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
Vvi2g1162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1163 . . . . Adu05g00283 . Aed11g1088 . . . . . . . . . . . . . Arst5g00357 . Bach4g00855 . . . . . . . Cca06g01141 . . . . . . . . . Gma01g01589 . . . Gso1g1320 . . . Lal15g0320 . . . . . Lan18g0849 . . . . . Lapu2g00986 . Lasa2g03583 . . . . . . . . . . . Mal6g0846 . Mepo5g01153 . Mesa17g01228 . . . Mtr5g1026 . . . Phco4g00720 . . . . . Pste1g03508 . Pte14g00788 Pte12g00584 . . Pumo8g01598 . Pvu2g1245 . Rops1g01409 . Seca10g01145 . Spst2g01047 . Ssu2g2123 . . . Tpr2g1249 . Trre9g01485 . Tsu05g00995 . Vian10g00932 . Vifa1g06234 . Vimu7g03251 . Viun2g01677 . Vivi2g02685 . Vra11g0903 .
Vvi2g1164 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1165 . . . . Adu05g00284 . Aed11g1089 . . . . . . . . . . . Apr7g0303 . Arst5g00358 . Bach4g00854 . . . Bva08g00995 . . . Cca06g01142 . . . . . . . . . Gma01g01590 Gma11g00820 . . Gso1g1321 Gso1g1321 . . . . . . . Lal23g1179 . . . . . . Lapu2g00988 . Lasa2g03582 . . . . . . . . . Lja2g0671 . Mal6g0847 . Mepo5g01151 . Mesa17g01220 . . . Mtr5g1024 . . . Phco4g00721 . . . . . Pste1g03505 . . . . . Pumo8g01599 . Pvu2g1244 . Rops1g01412 . Seca10g01144 . Spst2g01046 . . . Sto6g4067 . Tpr2g1248 . Trre9g01483 . Tsu05g00994 . Vian10g00931 . Vifa1g06235 . Vimu7g03248 . Viun2g01678 . Vivi2g02686 . Vra11g0902 .
Vvi2g1166 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1167 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1168 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1169 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0001 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g00159 Bva14g00231 . . . . . . . . . . . . . . Gma11g01048 . . . . . Lal1g0209 . . . . . Lan13g0216 . . . . . Lapu9g02424 . Lasa5g04719 . . . . . . . . . . . . . . . . . . . . . Phac9g02030 . Phco7g00129 . . . . . . . . . . . . . Pvu9g0051 . . . . . Spst9g00119 . . . . . . . . . . . . . . . Vimu10g03650 . . . Vivi3g00961 . . .
Vvi3g0002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma04g00089 Gma06g00084 . . Gso4g0084 Gso4g0084 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g3230 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi2g1162 Chr2 18562635 18582606 -
Vvi Vvi2g1163 Chr2 18588968 18590737 -
Adu Adu05g00283 Chr05 3021129 3023724 -
Aed Aed11g1088 Chr11 16528946 16531424 -
Arst Arst5g00357 Chr5 3040848 3042992 -
Bach Bach4g00855 Chr4 5707163 5708965 +
Cca Cca06g01141 Chr06 25680809 25682629 -
Gma Gma01g01589 Chr01 51488727 51491636 -
Gso Gso1g1320 Chr1 49763094 49765867 -
Lal Lal15g0320 Chr15 2133666 2137527 +
Lan Lan18g0849 Chr18 13833679 13836332 -
Lapu Lapu2g00986 Chr2 9200201 9203120 -
Lasa Lasa2g03583 Chr2 542696988 542698727 +
Mal Mal6g0846 Chr6 12672209 12672916 +
Mepo Mepo5g01153 Chr5 11686695 11688431 -
Mesa Mesa17g01228 Chr17 15750163 15750627 -
Mtr Mtr5g1026 Chr5 10258481 10260440 -
Phco Phco4g00720 Chr4 5502547 5504565 -
Pste Pste1g03508 Chr1 16431944 16433778 +
Pte Pte14g00788 Chr14 29434328 29437558 -
Pte Pte12g00584 Chr12 5229442 5231307 +
Pumo Pumo8g01598 Chr8 51243735 51245067 -
Pvu Pvu2g1245 Chr2 24398916 24401466 +
Rops Rops1g01409 Chr1 31284023 31284550 +
Seca Seca10g01145 Chr10 11040273 11042048 +
Spst Spst2g01047 Chr2 9159016 9160995 +
