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
Vvi4g1334 . . . . Adu01g00788 . . . . . . . . . . . . . . . Arst1g01065 . . . . . Bva08g00878 . . . . . . . . . . . . . . . Gma02g00420 Gma16g01093 . . . . . Lal15g1521 . . . . . . . . . . . . Lasa4g02200 . . . . . . . . . . . . Mal5g3307 Mepo1g02157 . Mesa29g02320 . . . . Mtr8g2388 Phac3g04142 . Phco8g00381 . . . . Psa4g2375 Pste7g01742 . . . . . Pumo4g02235 . Pvu3g2726 . Rops2g03233 . Seca12g02956 . . . . . . . . Tpr4g4303 . . . Tsu04g03539 Vian1g01858 . Vifa4g02304 . Vimu11g00768 . Viun3g03543 . . . . .
Vvi4g1335 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva08g00879 . . . