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
Vvi5g0044 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g0045 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g0046 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g0047 . . . . . Adu04g00818 . . . Aev04g1044 . Ahy14g0898 . Aip04g00982 . . . Amo14g1314 . Apr1g2038 . Arst4g01226 . . . . Bva05g01253 . . . . Cca08g01786 . . . Dod03g1193 . . . . . . . . . . . . . . . . . . . . . . . . . Lapu6g01871 . . . . . . . . . . . Lja6g2765 . . . . . . . . . . . . . Phco11g01150 . . . . . . . . . . . Pumo2g00076 . Pvu6g1254 . . . . . Spst6g01517 . Ssu1g1200 . . . . . . . . . . . . . Vimu2g01459 . . . Vivi5g04872 . Vra10g0754
Vvi5g0048 . . . . Adu01g02526 . Aed6g2290 . . . Ahy11g2698 . Aip01g02944 . . . . . Apr9g2334 . . . . . . . . . Car07g00480 . Cca11g02670 . . . . . . . . . Gma17g00339 Gma07g02289 . . Gso17g0300 Gso17g0300 . . Lal14g1592 . Lal19g1139 . . . Lan12g0908 . Lan12g0908 . . . . . Lasa4g03923 . . . . . . . . . Lja4g1383 . Mal5g4962 . Mepo1g00652 . Mesa29g00626 . . . Mtr4g4483 . . . . . . . . . . . . . . . . . Pvu3g1217 . . . . . . . Ssu6g0442 . Sto3g0780 . Tpr4g1893 . Trre15g04963 . . . . . . . Vimu7g01685 . . . Vivi1g00967 . Vra7g2751 .
Vvi5g0049 . . . . Adu01g02529 . . . Aev01g2848 Aev04g1045 Ahy11g2695 . Aip01g02942 Aip04g00985 . . . Amo14g1317 Apr9g2333 Apr1g2039 Arst1g03285 . Bach5g01044 . . . Bva05g01255 . Car07g00483 . . . . . Dod05g2558 Dod03g1194 . . . . Gma17g00338 . . . Gso17g0299 . . . Lal14g1591 . . . . . Lan12g0907 . . . . . Lapu3g00358 . Lasa4g03922 . . . . . . . . . Lja4g1382 . . . Mepo1g00654 . Mesa29g00630 . . . Mtr4g4480 . . . Phco8g02107 . . . . . Pste6g03957 . . . . . . . Pvu3g1216 . Rops2g04993 . Seca12g00455 . Spst3g02922 . . . . . Tpr4g1900 . Trre15g04961 . Tsu04g04341 . Vian1g00371 . Vifa4g04088 . . . Viun3g05619 . Vivi1g00972 . . .
Vvi5g0050 . . . . . . Aed6g2292 . . Aev04g1046 Ahy11g2679 Ahy14g0900 Aip01g02928 Aip04g00986 . . . . Apr9g2332 Apr1g2040 Arst1g03289 . Bach5g01045 . . . Bva05g01256 . Car07g00485 Car01g00917 Cca11g02671 Cca08g01785 . . . Dod03g1195 . . . . . . Gma09g00302 Gma15g01286 . . . . Lal14g1590 . Lal19g1138 . . . Lan12g0906 . Lan12g0906 . . . . . Lasa4g03917 . . . . . . . . . . Lja6g2767 Mal5g4950 . Mepo1g00657 . Mesa29g00635 . . . Mtr4g4478 Mtr2g1182 . . Phco8g02108 . . . . Psa4g0499 . . . . . . Pumo4g00482 . Pvu3g1215 . Rops2g04991 . Seca12g00454 . . . Ssu6g0440 Ssu1g1202 Sto3g0781 Sto12g1508 Tpr4g1903 Tpr5g1177 Trre15g04957 . Tsu04g04339 Tsu07g01690 Vian1g00368 . Vifa4g04075 . Vimu7g01687 . Viun3g05622 . Vivi1g00977 . Vra7g2753 Vra10g0755