Ssu Ssu2g2123 Chr2 76833501 76835955 -
Tpr Tpr2g1249 Chr2 14613989 14618597 +
Trre Trre9g01485 Chr9 12706539 12708284 +
Tsu Tsu05g00995 Chr05 8630541 8634009 +
Vian Vian10g00932 Chr10 9657938 9659825 +
Vifa Vifa1g06234 Chr1 974688368 974690089 -
Vimu Vimu7g03251 Chr7 27499085 27500964 +
Viun Viun2g01677 Chr2 26371502 26373962 -
Vivi Vivi2g02685 Chr2 120288381 120290813 -
Vra Vra11g0903 Chr11 7738825 7741099 +
Vvi Vvi2g1164 Chr2 18594380 18607338 -
Vvi Vvi2g1165 Chr2 18609801 18617173 -
Adu Adu05g00284 Chr05 3031942 3033352 -
Aed Aed11g1089 Chr11 16533787 16535058 -
Apr Apr7g0303 Chr7 8383692 8385908 +
Arst Arst5g00358 Chr5 3051231 3052680 -
Bach Bach4g00854 Chr4 5702652 5703977 +
Bva Bva08g00995 Chr08 5072787 5075888 +
Cca Cca06g01142 Chr06 25697118 25698386 -
Gma Gma01g01590 Chr01 51500785 51502056 -
Gma Gma11g00820 Chr11 6887226 6890009 +
Gso Gso1g1321 Chr1 49774953 49776556 -
Gso Gso1g1321 Chr1 49774953 49776556 -
Lal Lal23g1179 Chr23 13167036 13168328 -
Lapu Lapu2g00988 Chr2 9215634 9217091 -
Lasa Lasa2g03582 Chr2 542672440 542673702 +
Lja Lja2g0671 Chr2 6076031 6078340 +
Mal Mal6g0847 Chr6 12696327 12697604 -
Mepo Mepo5g01151 Chr5 11672792 11674623 +
Mesa Mesa17g01220 Chr17 15657545 15658801 +
Mtr Mtr5g1024 Chr5 10243822 10245445 +
Phco Phco4g00721 Chr4 5512670 5513938 -
Pste Pste1g03505 Chr1 16418439 16419695 +
Pumo Pumo8g01599 Chr8 51253559 51255220 -
Pvu Pvu2g1244 Chr2 24379460 24380942 +
Rops Rops1g01412 Chr1 31300644 31301936 -
Seca Seca10g01144 Chr10 11034465 11035721 +
Spst Spst2g01046 Chr2 9151456 9152733 +
Sto Sto6g4067 Chr6 44285508 44286475 +
Tpr Tpr2g1248 Chr2 14605930 14607465 +
Trre Trre9g01483 Chr9 12685531 12686823 +
Tsu Tsu05g00994 Chr05 8621773 8622908 +
Vian Vian10g00931 Chr10 9638566 9639816 +
Vifa Vifa1g06235 Chr1 974763773 974765035 -
Vimu Vimu7g03248 Chr7 27492296 27493704 +
Viun Viun2g01678 Chr2 26381682 26383110 -
Vivi Vivi2g02686 Chr2 120296033 120297749 -
Vra Vra11g0902 Chr11 7736080 7737504 +
Vvi Vvi2g1166 Chr2 18707208 18708404 -
Vvi Vvi2g1167 Chr2 18719865 18720236 +
Vvi Vvi2g1168 Chr2 18746619 18751138 +
Vvi Vvi2g1169 Chr2 18775046 18778401 +
Vvi Vvi3g0001 Chr3 3056 5194 +
Bva Bva13g00159 Chr13 779708 783777 -
Bva Bva14g00231 Chr14 1205794 1211007 -
Gma Gma11g01048 Chr11 8893020 8893520 -
Lal Lal1g0209 Chr1 1253985 1254461 -
Lan Lan13g0216 Chr13 1359795 1360914 -
Lapu Lapu9g02424 Chr9 38690533 38690966 +
Lasa Lasa5g04719 Chr5 691405841 691406195 +
Phac Phac9g02030 Chr9 18995183 18995839 +
Phco Phco7g00129 Chr7 856417 856818 -
Pvu Pvu9g0051 Chr9 882049 882567 -
Spst Spst9g00119 Chr9 970635 971068 -
Vimu Vimu10g03650 Chr10 45671994 45672379 +
Vivi Vivi3g00961 Chr3 15947975 15948666 +
Vvi Vvi3g0002 Chr3 7116 7422 +
Gma Gma04g00089 Chr04 784995 788210 +
Gma Gma06g00084 Chr06 758686 761587 +
Gso Gso4g0084 Chr4 770167 774486 +
Gso Gso4g0084 Chr4 770167 774486 +
Psa Psa7g3230 Chr7 242063466 242065339 -
Bva Bva13g00159 Chr13 779708 783777 -
Bva Bva14g00231 Chr14 1205794 1211007 -
Gma Gma04g00089 Chr04 784995 788210 +
Gma Gma06g00084 Chr06 758686 761587 +
Gso Gso4g0084 Chr4 770167 774486 +
Gso Gso4g0084 Chr4 770167 774486 +
Gma Gma04g00089 Chr04 784995 788210 +
Gso Gso4g0084 Chr4 770167 774486 +
Gso Gso4g0084 Chr4 770167 774486 +
Gma Gma06g00084 Chr06 758686 761587 +