chr9 55377151 55377657 -
Tsu Tsu05g03801 Chr05 49225032 49227438 -
Vian Vian7g01225 Chr7 20466909 20467430 +
Vifa Vifa1g03212 Chr1 502718404 502718928 -
Vimu Vimu1g00468 Chr1 2839921 2840442 +
Viun Viun8g02774 Chr8 36264835 36267460 -
Vivi Vivi7g02782 Chr7 91956506 91957033 +
Vra Vra6g0268 Chr6 1986195 1989205 +
Vvi Vvi19g0554 Chr19 6198352 6205465 -
Vvi Vvi19g0555 Chr19 6210099 6210900 +
Vvi Vvi19g0556 Chr19 6213932 6214126 -
Vvi Vvi19g0557 Chr19 6218326 6218538 +
Vvi Vvi19g0558 Chr19 6224950 6230859 +
Adu Adu01g00129 Chr01 1829896 1833658 +
Aed Aed4g2525 Chr4 27185198 27191403 -
Aev Aev01g1834 Chr01 23337837 23342215 +
Ahy Ahy11g0154 Chr11 1585546 1590480 -
Aip Aip01g00143 Chr01 1477004 1482210 -
Amo Amo11g0021 Chr11 178919 184033 +
Apr Apr2g0139 Chr2 2014629 2020118 +
Arst Arst1g00894 Chr1 9044893 9050068 +
Bach Bach12g01480 Chr12 10474562 10479739 -
Bva Bva12g02770 Chr12 20103703 20109240 -
Car Car05g00954 Chr05 49891013 49897683 +
Cca Cca09g01052 Chr09 31110714 31116575 +
Dod Dod05g0280 Chr05 3544547 3550190 -
Gma Gma08g02941 Chr08 45860742 45866997 +
Gma Gma18g00900 Chr18 10561714 10572802 -
Gso Gso8g2597 Chr8 43588817 43595191 +
Gso Gso8g2597 Chr8 43588817 43595191 +
Lal Lal11g1054 Chr11 14149591 14155501 -
Lasa Lasa5g00968 Chr5 262835575 262843439 +
Mepo Mepo3g04518 Chr3 55674749 55681480 +
Mesa Mesa9g01593 Chr9 36724987 36731627 +
Phco Phco11g02072 Chr11 17180694 17187536 -
Pste Pste7g01217 Chr7 11263392 11269806 +
Pumo Pumo1g00940 Chr1 14503492 14510294 -
Pvu Pvu6g0411 Chr6 14895274 14902710 +
Rops Rops11g02900 Chr11 50710824 50717089 -
Spst Spst6g02240 Chr6 31155055 31160969 +
Ssu Ssu9g0892 Chr9 38271726 38277285 +
Sto Sto5g1949 Chr5 14547431 14553333 -
Trre Trre5g01420 Chr5 10054149 10059612 -
Vian Vian6g00126 Chr6 3439910 3442299 -
Vifa Vifa2g00880 Chr2 232073288 232080526 +
Vimu Vimu2g02902 Chr2 27480377 27485165 -
Viun Viun6g00706 Chr6 17054229 17062352 +
Vivi Vivi3g05785 Chr3 134287237 134294220 +
Vvi Vvi19g0559 Chr19 6231742 6232754 -
Aev Aev01g1836 Chr01 23352918 23356712 -
Ahy Ahy17g0439 Chr17 4264177 4267043 +
Ahy Ahy11g0152 Chr11 1572787 1575553 +
Aip Aip07g00368 Chr07 3225185 3227999 +
Aip Aip01g00141 Chr01 1459141 1461660 +
Amo Amo11g0023 Chr11 192752 196628 -
Apr Apr2g0141 Chr2 2036757 2039863 -
Apr Apr9g1719 Chr9 26347474 26349981 -
Bva Bva12g02769 Chr12 20100121 20102829 +
Car Car02g02021 Chr02 50669640 50673814 -
Car Car05g00957 Chr05 49974561 49978091 -
Cca Cca05g01913 Chr05 38963402 38967289 -
Cca Cca09g01054 Chr09 31136621 31148075 -
Dod Dod05g0278 Chr05 3529840 3532546 +
Gma Gma08g02944 Chr08 45919012 45922021 -
Gma Gma02g02722 Chr02 52921246 52923925 -
Gma Gma14g00217 Chr14 1855412 1858215 +
Gso Gso8g2600 Chr8 43640055 43643488 -
Gso Gso8g2600 Chr8 43640055 43643488 -
Gso Gso8g2600 Chr8 43640055 43643488 -
Lal Lal18g1554 Chr18 17247291 17249783 -
Lan Lan2g1295 Chr2 23863666 23866181 -
Lja Lja6g2399 Chr6 52896417 52899346 -
Mal Mal8g0495 Chr8 7436890 7439845 +
Mtr Mtr5g3258 Chr5 41412725 41415670 -
Ssu Ssu6g3434 Chr6 76986600 76989380 -
Sto Sto5g1944 Chr5 14510015 14514766 -
Tpr Tpr4g3258 Chr4 38623551 38626686 +
Tsu Tsu05g03803 Chr05 49236912 49239670 -
Vra Vra6g0266 Chr6 1974205 1976505 +
Vra Vra6g0266 Chr6 1974205 1976505 +
Lal Lal3g0951 Chr3 10161195 10163764 -