Vvi5g0051 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g0052 . . . . . . Aed6g2293 . Aev01g2850 Aev04g1047 Ahy11g2678 Ahy14g0901 Aip01g02927 Aip04g00987 . . . Amo14g1318 Apr9g2331 Apr1g2041 . . . . . . Bva05g01257 . Car07g00486 Car01g00918 Cca11g02672 Cca08g01784 . . Dod05g2567 Dod03g1196 . . . . Gma17g00335 Gma07g02292 Gma09g00303 Gma15g01287 Gso17g0296 Gso17g0296 Gso17g0296 Gso17g0296 Lal14g1589 Lal7g0985 . . . . Lan12g0905 Lan12g0905 . . . . . . . . . . . . . . . . Lja4g1380 Lja6g2768 Mal5g4947 . . . . . . . Mtr4g4474 Mtr2g1183 . . . . . . . Psa4g0509 . . . . . . . . . . . . . . . . Ssu6g0439 Ssu1g1203 Sto3g0783 Sto12g1510 Tpr4g1905 Tpr5g1176 . . . Tsu07g01694 . . . . . . . . . . Vra7g2754 Vra10g0756
Vvi5g0053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi5g0044 Chr5 441759 444705 -
Vvi Vvi5g0045 Chr5 450116 450364 +
Vvi Vvi5g0046 Chr5 454099 454377 +
Vvi Vvi5g0047 Chr5 455427 464524 +
Adu Adu04g00818 Chr04 11956614 11960361 +
Aev Aev04g1044 Chr04 6541092 6544517 +
Ahy Ahy14g0898 Chr14 14430969 14434706 +
Aip Aip04g00982 Chr04 13833696 13837447 +
Amo Amo14g1314 Chr14 21370272 21374082 +
Apr Apr1g2038 Chr1 29934435 29939028 +
Arst Arst4g01226 Chr4 11920248 11924011 +
Bva Bva05g01253 Chr05 6564337 6568385 +
Cca Cca08g01786 Chr08 50101405 50106186 -
Dod Dod03g1193 Chr03 14904682 14909406 +
Lapu Lapu6g01871 Chr6 18547777 18562693 +
Lja Lja6g2765 Chr6 56758551 56763653 +
Phco Phco11g01150 Chr11 8604164 8619846 +
Pumo Pumo2g00076 Chr2 1573569 1574074 +
Pvu Pvu6g1254 Chr6 23499953 23509477 -
Spst Spst6g01517 Chr6 14231511 14238641 +
Ssu Ssu1g1200 Chr1 26571464 26575292 +
Vimu Vimu2g01459 Chr2 9990595 9995341 +
Vivi Vivi5g04872 Chr5 148213095 148215465 -
Vra Vra10g0754 Chr10 13608852 13614009 +
Vvi Vvi5g0048 Chr5 474053 474586 +
Adu Adu01g02526 Chr01 94450744 94451222 -
Aed Aed6g2290 Chr6 24961463 24961990 +
Ahy Ahy11g2698 Chr11 143497001 143497778 -
Aip Aip01g02944 Chr01 131668377 131668892 +
Apr Apr9g2334 Chr9 30961697 30962297 -
Car Car07g00480 Chr07 4265186 4266035 +
Cca Cca11g02670 Chr11 54104370 54105313 +
Gma Gma17g00339 Chr17 2710391 2711394 -
Gma Gma07g02289 Chr07 45758817 45759353 +
Gso Gso17g0300 Chr17 2670864 2671727 -
Gso Gso17g0300 Chr17 2670864 2671727 -
Lal Lal14g1592 Chr14 16435676 16436221 -
Lal Lal19g1139 Chr19 14927706 14928203 -
Lan Lan12g0908 Chr12 16054580 16055411 +
Lan Lan12g0908 Chr12 16054580 16055411 +
Lasa Lasa4g03923 Chr4 633087353 633087874 -
Lja Lja4g1383 Chr4 12357191 12360561 -
Mal Mal5g4962 Chr5 123138566 123139093 -
Mepo Mepo1g00652 Chr1 6252324 6252942 +
Mesa Mesa29g00626 Chr29 8036551 8037078 +
Mtr Mtr4g4483 Chr4 58805808 58806896 -
Pvu Pvu3g1217 Chr3 29248388 29248930 -
Ssu Ssu6g0442 Chr6 6857633 6858175 -
Sto Sto3g0780 Chr3 5411033 5411548 +
Tpr Tpr4g1893 Chr4 19903284 19903811 -
Trre Trre15g04963 Chr15 59612522 59613052 -
Vimu Vimu7g01685 Chr7 15631732 15633238 +
Vivi Vivi1g00967 Chr1 20288960 20289587 +
Vra Vra7g2751 Chr7 47772749 47773510 +
Vvi Vvi5g0049 Chr5 475375 475884 +
