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
Vvi17g0663 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0664 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0666 . . . . . . Aed10g1080 Aed6g1603 Aev01g2152 . Ahy11g1972 . Aip01g02187 . . . . . Apr1g0953 Apr9g2975 . . . . . . Bva06g01184 Bva05g00515 Car07g00913 Car05g00720 Cca03g00620 Cca11g01988 . . Dod05g1768 . . . . . Gma06g01780 Gma04g01603 Gma05g00232 Gma17g00972 Gso6g1671 Gso6g1671 Gso6g1671 Gso6g1671 . Lal7g1371 Lal14g1896 . . . . . . . . . . . . . . . . . . . . . Lja1g5550 Lja4g2112 Mal5g4297 Mal2g4306 . . . . . . Mtr4g3959 Mtr3g0863 . . . . . . Psa4g1144 Psa5g4629 . . . . . . . . . . . . . . . . Ssu1g2076 Ssu6g1229 Sto3g1592 Sto12g0932 Tpr3g4436 Tpr3g4436 . . Tsu04g03732 Tsu03g01678 . . . . . . . . . . . Vra7g1919
Vvi17g0667 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0668 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g01183 . . . . . . . . . . . . . Gma06g01781 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto3g1593 . . . . . . . . . . . . . . . . . . .
Vvi17g0669 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0670 . . . . Adu01g03232 . . Aed6g1604 . . Ahy11g1973 . Aip01g02188 . . . . . Apr1g0954 . Arst1g04184 . Bach5g00443 . . . Bva06g01181 Bva05g00516 . . . Cca11g01989 . . Dod05g1769 . . . . . Gma06g01782 . Gma05g00231 . Gso6g1672 . Gso6g1672 . . . . . . . . . . . . . Lapu3g00996 . . . . . . . . . . . . Lja4g2111 . . . . . . . . . . . . Phco8g01383 . . . . . Pste6g02626 . Pte3g00425 . . . Pumo4g01255 . Pvu3g1933 . . . Seca4g03296 . Spst3g04733 . . Ssu6g1228 . . . . . . . . Vian1g00807 . . . Vimu7g00832 . Viun3g04619 . . . . Vra7g1920
Vvi17g0671 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0672 . . . . . . Aed10g1082 . . . . . . . . . . . Apr1g0955 . . . . . . . Bva06g01179 Bva05g00517 Car07g00912 . Cca03g00622 . . . . . . . . . Gma06g01783 Gma04g01600 . . Gso6g1673 Gso6g1673 . . . Lal7g1370 Lal14g1895 . . . . . . . . . . . . . . . . . . . . . . Lja4g2109 Mal5g4298 . . . . . . . Mtr4g3960 . . . . . . . Psa4g1143 . . . . . . . . . . . . . . . . . Ssu1g2070 . . Sto12g0934 Tpr5g3068 . . . Tsu04g03733 . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi17g0663 Chr17 7269914 7271213 +
Vvi Vvi17g0664 Chr17 7294538 7295111 +
Vvi Vvi17g0665 Chr17 7296679 7297814 -
Vvi Vvi17g0666 Chr17 7307383 7310795 +
Aed Aed10g1080 Chr10 9795575 9800676 +
Aed Aed6g1603 Chr6 20010006 20014278 +
Aev Aev01g2152 Chr01 25858394 25863645 +
Ahy Ahy11g1972 Chr11 126481700 126485797 +
Aip Aip01g02187 Chr01 115782530 115785930 +
Apr Apr1g0953 Chr1 13900993 13905298 +
Apr Apr9g2975 Chr9 36641009 36644792 -
Bva Bva06g01184 Chr06 9282544 9286712 -
Bva Bva05g00515 Chr05 2530109 2534069 +
Car Car07g00913 Chr07 8101374 8105162 -
Car Car05g00720 Chr05 40446562 40450843 -
Cca Cca03g00620 Chr03 10882670 10886269 +
Cca Cca11g01988 Chr11 45300781 45304910 +
Dod Dod05g1768 Chr05 43100454 43104517 +
Gma Gma06g01780 Chr06 18425237 18429230 +
Gma Gma04g01603 Chr04 43556142 43559732 -
Gma Gma05g00232 Chr05 2127415 2130839 -
Gma Gma17g00972 Chr17 8290043 8292091 +
Gso Gso6g1671 Chr6 17992542 17996599 +
Gso Gso6g1671 Chr6 17992542 17996599 +
