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
Vvi17g0683 Acco04g2783 . . . Adu01g03226 . Aed10g1092 Aed6g1610 . . . . . . Alju06g2744 . . . Apr1g0960 Apr9g2970 Arst1g04174 . Bach10g01095 . Bisa08g1769 . Bva06g01170 . . Car05g00729 Cca03g00631 Cca11g01995 Dere03g0968 . . . Enph6g0742 . . . . Gma04g01588 Gma05g00224 . . . . . . Lal7g1365 Lal14g1892 . . . . . . . . . Lapu3g00989 . Lasa4g03320 . Lele21g1935 Lele22g1902 Lele23g0076 Lele24g1852 . . . . . Lja4g2102 Mal5g4306 Mal2g5076 Mepo1g01224 . Mesa29g01257 . Mibi09g0084 . Mtr4g3967 Mtr3g0583 Phac3g02857 . Phco8g01389 . Prci4g3095 . . . Pste6g02641 . Pte14g00057 Pte2g02213 . . Pumo4g01248 . Pvu3g1927 . Rops2g03841 . Seca4g03306 . Spst3g04739 . Ssu1g2062 Ssu6g1220 Sto3g1598 . Tpr3g4448 Tpr3g4448 Trre15g04270 . Tsu04g03737 Tsu03g01705 Vian1g00814 . Vifa2g00567 . Vimu7g00838 . Viun3g04628 . Vivi1g01874 . . Vra7g1925
Vvi17g0684 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva05g00524 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0685 . . . . . . Aed10g0993 . Aev01g2157 . Ahy11g1981 . Aip01g02192 . . . . . . . . . . . . . . . . Car05g00730 Cca03g00523 . . . Dod05g1774 . . . . . Gma06g01801 . . Gma17g00722 Gso6g1689 . . Gso6g1689 . . . . . . . . . . . . . . . . . . . . . . . . Lja1g5566 . . Mal2g5078 . . . . . . . Mtr3g0580 . . . . . . Psa4g1134 . . . . . . . . . . . . . . . . . Ssu1g2174 . . Sto12g0942 . . . . . . . . . . . . . . . . . .
Vvi17g0686 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0687 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0688 . . . . . . . . . . . . . . . . . . Apr1g0867 . . . . . . . . . . . . . . . . . . . . . Gma06g01676 . . . Gso6g1578 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal2g4906 . . . . . . . Mtr3g0569 . . . . . . . Psa5g4556 . . . . . . . . . . . . . . . . . . . . . Tpr3g4443 . . . Tsu03g01699 . . . . . . . . . . . .
Vvi17g0689 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal2g4910 . . . . . . . Mtr3g0563 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr3g4442 . . . Tsu03g01698 . . . . . . . . . . . .
Vvi17g0690 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi17g0691 . . . . . . Aed10g1100 . . . . . . . . . . . Apr1g0964 . . . . . . . Bva06g01165 Bva05g00529 . Car05g00732 Cca03g00637 . . . . . . . . . Gma06g01808 Gma04g01584 . . Gso6g1704 Gso6g1704 . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g5573 . . Mal2g5071 . Mepo5g02839 . Mesa9g00706 . . . Mtr3g0589 . . . Phco7g02322 . . . . . . . . Pte3g00410 . . Pumo10g02219 . Pvu9g2001 . Rops10g00478 . Seca4g03313 . . Ssu1g2056 . Sto3g1601 Sto12g0947 . Tpr3g4453 . Trre5g01749 . Tsu03g01710 . . . Vifa2g00563 . Vimu10g00958 . . . . Vra3g1129 .
