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
Vvi4g1184 . . Accr10g00014 . . . . . . . . . . . Alju12g0040 . . . . . Arst3g00662 . . . Bisa01g3991 . Bva08g00775 . . . . . Dere13g0670 . . . . . Glsi09g0585 . . . . Gma16g01256 . . . . . . . . . . . . . . . . . . Lasa4g02317 . . . Lele55g1461 Lele56g1395 . . . . . . . . . . . . Mibi10g0035 . . . Phac3g04022 . . . Prci5g0993 . . . Pste6g00165 . . . . . Pumo4g02136 . Pvu3g2634 . Rops2g03339 . Seca12g02751 . . . . . . . . . . . . . Vian1g01787 . Vifa4g02422 . Vimu11g00659 . Viun3g03653 . Vivi1g03050 . . .
Vvi4g1185 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1186 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto11g1527 . . . . . . . . . . . . . . . . . .
Vvi4g1187 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1188 Acco12g2112 . Accr10g00013 . . . . . . . . . . . Alju12g0039 . . . . . Arst3g00661 . . . Bisa01g3992 . . . . . . . Dere13g0672 . . . Enph14g0571 . . . . . . Gma16g01255 . . . . . . . . . . . . . . . . Lapu3g01668 . Lasa4g02316 . . Lele54g0032 . . . . . . . . . . . . . . Mibi10g0034 . . . Phac3g04023 . . . Prci5g0992 . . . Pste7g01525 . . Pte12g00447 . . . . Pvu3g2635 . . . . . . . . . . . . . . . . . . . . . . . . . Vivi1g03051 . . .
Vvi4g1189 Acco12g2113 . Accr10g00012 . . . . . . . . . . . Alju12g0038 . . . . . Arst3g00660 . . . Bisa01g3996 . . . . . . . Dere13g0673 . . . Enph14g0572 . Glsi09g0586 . . . Gma02g00491 . . . . . . . . . . . . . . . . . . . Lasa4g02315 . . . . Lele56g1396 . . . . . . . . . . . . . . . . . . Phco8g00462 . Prci5g0991 . . Psa4g2214 Pste7g01528 . Pte14g00899 . . . Pumo4g02147 . Pvu3g2636 . Rops2g03337 . Seca12g02757 . Spst3g03867 . . . . . . . . . . . Vian1g01788 . Vifa4g02417 . Vimu11g00660 . Viun3g03652 . Vivi1g03052 . . .
Vvi4g1190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1191 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma16g01254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja4g3204 . . . . . . . . . . . . . . . . . Psa4g2215 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1192 Acco12g2115 . . . . . . . . . . . . . Alju12g0037 . . . . . Arst3g00659 . . . Bisa01g3997 . . . . . . . Dere13g0682 . . . Enph14g0573 . . . . Gma01g01751 Gma02g00489 . . . . . . . . . . . . . . . . . . . . . . . . Lele56g1397 . . . . . . . . . . . . Mibi10g0032 . . . . . Phco8g00461 . Prci5g0942 . . Psa4g2223 Pste6g00123 . . Pte12g00467 . . Pumo4g02148 . Pvu3g2639 . Rops2g03335 . . . Spst3g03866 . . . . Sto11g1526 . . . . . . . . Vifa4g02414 . Vimu7g02994 . . . Vivi1g03053 . . .
Vvi4g1193 . . . . . . . . . . . . . . . . . . . . . . . Bach4g01363 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco4g01944 . . . . . Pste3g04004 . . . . . . . Pvu2g1732 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi4g1184 Chr4 18735818 18737368 -
Accr Accr10g00014 Chr10 237461 239066 +
Alju Alju12g0040 Chr12 668477 670040 +
Arst Arst3g00662 Chr3 4606432 4618623 +
Bisa Bisa01g3991 Chr01 96015130 96018160 -
Bva Bva08g00775 Chr08 3988724 3993948 -
Dere Dere13g0670 Chr13 8308478 8310109 -
Glsi Glsi09g0585 Chr09 4056326 4059502 -
Gma Gma16g01256 Chr16 30729622 30731902 -
Lasa Lasa4g02317 Chr4 457589650 457591146 +
Lele Lele55g1461 Chr55 20777225 20777963 +
Lele Lele56g1395 Chr56 17023886 17025281 -
Mibi Mibi10g0035 Chr10 669958 671576 +
Phac Phac3g04022 Chr3 39761047 39764468 +
Prci Prci5g0993 Chr5 28085256 28089224 +
Pste Pste6g00165 Chr6 539461 544116 -
Pumo Pumo4g02136 Chr4 30623020 30625812 +
Pvu Pvu3g2634 Chr3 48387488 48389492 +
Rops Rops2g03339 Chr2 61364052 61366292 -
Seca Seca12g02751 Chr12 48505225 48508464 +
Vian Vian1g01787 Chr1 21024040 21025727 +
Vifa Vifa4g02422 Chr4 730070178 730071633 +