Gso Gso6g1671 Chr6 17992542 17996599 +
Gso Gso6g1671 Chr6 17992542 17996599 +
Lal Lal7g1371 Chr7 18799164 18804384 -
Lal Lal14g1896 Chr14 18368395 18372885 -
Lja Lja1g5550 Chr1 96379813 96384012 +
Lja Lja4g2112 Chr4 22666277 22670304 -
Mal Mal5g4297 Chr5 114075942 114079378 +
Mal Mal2g4306 Chr2 81977256 81981046 +
Mtr Mtr4g3959 Chr4 53355994 53359892 +
Mtr Mtr3g0863 Chr3 12748814 12753306 -
Psa Psa4g1144 Chr4 82302501 82306395 -
Psa Psa5g4629 Chr5 409614153 409618158 +
Ssu Ssu1g2076 Chr1 59080015 59083638 -
Ssu Ssu6g1229 Chr6 20078897 20081530 -
Sto Sto3g1592 Chr3 11881185 11884733 +
Sto Sto12g0932 Chr12 5777535 5780944 +
Tpr Tpr3g4436 Chr3 49417921 49423216 +
Tpr Tpr3g4436 Chr3 49417921 49423216 +
Tsu Tsu04g03732 Chr04 46296480 46300116 -
Tsu Tsu03g01678 Chr03 16984983 16990253 +
Vra Vra7g1919 Chr7 38701376 38705334 +
Vvi Vvi17g0667 Chr17 7311700 7311955 -
Vvi Vvi17g0668 Chr17 7313854 7315836 +
Bva Bva06g01183 Chr06 9279956 9281329 -
Gma Gma06g01781 Chr06 18430514 18432921 +
Sto Sto3g1593 Chr3 11885365 11886866 +
Vvi Vvi17g0669 Chr17 7318794 7319944 +
Vvi Vvi17g0670 Chr17 7322936 7323444 +
Adu Adu01g03232 Chr01 104765358 104765830 -
Aed Aed6g1604 Chr6 20016082 20017321 +
Ahy Ahy11g1973 Chr11 126489301 126489991 +
Aip Aip01g02188 Chr01 115788809 115789639 +
Apr Apr1g0954 Chr1 13924149 13924655 -
Arst Arst1g04184 Chr1 104032643 104033378 -
Bach Bach5g00443 Chr5 3003753 3004226 +
Bva Bva06g01181 Chr06 9273536 9274267 -
Bva Bva05g00516 Chr05 2535756 2536330 +
Cca Cca11g01989 Chr11 45313703 45314584 +
Dod Dod05g1769 Chr05 43111376 43112789 +
Gma Gma06g01782 Chr06 18433600 18434155 -
Gma Gma05g00231 Chr05 2121148 2121618 -
Gso Gso6g1672 Chr6 18000848 18001535 -
Gso Gso6g1672 Chr6 18000848 18001535 -
Lapu Lapu3g00996 Chr3 10697577 10698322 -
Lja Lja4g2111 Chr4 22662755 22663675 -
Phco Phco8g01383 Chr8 14361219 14361740 +
Pste Pste6g02626 Chr6 13695110 13695814 +
Pte Pte3g00425 Chr3 3481331 3482760 -
Pumo Pumo4g01255 Chr4 16040914 16041909 -
Pvu Pvu3g1933 Chr3 39902499 39903440 -
Seca Seca4g03296 Chr4 56774173 56775746 -
Spst Spst3g04733 Chr3 99086829 99087320 +
Ssu Ssu6g1228 Chr6 20059314 20059779 -
Vian Vian1g00807 Chr1 8452780 8453250 +
Vimu Vimu7g00832 Chr7 8222971 8224097 +
Viun Viun3g04619 Chr3 53745915 53746706 +
Vra Vra7g1920 Chr7 38725437 38726095 +
Vvi Vvi17g0671 Chr17 7330090 7331247 +
Vvi Vvi17g0672 Chr17 7340062 7342035 +
Aed Aed10g1082 Chr10 9838791 9844739 +
Apr Apr1g0955 Chr1 14031208 14037284 +
Bva Bva06g01179 Chr06 9263216 9269410 -
Bva Bva05g00517 Chr05 2538965 2544887 +
Car Car07g00912 Chr07 8087697 8094528 -
Cca Cca03g00622 Chr03 10929668 10933972 +
Gma Gma06g01783 Chr06 18456359 18462378 +
Gma Gma04g01600 Chr04 43491602 43495142 -
Gso Gso6g1673 Chr6 18023392 18029279 +
Gso Gso6g1673 Chr6 18023392 18029279 +
Lal Lal7g1370 Chr7 18792673 18797785 -
Lal Lal14g1895 Chr14 18362490 18367151 -
Lja Lja4g2109 Chr4 22633438 22638553 -
Mal Mal5g4298 Chr5 114088504 114092434 +
Mtr Mtr4g3960 Chr4 53366200 53370698 +
Psa Psa4g1143 Chr4 82278885 82283665 -
Ssu Ssu1g2070 Chr1 58936284 58938005 -
Sto Sto12g0934 Chr12 5791994 5795424 +
Tpr Tpr5g3068 Chr5 53544230 53548422 +
Tsu Tsu04g03733 Chr04 46320590 46323378 +