Vvi17g0692 Acco06g1641 . Accr5g01452 . Adu10g02285 . Aed10g1101 . . . . Ahy20g2444 . Aip10g02877 Alju03g1742 . . Amo20g3201 Apr1g0965 . . . Bach1g01068 . Bisa07g2527 . . Bva05g00531 . Car05g00733 Cca03g00639 . Dere02g2021 . . Dod09g0467 Enph4g1079 . Glsi11g1912 . Gma06g01809 . . . Gso6g1705 . . . . . . . . . . . . . . . Lapu4g01395 . Lasa1g04783 . . . . . . . . . . . . Mal2g5068 Mepo5g03676 Mepo5g02840 Mesa22g00339 . Mibi06g1428 . . Mtr3g0590 . . . Phco7g02320 . . . . Pste9g00551 Pste2g00498 . . . . Pumo2g02517 . Pvu4g0287 Pvu9g1998 Rops5g01352 . . . . . . . Sto3g1604 . . Tpr3g4454 . . . . Vian8g00272 . . . . Vimu10g00961 . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Mal Mal2g5071 Chr2 118803677 118809454 +
Mtr Mtr3g0589 Chr3 7776727 7782255 -
Tpr Tpr3g4453 Chr3 49565118 49571179 -
Tsu Tsu03g01710 Chr03 17462203 17469006 -
Vvi Vvi17g0683 Chr17 7520884 7524286 +
Acco Acco04g2783 Chr04 44602257 44604795 -
Adu Adu01g03226 Chr01 104661924 104663432 +
Aed Aed10g1092 Chr10 9949206 9953725 -
Aed Aed6g1610 Chr6 20052891 20056023 -
Alju Alju06g2744 Chr06 54407864 54410247 -
Apr Apr1g0960 Chr1 14179064 14181592 -
Apr Apr9g2970 Chr9 36572825 36575864 +
Arst Arst1g04174 Chr1 103928651 103931116 +
Bach Bach10g01095 Chr10 8112492 8114356 -
Bisa Bisa08g1769 Chr08 42188171 42190742 +
Bva Bva06g01170 Chr06 9218359 9221219 +
Car Car05g00729 Chr05 41377243 41381699 +
Cca Cca03g00631 Chr03 11093769 11096274 -
Cca Cca11g01995 Chr11 45377702 45380867 -
Dere Dere03g0968 Chr03 14835999 14838921 -
Enph Enph6g0742 Chr6 10381260 10385346 -
Gma Gma04g01588 Chr04 43204954 43206847 +
Gma Gma05g00224 Chr05 2061091 2063967 +
Lal Lal7g1365 Chr7 18769857 18774411 +
Lal Lal14g1892 Chr14 18348965 18351702 +
Lapu Lapu3g00989 Chr3 10648563 10651625 +
Lasa Lasa4g03320 Chr4 583984679 583986681 -
Lele Lele21g1935 Chr21 26487214 26489097 -
Lele Lele22g1902 Chr22 23795395 23797796 -
Lele Lele23g0076 Chr23 505436 507336 +
Lele Lele24g1852 Chr24 23388017 23393191 -
Lja Lja4g2102 Chr4 22582316 22585323 +
Mal Mal5g4306 Chr5 114151004 114152831 -
Mal Mal2g5076 Chr2 118863049 118865349 +
Mepo Mepo1g01224 Chr1 11980888 11983467 +
Mesa Mesa29g01257 Chr29 16283622 16285390 +
Mibi Mibi09g0084 Chr09 1391126 1393402 +
Mtr Mtr4g3967 Chr4 53430310 53432786 -
Mtr Mtr3g0583 Chr3 7733057 7736973 -
Phac Phac3g02857 Chr3 30431778 30434888 +
Phco Phco8g01389 Chr8 14406824 14408513 -
Prci Prci4g3095 Chr4 42336196 42339518 -
Pste Pste6g02641 Chr6 13840607 13842894 -
Pte Pte14g00057 Chr14 2884605 2885984 +
Pte Pte2g02213 Chr2 41931127 41934016 -
Pumo Pumo4g01248 Chr4 15966675 15969818 +
