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
Vvi17g0823 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0824 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0825 . . . . . . . . . . . . . . . . . . Apr1g0814 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0826 . Acco13g0611 . Accr12g00549 . . . . . . . . . . . . . . . . . Arst10g02879 . Bach2g02133 . Bisa02g1305 . . . Car05g01735 . . . . . . . Enph5g0488 . . . . . . . . . . . . . . . . . . . . . . . Lapu9g00730 . Lasa5g02209 . . . . . . Lele19g0517 . . . . . . Mepo3g05852 . Mesa9g03316 . Mibi13g0604 . . . Phac9g02964 . Phco7g02132 . Prci9g1678 . . . Pste2g00802 . . Pte3g00247 . . Pumo10g02035 . Pvu9g1842 . . . Seca4g03075 . Spst9g02203 . . . . . . . Trre5g02686 . . . . . Vifa2g02035 . Vimu10g01230 . . . Vivi3g03901 . .
Vvi17g0827 . . . . . . Aed10g0941 . . . . . . . . . . . . . . . . . . . . . . . Cca03g00471 . . . . . . . . . . Gma04g01773 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0828 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma04g01774 . . . . . . Lal19g1081 . . . Lal4g1126 . Lan1g1411 . . . Lan1g1411 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto12g0792 . . . . . . . . . . . . . . . . . .
Vvi17g0829 . . . . Adu05g02931 . . . . . . . . . . . . . . . Arst5g03712 . Bach1g01677 . . . . Bva05g00369 . . . . . . . . . . . . Gma06g01628 Gma04g01776 . . Gso6g1532 Gso6g1532 . . . . . . . . . . . . . . . . Lasa1g03617 . . . . . . . . . . . Mal5g4109 . Mepo5g03875 . Mesa22g00136 . . . Mtr4g3813 . . . Phco5g01800 . . . . Psa5g2678 Pste9g00252 . . Pte6g01002 . . . . Pvu4g0156 . Rops5g02236 . Seca10g02909 . Spst4g00060 . . . Sto3g1419 . Tpr5g2924 . Trre11g00209 . Tsu04g02634 . Vian8g00061 . Vifa1g06148 . Vimu8g01082 . . . Vivi2g04498 . . .
Vvi17g0830 . . . . . . . Aed6g1459 Aev01g2018 . Ahy11g1718 . Aip01g01893 . . . . . . . . . . . . . Bva06g01352 . . . . Cca11g01844 . . Dod05g1621 . . . . . . . . Gma17g00842 . . . . . . Lal14g1520 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu6g1372 . . . . . . . . . . . . . . . . . . . Vra7g1636
Vvi17g0831 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0832 Acco04g2581 . Accr8g00169 . Adu01g01871 . . . . . . . . . Alju06g2555 . . . . Apr9g3099 Arst1g02463 . Bach5g00313 . Bisa08g1972 . . . . . . . Dere03g0787 . . . Enph6g0608 . Glsi02g0707 . . . Gma05g00355 . . . . . . Lal7g0923 . . . . . . . . . . Lapu3g01117 . Lasa4g03140 . . Lele22g1766 Lele23g0218 Lele24g1727 . . . . . Lja4g2267 . . Mepo1g01386 . . . Mibi09g0255 . . . Phac3g03079 . . . Prci4g2865 . Psa4g1349 . Pste6g02224 . . . . . Pumo4g01407 . Pvu3g2068 . Rops2g04006 . Seca12g01542 . Spst3g04573 . . . . . . . Trre15g02857 . . . Vian1g01188 . Vifa4g03230 . Vimu7g00674 . Viun3g04427 . . . . .