Adu Adu01g02529 Chr01 94498639 94499312 +
Aev Aev01g2848 Chr01 30809891 30810382 +
Aev Aev04g1045 Chr04 6546603 6547148 +
Ahy Ahy11g2695 Chr11 143459124 143459852 -
Aip Aip01g02942 Chr01 131655124 131655915 -
Aip Aip04g00985 Chr04 13857007 13857486 +
Amo Amo14g1317 Chr14 21404109 21404736 +
Apr Apr9g2333 Chr9 30958925 30959485 -
Apr Apr1g2039 Chr1 29942060 29942590 +
Arst Arst1g03285 Chr1 93935199 93935993 -
Bach Bach5g01044 Chr5 7386563 7387108 +
Bva Bva05g01255 Chr05 6571897 6574637 +
Car Car07g00483 Chr07 4281553 4282065 -
Dod Dod05g2558 Chr05 51847183 51848067 +
Dod Dod03g1194 Chr03 14916027 14916817 +
Gma Gma17g00338 Chr17 2707351 2708334 -
Gso Gso17g0299 Chr17 2667769 2668722 -
Lal Lal14g1591 Chr14 16433582 16434799 -
Lan Lan12g0907 Chr12 16048983 16049820 -
Lapu Lapu3g00358 Chr3 3587874 3588626 -
Lasa Lasa4g03922 Chr4 633002874 633003389 -
Lja Lja4g1382 Chr4 12355887 12356775 -
Mepo Mepo1g00654 Chr1 6292252 6293129 +
Mesa Mesa29g00630 Chr29 8085980 8086300 +
Mtr Mtr4g4480 Chr4 58776723 58777687 -
Phco Phco8g02107 Chr8 22515871 22516413 +
Pste Pste6g03957 Chr6 28837846 28838758 +
Pvu Pvu3g1216 Chr3 29228042 29228584 -
Rops Rops2g04993 Chr2 89689462 89689989 -
Seca Seca12g00455 Chr12 3958851 3959387 -
Spst Spst3g02922 Chr3 78872101 78872784 +
Tpr Tpr4g1900 Chr4 19941692 19942578 +
Trre Trre15g04961 Chr15 59602677 59603204 +
Tsu Tsu04g04341 Chr04 51352627 51353575 -
Vian Vian1g00371 Chr1 3295541 3296083 -
Vifa Vifa4g04088 Chr4 1303099202 1303099750 -
Viun Viun3g05619 Chr3 61888857 61890098 +
Vivi Vivi1g00972 Chr1 20372520 20373038 +
Vvi Vvi5g0050 Chr5 476921 477430 +
Aed Aed6g2292 Chr6 24966980 24967546 +
Aev Aev04g1046 Chr04 6551743 6552081 +
Ahy Ahy11g2679 Chr11 143131936 143132793 -
Ahy Ahy14g0900 Chr14 14483290 14484181 +
Aip Aip01g02928 Chr01 131351800 131352736 -
Aip Aip04g00986 Chr04 13865703 13866378 +
Apr Apr9g2332 Chr9 30953401 30954141 -
Apr Apr1g2040 Chr1 29944091 29944807 +
Arst Arst1g03289 Chr1 93983284 93984143 +
Bach Bach5g01045 Chr5 7390775 7391350 +
Bva Bva05g01256 Chr05 6576143 6576988 +
Car Car07g00485 Chr07 4289419 4289940 +
Car Car01g00917 Chr01 8457185 8457972 +
Cca Cca11g02671 Chr11 54111459 54112248 +
Cca Cca08g01785 Chr08 50078773 50079600 -
Dod Dod03g1195 Chr03 14920816 14921547 +
Gma Gma09g00302 Chr09 2847854 2848507 +
Gma Gma15g01286 Chr15 11391967 11392533 +
Lal Lal14g1590 Chr14 16432307 16432870 -
Lal Lal19g1138 Chr19 14925076 14925648 -
Lan Lan12g0906 Chr12 16044585 16045626 -
Lan Lan12g0906 Chr12 16044585 16045626 -
Lasa Lasa4g03917 Chr4 632882165 632882698 +
Lja Lja6g2767 Chr6 56775936 56776490 +
Mal Mal5g4950 Chr5 123064270 123064785 -
Mepo Mepo1g00657 Chr1 6304698 6305596 +
Mesa Mesa29g00635 Chr29 8124697 8125230 +
Mtr Mtr4g4478 Chr4 58759003 58759751 -
Mtr Mtr2g1182 Chr2 12872104 12872879 +
