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
Vvi18g0006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma17g02504 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g3369 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0007 . . . . Adu08g00107 . . . . . . . . . . . . . . . Arst8g00129 . Bach12g00137 . . . Bva06g01806 . . Car05g03367 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g3369 Mal1g6167 Mal2g0336 . . . . . . Mtr1g0773 Mtr3g4382 . . Phco7g00333 . . . . . Pste2g00776 . . . . . . . Pvu9g0133 . Rops10g02420 . Seca4g00502 . Spst9g00330 . . . . Sto9g3768 . Tpr7g0126 . . . Tsu07g00141 Vian4g02352 . . . Vimu10g03440 . Viun9g03621 . Vivi4g05853 . . .
Vvi18g0008 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g3767 . . . . . . . . . . . . . . . . . .
Vvi18g0009 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0010 . . . . . Adu06g01341 Aed11g0001 . . Aev07g2399 . Ahy16g0001 . Aip06g00001 . . . . Apr9g0701 . . Arst6g01770 . Bach3g02521 . Bisa05g0476 Bva06g01807 . . . Cca05g00439 . . . . Dod08g2339 . . . Glsi10g0004 . . Gma14g02189 Gma17g02504 . . . . . . . . . . . . . . . . . Lapu8g01075 . Lasa6g00347 . . . . . . . . . Lja5g3367 Mal1g6164 . . Mepo4g01954 . Mesa1g00002 . . Mtr1g0772 . . . . Phco2g00006 . . . . . Pste8g01500 . . Pte3g01459 . . . . Pvu1g0005 . Rops9g02522 . Seca8g04176 . Spst8g02096 . . Sto5g0002 Sto9g3766 . . . . Tsu01g00149 . . Vian7g00965 . . . . . . . Vivi4g06004 Vra6g1981 .
Vvi18g0011 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0012 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0013 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0015 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Gma Gma14g02189 Chr14 53026889 53032132 -
Vvi Vvi18g0006 Chr18 93872 95154 +
Gma Gma17g02504 Chr17 43038198 43042322 -
Lja Lja5g3369 Chr5 65816264 65823803 -
Vvi Vvi18g0007 Chr18 99836 105167 +
Adu Adu08g00107 Chr08 1428022 1429765 +
Arst Arst8g00129 Chr8 1427940 1430543 +
Bach Bach12g00137 Chr12 960248 968386 -
Bva Bva06g01806 Chr06 12478620 12482226 +
Car Car05g03367 Chr05 78305778 78308078 -
Lja Lja5g3369 Chr5 65816264 65823803 -
Mal Mal1g6167 Chr1 140853491 140856370 -
Mal Mal2g0336 Chr2 3759954 3762033 -
Mtr Mtr1g0773 Chr1 8690979 8694191 -
Mtr Mtr3g4382 Chr3 57750012 57752442 +
Phco Phco7g00333 Chr7 2372152 2374870 -
Pste Pste2g00776 Chr2 8221911 8224863 -
Pvu Pvu9g0133 Chr9 2044053 2047408 +
Rops Rops10g02420 Chr10 42407344 42410307 +
Seca Seca4g00502 Chr4 8218181 8221189 -
Spst Spst9g00330 Chr9 3140329 3142494 -
Sto Sto9g3768 Chr9 35768860 35772838 -
Tpr Tpr7g0126 Chr7 1009745 1012333 -
Tsu Tsu07g00141 Chr07 1073505 1076347 -
Vian Vian4g02352 Chr4 40219877 40222586 +
Vimu Vimu10g03440 Chr10 44198504 44200887 +
Viun Viun9g03621 Chr9 41664864 41668109 +
Vivi Vivi4g05853 Chr4 195051674 195054464 +
Vvi Vvi18g0008 Chr18 139909 154055 +
Sto Sto9g3767 Chr9 35758124 35765252 -
Vvi Vvi18g0009 Chr18 160192 165198 -
Vvi Vvi18g0010 Chr18 170677 177316 +
Adu Adu06g01341 Chr06 18627835 18632279 +
Aed Aed11g0001 Chr11 8571 14549 +
Aev Aev07g2399 Chr07 24643110 24647066 -
Ahy Ahy16g0001 Chr16 14387 18970 -
Aip Aip06g00001 Chr06 10217 14708 -
Apr Apr9g0701 Chr9 11721112 11726448 -
Arst Arst6g01770 Chr6 18660722 18665123 +
Bach Bach3g02521 Chr3 31117413 31120249 +
Bisa Bisa05g0476 Chr05 7728837 7733759 +
Bva Bva06g01807 Chr06 12484522 12489067 +
Cca Cca05g00439 Chr05 9593074 9600271 +
Dod Dod08g2339 Chr08 51575675 51582827 -
Glsi Glsi10g0004 Chr10 66812 72915 +
Gma Gma14g02189 Chr14 53026889 53032132 -
Gma Gma17g02504 Chr17 43038198 43042322 -
Lapu Lapu8g01075 Chr8 28716629 28725178 +
Lasa Lasa6g00347 Chr6 9883736 9887434 -
Lja Lja5g3367 Chr5 65780025 65786267 -
Mal Mal1g6164 Chr1 140791785 140796788 -
Mepo Mepo4g01954 Chr4 24766891 24771126 -
Mesa Mesa1g00002 Chr1 51038 52807 +
Mtr Mtr1g0772 Chr1 8681814 8686114 -
Phco Phco2g00006 Chr2 95947 102544 +
Pste Pste8g01500 Chr8 8235365 8243011 -
Pte Pte3g01459 Chr3 12848171 12850696 -
Pvu Pvu1g0005 Chr1 125452 132387 +
Rops Rops9g02522 Chr9 47471560 47478001 -
Seca Seca8g04176 Chr8 118966681 118966887 -
Spst Spst8g02096 Chr8 29216396 29218805 -
Sto Sto5g0002 Chr5 23549 24966 +
Sto Sto9g3766 Chr9 35747620 35752102 -
Tsu Tsu01g00149 Chr01 1145378 1156473 +
Vian Vian7g00965 Chr7 17855918 17856472 +
Vivi Vivi4g06004 Chr4 197262430 197266378 -
Vra Vra6g1981 Chr6 36440209 36447937 +
Vvi Vvi18g0011 Chr18 180008 216858 -
Vvi Vvi18g0012 Chr18 227521 228027 +
Vvi Vvi18g0013 Chr18 229614 232675 -
Vvi Vvi18g0014 Chr18 233919 235470 -
Vvi Vvi18g0015 Chr18 249632 255426 +
Adu Adu08g00107 Chr08 1428022 1429765 +
Arst Arst8g00129 Chr8 1427940 1430543 +
Bach Bach12g00137 Chr12 960248 968386 -
Phco Phco7g00333 Chr7 2372152 2374870 -
Pste Pste2g00776 Chr2 8221911 8224863 -
Pvu Pvu9g0133 Chr9 2044053 2047408 +
Rops Rops10g02420 Chr10 42407344 42410307 +
Seca Seca4g00502 Chr4 8218181 8221189 -
Spst Spst9g00330 Chr9 3140329 3142494 -
Vian Vian4g02352 Chr4 40219877 40222586 +
Vimu Vimu10g03440 Chr10 44198504 44200887 +
Viun Viun9g03621 Chr9 41664864 41668109 +
Vivi Vivi4g05853 Chr4 195051674 195054464 +
Vivi Vivi4g05853 Chr4 195051674 195054464 +