   
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Select Species Gene Chromosome Start End Strand
Adu Adu05g02931 Chr05 98765893 98767070 +
Vvi Vvi17g0823 Chr17 9403896 9404797 +
Vvi Vvi17g0824 Chr17 9406972 9411665 +
Vvi Vvi17g0825 Chr17 9433647 9439744 +
Apr Apr1g0814 Chr1 10234209 10313551 +
Vvi Vvi17g0826 Chr17 9468816 9484795 +
Acco Acco13g0611 Chr13 4445969 4501452 +
Accr Accr12g00549 Chr12 5196217 5219150 +
Arst Arst10g02879 Chr10 95694875 95737877 +
Bach Bach2g02133 Chr2 28425814 28462103 -
Bisa Bisa02g1305 Chr02 22248986 22277977 +
Car Car05g01735 Chr05 62349690 62407466 +
Enph Enph5g0488 Chr5 3951474 4003887 +
Lapu Lapu9g00730 Chr9 9467036 9551450 +
Lasa Lasa5g02209 Chr5 461650786 461666855 +
Lele Lele19g0517 Chr19 2981591 3006195 +
Mepo Mepo3g05852 Chr3 72838129 72863930 +
Mesa Mesa9g03316 Chr9 63944928 63985763 +
Mibi Mibi13g0604 Chr13 7896425 7928980 +
Phac Phac9g02964 Chr9 28774913 28837252 +
Phco Phco7g02132 Chr7 37674217 37770332 +
Prci Prci9g1678 Chr9 28975908 28988902 -
Pste Pste2g00802 Chr2 8556987 8569276 +
Pte Pte3g00247 Chr3 2094453 2113951 +
Pumo Pumo10g02035 Chr10 27047714 27112568 +
Pvu Pvu9g1842 Chr9 26097296 26161892 +
Seca Seca4g03075 Chr4 52772812 52789260 +
Spst Spst9g02203 Chr9 49291459 49308393 +
Trre Trre5g02686 Chr5 21246065 21310535 -
Vifa Vifa2g02035 Chr2 529336614 529351541 +
Vimu Vimu10g01230 Chr10 12243783 12288012 -
Vivi Vivi3g03901 Chr3 67438400 67528252 -
Vvi Vvi17g0827 Chr17 9499539 9556779 +
Aed Aed10g0941 Chr10 7986675 8048895 +
Cca Cca03g00471 Chr03 7448087 7545338 +
Gma Gma04g01773 Chr04 47344833 47421175 +
Vvi Vvi17g0828 Chr17 9558818 9560880 +
Gma Gma04g01774 Chr04 47456904 47459753 +
Lal Lal19g1081 Chr19 14509537 14512780 +
Lal Lal4g1126 Chr4 14608785 14612258 -
Lan Lan1g1411 Chr1 23842951 23845891 -
Lan Lan1g1411 Chr1 23842951 23845891 -
Sto Sto12g0792 Chr12 5005856 5007505 +
Vvi Vvi17g0829 Chr17 9575132 9576043 +
Adu Adu05g02931 Chr05 98765893 98767070 +
Arst Arst5g03712 Chr5 97443523 97444820 +
Bach Bach1g01677 Chr1 30236746 30237669 -
Bva Bva05g00369 Chr05 1831629 1832765 +
Gma Gma06g01628 Chr06 16024889 16026201 +
Gma Gma04g01776 Chr04 47506798 47508121 +
Gso Gso6g1532 Chr6 15705053 15706385 +
Gso Gso6g1532 Chr6 15705053 15706385 +
Lasa Lasa1g03617 Chr1 653958618 653961021 -
Mal Mal5g4109 Chr5 111472901 111473539 +
Mepo Mepo5g03875 Chr5 48355788 48356612 -
Mesa Mesa22g00136 Chr22 2248054 2248857 +
Mtr Mtr4g3813 Chr4 51875372 51876513 +
Phco Phco5g01800 Chr5 54001921 54002721 -
Psa Psa5g2678 Chr5 204049019 204050866 -
Pste Pste9g00252 Chr9 1141765 1142544 +
Pte Pte6g01002 Chr6 27871820 27873163 +
Pvu Pvu4g0156 Chr4 1411402 1412579 +
Rops Rops5g02236 Chr5 48760775 48761648 +
Seca Seca10g02909 Chr10 38687943 38688731 -
Spst Spst4g00060 Chr4 687625 688407 +
Sto Sto3g1419 Chr3 10363225 10372981 +
Tpr Tpr5g2924 Chr5 52295289 52297140 +
Trre Trre11g00209 Chr11 1676576 1677487 +
Tsu Tsu04g02634 Chr04 29782285 29782989 +
Vian Vian8g00061 Chr8 858041 858859 -
Vifa Vifa1g06148 Chr1 960903022 960903915 -
Vimu Vimu8g01082 Chr8 17925662 17926483 -
Vivi Vivi2g04498 Chr2 160030456 160031726 +
Vvi Vvi17g0830 Chr17 9583558 9590206 -
Aed Aed6g1459 Chr6 18894127 18898705 -
Aev Aev01g2018 Chr01 24873930 24877845 -
Ahy Ahy11g1718 Chr11 108848499 108852698 -
Aip Aip01g01893 Chr01 99753421 99757719 -
Bva Bva06g01352 Chr06 10066883 10071013 +
Cca Cca11g01844 Chr11 43497320 43502871 -
Dod Dod05g1621 Chr05 41300745 41306083 -
Gma Gma17g00842 Chr17 7126148 7132205 -
Lal Lal14g1520 Chr14 16015783 16020732 -
Ssu Ssu6g1372 Chr6 22559081 22565200 +
Vra Vra7g1636 Chr7 34822377 34827066 -
Vvi Vvi17g0831 Chr17 9600692 9601123 +
Vvi Vvi17g0832 Chr17 9603536 9610278 -
Acco Acco04g2581 Chr04 42695116 42701007 -
Accr Accr8g00169 Chr8 2373267 2378953 +
Adu Adu01g01871 Chr01 78164693 78169008 -
Alju Alju06g2555 Chr06 52567173 52575017 -
Apr Apr9g3099 Chr9 37806685 37813868 +
Arst Arst1g02463 Chr1 78393804 78398084 -
Bach Bach5g00313 Chr5 2200192 2202819 -
Bisa Bisa08g1972 Chr08 47339486 47350487 +
Dere Dere03g0787 Chr03 12400826 12406844 -
Enph Enph6g0608 Chr6 9325089 9333388 -
Glsi Glsi02g0707 Chr02 4625926 4631959 -
Gma Gma05g00355 Chr05 3322661 3329787 +
Lal Lal7g0923 Chr7 15660853 15666438 -
Lapu Lapu3g01117 Chr3 12053573 12068943 +
Lasa Lasa4g03140 Chr4 569096855 569105802 -
Lele Lele22g1766 Chr22 22896866 22902222 -
Lele Lele23g0218 Chr23 1478167 1485341 +
Lele Lele24g1727 Chr24 22546442 22551824 -
Lja Lja4g2267 Chr4 24926518 24935353 +
Mepo Mepo1g01386 Chr1 13694377 13701446 +
Mibi Mibi09g0255 Chr09 3150998 3155622 +
Phac Phac3g03079 Chr3 31976671 31989061 +
Prci Prci4g2865 Chr4 40644666 40650900 -
Psa Psa4g1349 Chr4 94380261 94389997 +
Pste Pste6g02224 Chr6 10574905 10583652 -
Pumo Pumo4g01407 Chr4 17847642 17856014 +
Pvu Pvu3g2068 Chr3 41344917 41359097 +
Rops Rops2g04006 Chr2 73258703 73264949 +
Seca Seca12g01542 Chr12 16259264 16262531 +
Spst Spst3g04573 Chr3 97469907 97477614 -
Trre Trre15g02857 Chr15 24722170 24727639 +
Vian Vian1g01188 Chr1 12760147 12769588 +
Vifa Vifa4g03230 Chr4 1016645608 1016652775 -
Vimu Vimu7g00674 Chr7 6717674 6725725 -
Viun Viun3g04427 Chr3 52047419 52056701 -