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
Vvi18g0706 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0707 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0708 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0709 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0710 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0711 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0713 . . . . . Adu06g03101 Aed6g0393 . . Aev07g0918 . Ahy16g3436 . Aip06g03698 . . . Amo16g4157 Apr9g0358 . . Arst6g03997 . Bach3g02173 . . . Bva10g00633 Car04g03377 . Cca05g00086 . . . . Dod08g1995 . . . . . . Gma14g00789 Gma17g02250 . . . . . . . Lal8g0683 Lal10g0771 Lal25g0612 . . . . . . . . . Lasa6g00033 . . . . . . . . Lja1g4095 Lja5g3075 Mal1g5692 . . Mepo4g00345 . Mesa1g00383 . . Mtr1g0446 . . Phac1g00374 . Phco2g00339 . . . . . Pste8g00783 . . Pte3g01281 . . Pumo9g00350 . Pvu1g0290 . Rops9g02134 . Seca4g01350 . Spst8g02267 Ssu5g0334 . . . Tpr1g3618 . . Trre1g00416 Tsu01g00466 . . Vian7g00657 . Vifa3g04827 . Vimu1g02905 . Viun8g00417 . Vivi4g05519 Vra6g1796 .
Vvi18g0714 . . . . . Adu06g03102 Aed6g0391 . . Aev07g0916 . Ahy16g3437 . Aip06g03699 . . . Amo16g4158 Apr9g0359 . . Arst6g03998 . . . . Bva06g02163 . . . Cca05g00087 . . . . Dod08g1996 . . . . . . Gma14g00788 Gma17g02251 . . . . . . . . . . . . . . . . . Lapu8g00816 . . . . . . . . . . . Lja5g3076 . . . . . . . . . . . Phac1g00373 . Phco2g00338 . . . . . . . . . Pte2g01123 . Pumo9g00349 . Pvu1g0289 . Rops9g02135 . Seca8g03554 . . Ssu5g0333 . . Sto9g3490 . . . . . . . Vian7g00658 . . . Vimu1g02906 . . . . Vra6g1797 .
Vvi18g0715 . Acco05g2011 . Accr3g00976 . Adu06g03104 Aed6g0390 . . Aev07g0914 . Ahy16g3438 . Aip06g03700 . Alju07g1975 . Amo16g4160 Apr9g0360 . . Arst6g04001 . Bach3g02175 . Bisa05g0141 . Bva10g00634 Car04g03378 . Cca05g00088 . . Dere05g1709 . Dod08g1997 . Enph7g0774 . Glsi10g0429 . . Gma14g00787 Gma17g02252 . . . . . . . Lal8g0682 . . . . . . . . . Lapu8g00817 . Lasa6g00034 . . . . Lele25g0815 Lele26g0827 Lele27g1263 Lele28g0812 . Lja5g3078 Mal1g5694 . . Mepo4g00344 . Mesa1g00382 . Mibi08g1736 Mtr1g0447 . . . . Phco2g00337 . Prci2g1300 . . . Pste8g00785 . . . . . Pumo9g00348 . Pvu1g0288 . Rops9g02136 . Seca8g03556 . . Ssu5g0332 . Sto5g1102 . Tpr1g3619 . . Trre1g00415 Tsu01g00465 . . Vian7g00659 . Vifa3g04829 . Vimu1g02909 . Viun8g00416 . Vivi4g05521 Vra6g1798 .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi18g0706 Chr18 7481275 7481835 +
Vvi Vvi18g0707 Chr18 7483891 7484538 -
Vvi Vvi18g0708 Chr18 7484813 7485994 -
Vvi Vvi18g0709 Chr18 7495984 7497239 -
Vvi Vvi18g0710 Chr18 7500196 7511898 -