Phco Phco8g02108 Chr8 22529168 22529710 +
Psa Psa4g0499 Chr4 30545678 30546567 +
Pumo Pumo4g00482 Chr4 6342980 6343723 -
Pvu Pvu3g1215 Chr3 29216861 29217699 -
Rops Rops2g04991 Chr2 89677699 89678473 -
Seca Seca12g00454 Chr12 3953170 3956131 -
Ssu Ssu6g0440 Chr6 6844569 6845123 -
Ssu Ssu1g1202 Chr1 26618426 26618992 +
Sto Sto3g0781 Chr3 5414159 5414680 +
Sto Sto12g1508 Chr12 10404530 10406030 +
Tpr Tpr4g1903 Chr4 19948792 19949558 +
Tpr Tpr5g1177 Chr5 23213444 23214117 -
Trre Trre15g04957 Chr15 59596276 59596803 +
Tsu Tsu04g04339 Chr04 51337397 51338126 -
Tsu Tsu07g01690 Chr07 16505588 16505929 +
Vian Vian1g00368 Chr1 3289511 3290071 -
Vifa Vifa4g04075 Chr4 1300130059 1300130448 -
Vimu Vimu7g01687 Chr7 15633999 15634532 +
Viun Viun3g05622 Chr3 61896708 61897300 +
Vivi Vivi1g00977 Chr1 20746819 20747656 +
Vra Vra7g2753 Chr7 47776652 47779079 +
Vra Vra10g0755 Chr10 13617262 13619406 +
Vvi Vvi5g0051 Chr5 478688 479077 -
Vvi Vvi5g0052 Chr5 480742 482540 -
Aed Aed6g2293 Chr6 24969507 24972861 -
Aev Aev01g2850 Chr01 30817405 30819056 -
Aev Aev04g1047 Chr04 6553589 6556937 -
Ahy Ahy11g2678 Chr11 143127805 143130370 +
Ahy Ahy14g0901 Chr14 14485008 14488220 -
Aip Aip01g02927 Chr01 131348173 131350304 +
Aip Aip04g00987 Chr04 13868748 13870285 -
Amo Amo14g1318 Chr14 21416083 21419313 -
Apr Apr9g2331 Chr9 30944254 30947126 +
Apr Apr1g2041 Chr1 29946475 29948097 -
Bva Bva05g01257 Chr05 6577939 6580901 -
Car Car07g00486 Chr07 4295567 4298376 -
Car Car01g00918 Chr01 8464498 8467720 -
Cca Cca11g02672 Chr11 54114908 54118041 -
Cca Cca08g01784 Chr08 50073307 50076981 +
Dod Dod05g2567 Chr05 51921528 51923042 -
Dod Dod03g1196 Chr03 14922236 14925929 -
Gma Gma17g00335 Chr17 2694417 2697181 +
Gma Gma07g02292 Chr07 45770383 45773385 -
Gma Gma09g00303 Chr09 2850264 2852073 -
Gma Gma15g01287 Chr15 11394806 11398648 -
Gso Gso17g0296 Chr17 2654751 2657554 +
Gso Gso17g0296 Chr17 2654751 2657554 +
Gso Gso17g0296 Chr17 2654751 2657554 +
Gso Gso17g0296 Chr17 2654751 2657554 +
Lal Lal14g1589 Chr14 16429219 16430479 +
Lal Lal7g0985 Chr7 16127433 16129905 +
Lan Lan12g0905 Chr12 16041218 16043516 +
Lan Lan12g0905 Chr12 16041218 16043516 +
Lja Lja4g1380 Chr4 12348122 12350688 +
Lja Lja6g2768 Chr6 56781478 56785246 -
Mal Mal5g4947 Chr5 123045778 123046986 +
Mtr Mtr4g4474 Chr4 58733747 58736370 +
Mtr Mtr2g1183 Chr2 12875083 12878428 -
Psa Psa4g0509 Chr4 31776103 31777872 -
Ssu Ssu6g0439 Chr6 6839429 6841526 +
Ssu Ssu1g1203 Chr1 26621588 26623245 -
Sto Sto3g0783 Chr3 5426072 5427672 -
Sto Sto12g1510 Chr12 10421184 10422481 -
Tpr Tpr4g1905 Chr4 19957158 19960096 -
Tpr Tpr5g1176 Chr5 23191952 23194973 +
Tsu Tsu07g01694 Chr07 16556796 16558439 -
Vra Vra7g2754 Chr7 47780315 47782873 -
Vra Vra10g0756 Chr10 13619566 13622574 -
Vvi Vvi5g0053 Chr5 483214 487376 -