Pvu Pvu3g1927 Chr3 39853574 39856440 +
Rops Rops2g03841 Chr2 70687948 70691142 +
Seca Seca4g03306 Chr4 56971855 56975083 -
Spst Spst3g04739 Chr3 99148177 99149822 -
Ssu Ssu1g2062 Chr1 58677898 58679559 +
Ssu Ssu6g1220 Chr6 19948145 19949765 +
Sto Sto3g1598 Chr3 11909182 11911843 -
Tpr Tpr3g4448 Chr3 49527169 49531850 -
Tpr Tpr3g4448 Chr3 49527169 49531850 -
Trre Trre15g04270 Chr15 53330190 53332050 -
Tsu Tsu04g03737 Chr04 46353721 46355549 -
Tsu Tsu03g01705 Chr03 17409452 17412923 -
Vian Vian1g00814 Chr1 8498662 8500311 -
Vifa Vifa2g00567 Chr2 116994419 116996468 +
Vimu Vimu7g00838 Chr7 8267646 8269295 -
Viun Viun3g04628 Chr3 53796631 53799315 -
Vivi Vivi1g01874 Chr1 39873082 39876275 +
Vra Vra7g1925 Chr7 38763979 38766651 -
Vvi Vvi17g0684 Chr17 7530591 7530863 -
Bva Bva05g00524 Chr05 2582223 2582492 +
Vvi Vvi17g0685 Chr17 7532204 7537040 -
Aed Aed10g0993 Chr10 8711107 8715285 +
Aev Aev01g2157 Chr01 25898706 25901593 +
Ahy Ahy11g1981 Chr11 126724505 126729218 +
Aip Aip01g02192 Chr01 115991696 115996145 +
Car Car05g00730 Chr05 41382885 41396407 -
Cca Cca03g00523 Chr03 8683898 8687728 +
Dod Dod05g1774 Chr05 43149309 43155829 +
Gma Gma06g01801 Chr06 18652036 18656496 +
Gma Gma17g00722 Chr17 6114606 6119148 +
Gso Gso6g1689 Chr6 18223106 18228721 +
Gso Gso6g1689 Chr6 18223106 18228721 +
Lja Lja1g5566 Chr1 96990922 96996750 +
Mal Mal2g5078 Chr2 118876185 118880822 -
Mtr Mtr3g0580 Chr3 7714056 7726824 +
Psa Psa4g1134 Chr4 81614091 81620557 -
Ssu Ssu1g2174 Chr1 61990912 61993985 -
Sto Sto12g0942 Chr12 5848809 5852422 +
Vvi Vvi17g0686 Chr17 7542594 7554891 +
Vvi Vvi17g0687 Chr17 7556257 7557107 -
Vvi Vvi17g0688 Chr17 7593722 7599706 -
Apr Apr1g0867 Chr1 11551534 11555793 +
Gma Gma06g01676 Chr06 16753519 16758990 +
Gso Gso6g1578 Chr6 16375927 16380755 +
Mal Mal2g4906 Chr2 113261091 113280603 -
Mtr Mtr3g0569 Chr3 7516485 7532757 +
Psa Psa5g4556 Chr5 402067663 402090449 -
Tpr Tpr3g4443 Chr3 49479035 49495575 +
Tsu Tsu03g01699 Chr03 17352688 17369053 +
Vvi Vvi17g0689 Chr17 7601986 7602915 +
Mal Mal2g4910 Chr2 113386980 113390327 +
Mtr Mtr3g0563 Chr3 7435774 7438136 -
Tpr Tpr3g4442 Chr3 49466488 49469979 +
Tsu Tsu03g01698 Chr03 17347576 17349481 -
Vvi Vvi17g0690 Chr17 7609992 7612967 +
Vvi Vvi17g0691 Chr17 7617269 7632281 -
Aed Aed10g1100 Chr10 10043785 10051303 -
Apr Apr1g0964 Chr1 14240699 14249620 -
Bva Bva06g01165 Chr06 9189890 9195511 +
Bva Bva05g00529 Chr05 2603571 2606881 -
Car Car05g00732 Chr05 41441463 41449254 -
Cca Cca03g00637 Chr03 11209376 11218117 -
Gma Gma06g01808 Chr06 18819014 18826699 -