Vvi Vvi18g0711 Chr18 7515444 7516099 +
Vvi Vvi18g0712 Chr18 7519698 7520681 +
Vvi Vvi18g0713 Chr18 7524945 7526375 +
Adu Adu06g03101 Chr06 109182425 109184029 +
Aed Aed6g0393 Chr6 3405111 3406268 -
Aev Aev07g0918 Chr07 6501659 6502828 -
Ahy Ahy16g3436 Chr16 151638316 151640022 +
Aip Aip06g03698 Chr06 134518999 134521243 +
Amo Amo16g4157 Chr16 154255404 154257034 +
Apr Apr9g0358 Chr9 4806579 4807697 +
Arst Arst6g03997 Chr6 108290614 108291918 +
Bach Bach3g02173 Chr3 28859654 28860706 +
Bva Bva10g00633 Chr10 5537840 5538901 +
Car Car04g03377 Chr04 62304641 62305764 -
Cca Cca05g00086 Chr05 1939246 1941652 +
Dod Dod08g1995 Chr08 47103201 47104418 +
Gma Gma14g00789 Chr14 8165127 8166233 -
Gma Gma17g02250 Chr17 40373048 40374142 +
Lal Lal8g0683 Chr8 4810804 4811871 -
Lal Lal10g0771 Chr10 15444224 15445318 -
Lal Lal25g0612 Chr25 4630999 4634533 -
Lasa Lasa6g00033 Chr6 1283868 1285001 +
Lja Lja1g4095 Chr1 52004856 52006104 +
Lja Lja5g3075 Chr5 60381432 60382850 +
Mal Mal1g5692 Chr1 133531689 133532813 -
Mepo Mepo4g00345 Chr4 5268992 5270562 +
Mesa Mesa1g00383 Chr1 4746614 4747720 +
Mtr Mtr1g0446 Chr1 5164748 5166244 -
Phac Phac1g00374 Chr1 2469756 2472010 -
Phco Phco2g00339 Chr2 2803249 2804340 -
Pste Pste8g00783 Chr8 4029095 4030180 +
Pte Pte3g01281 Chr3 10972174 10973187 +
Pumo Pumo9g00350 Chr9 5491275 5492754 -
Pvu Pvu1g0290 Chr1 2633208 2634434 -
Rops Rops9g02134 Chr9 39309663 39310772 +
Seca Seca4g01350 Chr4 21890559 21891554 +
Spst Spst8g02267 Chr8 33257734 33259595 +
Ssu Ssu5g0334 Chr5 7007290 7008402 -
Tpr Tpr1g3618 Chr1 40348757 40350463 -
Trre Trre1g00416 Chr1 3008819 3009946 +
Tsu Tsu01g00466 Chr01 3982278 3983399 +
Vian Vian7g00657 Chr7 14679505 14681058 +
Vifa Vifa3g04827 Chr3 1396855018 1396856142 -
Vimu Vimu1g02905 Chr1 41460323 41460904 +
Viun Viun8g00417 Chr8 2845531 2847039 -
Vivi Vivi4g05519 Chr4 190112356 190114294 -
Vra Vra6g1796 Chr6 34402935 34404692 +
Vvi Vvi18g0714 Chr18 7529283 7531698 +
Adu Adu06g03102 Chr06 109187385 109190726 +
Aed Aed6g0391 Chr6 3385008 3387302 -
Aev Aev07g0916 Chr07 6485246 6489494 +
Ahy Ahy16g3437 Chr16 151643695 151647781 +
Aip Aip06g03699 Chr06 134523911 134527811 +
Amo Amo16g4158 Chr16 154260786 154264143 +
Apr Apr9g0359 Chr9 4809528 4812476 +
Arst Arst6g03998 Chr6 108295302 108298736 +
Bva Bva06g02163 Chr06 14222326 14224928 -
Cca Cca05g00087 Chr05 1985283 1987925 +
Dod Dod08g1996 Chr08 47125528 47129857 +
Gma Gma14g00788 Chr14 8152891 8155438 -
Gma Gma17g02251 Chr17 40379316 40382232 +
Lapu Lapu8g00816 Chr8 26346610 26348885 +
Lja Lja5g3076 Chr5 60404351 60407504 +
Phac Phac1g00373 Chr1 2462412 2464657 -
Phco Phco2g00338 Chr2 2795090 2797460 -