Vimu Vimu11g00659 Chr11 7074355 7076043 +
Viun Viun3g03653 Chr3 43384247 43386073 -
Vivi Vivi1g03050 Chr1 67237769 67240082 -
Vvi Vvi4g1185 Chr4 18738288 18740034 -
Vvi Vvi4g1186 Chr4 18747798 18748758 -
Sto Sto11g1527 Chr11 14461576 14462160 -
Vvi Vvi4g1187 Chr4 18748814 18770419 -
Vvi Vvi4g1188 Chr4 18771795 18772890 -
Acco Acco12g2112 Chr12 32602295 32603784 -
Accr Accr10g00013 Chr10 229962 231348 +
Alju Alju12g0039 Chr12 656645 658017 +
Arst Arst3g00661 Chr3 4605348 4618622 +
Bisa Bisa01g3992 Chr01 96058046 96060042 +
Dere Dere13g0672 Chr13 8371921 8373668 -
Enph Enph14g0571 Chr14 7571639 7573011 -
Gma Gma16g01255 Chr16 30701143 30721629 -
Lapu Lapu3g01668 Chr3 24611433 24615852 +
Lasa Lasa4g02316 Chr4 457414370 457415717 -
Lele Lele54g0032 Chr54 318749 321191 +
Mibi Mibi10g0034 Chr10 658947 661168 +
Phac Phac3g04023 Chr3 39771732 39774002 +
Prci Prci5g0992 Chr5 28085255 28089224 +
Pste Pste7g01525 Chr7 14000774 14004842 +
Pte Pte12g00447 Chr12 3780097 3781707 -
Pvu Pvu3g2635 Chr3 48409298 48411753 +
Vivi Vivi1g03051 Chr1 67248557 67250161 -
Vvi Vvi4g1189 Chr4 18778206 18779425 -
Acco Acco12g2113 Chr12 32611754 32613137 -
Accr Accr10g00012 Chr10 229893 231348 +
Alju Alju12g0038 Chr12 622700 625844 -
Arst Arst3g00660 Chr3 4599426 4618616 +
Bisa Bisa01g3996 Chr01 96144381 96146377 +
Dere Dere13g0673 Chr13 8399017 8400701 +
Enph Enph14g0572 Chr14 7579502 7581338 -
Glsi Glsi09g0586 Chr09 4065127 4066539 +
Gma Gma02g00491 Chr02 4940451 4946120 -
Lasa Lasa4g02315 Chr4 457321659 457323012 -
Lele Lele56g1396 Chr56 17034816 17038156 -
Phco Phco8g00462 Chr8 4359739 4361549 -
Prci Prci5g0991 Chr5 28085253 28089224 +
Psa Psa4g2214 Chr4 178559207 178560613 +
Pste Pste7g01528 Chr7 14028360 14044046 +
Pte Pte14g00899 Chr14 30730539 30731481 +
Pumo Pumo4g02147 Chr4 31081875 31083693 +
Pvu Pvu3g2636 Chr3 48419574 48421473 +
Rops Rops2g03337 Chr2 61287919 61290576 +
Seca Seca12g02757 Chr12 48817644 48821550 +
Spst Spst3g03867 Chr3 88737764 88740832 -
Vian Vian1g01788 Chr1 21044470 21045699 +
Vifa Vifa4g02417 Chr4 728845206 728847114 +
Vimu Vimu11g00660 Chr11 7092353 7094595 +
Viun Viun3g03652 Chr3 43356078 43358650 -
Vivi Vivi1g03052 Chr1 67253259 67260481 -
Vvi Vvi4g1190 Chr4 18798606 18803911 +
Vvi Vvi4g1191 Chr4 18807648 18813999 -
Gma Gma16g01254 Chr16 30682127 30684458 -
Lja Lja4g3204 Chr4 60586611 60588897 -
Psa Psa4g2215 Chr4 178794885 178796775 +
Vvi Vvi4g1192 Chr4 18815425 18816172 -
Acco Acco12g2115 Chr12 32659005 32660778 +
Alju Alju12g0037 Chr12 596303 598358 -
Arst Arst3g00659 Chr3 4587985 4590099 +
Bisa Bisa01g3997 Chr01 96187111 96190184 -
Dere Dere13g0682 Chr13 8613117 8614846 +
Enph Enph14g0573 Chr14 7600309 7602757 +
Gma Gma01g01751 Chr01 53183991 53188363 -
Gma Gma02g00489 Chr02 4931310 4935396 -
Lele Lele56g1397 Chr56 17046355 17047979 +
Mibi Mibi10g0032 Chr10 611559 613902 -
Phco Phco8g00461 Chr8 4322993 4325754 -
Prci Prci5g0942 Chr5 26546293 26548624 +
Psa Psa4g2223 Chr4 179538642 179540787 +
Pste Pste6g00123 Chr6 373086 379975 -
Pte Pte12g00467 Chr12 3978497 3980107 -
Pumo Pumo4g02148 Chr4 31118794 31121553 +
Pvu Pvu3g2639 Chr3 48435015 48436931 +
Rops Rops2g03335 Chr2 61240074 61242979 -
Spst Spst3g03866 Chr3 88721892 88724174 -
Sto Sto11g1526 Chr11 14447820 14470962 -
Vifa Vifa4g02414 Chr4 727533851 727535449 +
Vimu Vimu7g02994 Chr7 25211538 25214871 +
Vivi Vivi1g03053 Chr1 67343473 67345143 +
Vvi Vvi4g1193 Chr4 18830939 18831569 -
Bach Bach4g01363 Chr4 9565421 9570228 +
Phco Phco4g01944 Chr4 38548010 38550917 +
Pste Pste3g04004 Chr3 33961351 33966328 -
Pvu Pvu2g1732 Chr2 31094659 31098090 +
Gma Gma16g01255 Chr16 30701143 30721629 -
Gma Gma16g01254 Chr16 30682127 30684458 -