Gma Gma04g01584 Chr04 43035693 43044134 +
Gso Gso6g1704 Chr6 18476315 18483904 -
Gso Gso6g1704 Chr6 18476315 18483904 -
Lja Lja1g5573 Chr1 97112177 97121925 -
Mal Mal2g5071 Chr2 118803677 118809454 +
Mepo Mepo5g02839 Chr5 34395102 34401278 -
Mesa Mesa9g00706 Chr9 14352040 14357804 -
Mtr Mtr3g0589 Chr3 7776727 7782255 -
Phco Phco7g02322 Chr7 40811808 40819944 +
Pte Pte3g00410 Chr3 3377000 3381888 -
Pumo Pumo10g02219 Chr10 30515686 30522915 -
Pvu Pvu9g2001 Chr9 28696796 28706775 +
Rops Rops10g00478 Chr10 12792760 12797719 +
Seca Seca4g03313 Chr4 57062641 57070156 -
Ssu Ssu1g2056 Chr1 58455727 58463510 +
Sto Sto3g1601 Chr3 11935439 11939469 -
Sto Sto12g0947 Chr12 5878606 5889450 -
Tpr Tpr3g4453 Chr3 49565118 49571179 -
Trre Trre5g01749 Chr5 12826322 12832304 -
Tsu Tsu03g01710 Chr03 17462203 17469006 -
Vifa Vifa2g00563 Chr2 115618665 115622159 +
Vimu Vimu10g00958 Chr10 8591398 8604200 -
Vra Vra3g1129 Chr3 11841347 11848453 +
Vvi Vvi17g0692 Chr17 7650300 7658335 +
Acco Acco06g1641 Chr06 11716244 11722126 +
Accr Accr5g01452 Chr5 40602427 40608108 -
Adu Adu10g02285 Chr10 97500213 97507164 +
Aed Aed10g1101 Chr10 10051138 10066613 +
Ahy Ahy20g2444 Chr20 130278977 130293857 -
Aip Aip10g02877 Chr10 122794604 122809477 -
Alju Alju03g1742 Chr03 45546981 45552604 -
Amo Amo20g3201 Chr20 138019647 138034645 -
Apr Apr1g0965 Chr1 14269832 14291743 +
Bach Bach1g01068 Chr1 23566490 23574021 +
Bisa Bisa07g2527 Chr07 56397458 56403836 -
Bva Bva05g00531 Chr05 2609200 2618621 +
Car Car05g00733 Chr05 41484908 41506515 +
Cca Cca03g00639 Chr03 11229796 11242658 +
Dere Dere02g2021 Chr02 20544704 20552529 +
Dod Dod09g0467 Chr09 6865969 6884198 -
Enph Enph4g1079 Chr4 24149732 24157060 -
Glsi Glsi11g1912 Chr11 12002573 12017219 +
Gma Gma06g01809 Chr06 18839818 18878738 +
Gso Gso6g1705 Chr6 18501207 18535503 +
Lapu Lapu4g01395 Chr4 31033052 31083092 -
Lasa Lasa1g04783 Chr1 787533293 787534258 -
Mal Mal2g5068 Chr2 118604040 118630144 -
Mepo Mepo5g03676 Chr5 45777688 45785446 -
Mepo Mepo5g02840 Chr5 34408360 34427146 +
Mesa Mesa22g00339 Chr22 5468304 5475655 +
Mibi Mibi06g1428 Chr06 34649317 34655951 -
Mtr Mtr3g0590 Chr3 7794066 7811202 +
Phco Phco7g02320 Chr7 40785518 40810628 -
Pste Pste9g00551 Chr9 2806657 2814295 +
Pste Pste2g00498 Chr2 4580294 4604505 -
Pumo Pumo2g02517 Chr2 54798383 54805869 -
Pvu Pvu4g0287 Chr4 2620084 2627427 +
Pvu Pvu9g1998 Chr9 28673326 28695609 -
Rops Rops5g01352 Chr5 28202731 28211226 +
Sto Sto3g1604 Chr3 11956050 11962396 +
Tpr Tpr3g4454 Chr3 49578706 49595511 +
Vian Vian8g00272 Chr8 4438493 4445311 +
Vimu Vimu10g00961 Chr10 8637144 8670714 +