Pte Pte2g01123 Chr2 12192060 12194326 +
Pumo Pumo9g00349 Chr9 5482989 5485790 -
Pvu Pvu1g0289 Chr1 2624244 2626623 -
Rops Rops9g02135 Chr9 39316239 39318999 +
Seca Seca8g03554 Chr8 102393560 102396559 +
Ssu Ssu5g0333 Chr5 6991080 6994199 -
Sto Sto9g3490 Chr9 34180420 34182618 +
Vian Vian7g00658 Chr7 14686711 14689047 +
Vimu Vimu1g02906 Chr1 41466503 41468696 +
Vra Vra6g1797 Chr6 34409773 34412415 +
Vvi Vvi18g0715 Chr18 7533882 7536226 +
Acco Acco05g2011 Chr05 36474446 36476311 -
Accr Accr3g00976 Chr3 10944809 10946677 +
Adu Adu06g03104 Chr06 109201716 109204677 +
Aed Aed6g0390 Chr6 3382113 3384400 -
Aev Aev07g0914 Chr07 6475270 6477969 -
Ahy Ahy16g3438 Chr16 151660494 151663279 +
Aip Aip06g03700 Chr06 134541243 134544081 +
Alju Alju07g1975 Chr07 46010647 46012505 -
Amo Amo16g4160 Chr16 154274428 154277461 +
Apr Apr9g0360 Chr9 4813419 4815741 +
Arst Arst6g04001 Chr6 108309653 108312595 +
Bach Bach3g02175 Chr3 28866686 28868660 +
Bisa Bisa05g0141 Chr05 2180707 2182996 +
Bva Bva10g00634 Chr10 5539508 5541984 +
Car Car04g03378 Chr04 62329143 62331485 +
Cca Cca05g00088 Chr05 1996530 1998772 +
Dere Dere05g1709 Chr05 26771791 26774767 -
Dod Dod08g1997 Chr08 47130935 47134087 +
Enph Enph7g0774 Chr7 13630232 13634653 -
Glsi Glsi10g0429 Chr10 2743706 2745603 -
Gma Gma14g00787 Chr14 8149930 8152213 -
Gma Gma17g02252 Chr17 40384094 40386300 +
Lal Lal8g0682 Chr8 4806508 4808925 -
Lapu Lapu8g00817 Chr8 26350815 26353168 +
Lasa Lasa6g00034 Chr6 1309475 1311335 +
Lele Lele25g0815 Chr25 5252010 5253667 +
Lele Lele26g0827 Chr26 5311914 5313349 +
Lele Lele27g1263 Chr27 19439751 19441410 -
Lele Lele28g0812 Chr28 5223252 5225135 +
Lja Lja5g3078 Chr5 60454787 60457046 +
Mal Mal1g5694 Chr1 133546954 133548741 +
Mepo Mepo4g00344 Chr4 5259974 5262273 -
Mesa Mesa1g00382 Chr1 4737317 4739168 -
Mibi Mibi08g1736 Chr08 34065896 34067806 -
Mtr Mtr1g0447 Chr1 5172153 5174565 +
Phco Phco2g00337 Chr2 2791744 2793679 -
Prci Prci2g1300 Chr2 9760097 9762708 +
Pste Pste8g00785 Chr8 4039098 4040974 +
Pumo Pumo9g00348 Chr9 5479031 5481518 -
Pvu Pvu1g0288 Chr1 2620429 2622843 -
Rops Rops9g02136 Chr9 39319930 39322248 +
Seca Seca8g03556 Chr8 102438682 102440642 +
Ssu Ssu5g0332 Chr5 6982400 6984141 -
Sto Sto5g1102 Chr5 7404591 7406423 +
Tpr Tpr1g3619 Chr1 40358392 40360713 +
Trre Trre1g00415 Chr1 3000811 3002628 -
Tsu Tsu01g00465 Chr01 3972582 3975083 -
Vian Vian7g00659 Chr7 14690532 14692405 +
Vifa Vifa3g04829 Chr3 1397150814 1397152633 +
Vimu Vimu1g02909 Chr1 41469942 41471825 +
Viun Viun8g00416 Chr8 2834300 2836634 -
Vivi Vivi4g05521 Chr4 190127859 190130179 +
Vra Vra6g1798 Chr6 34413353 34415580 +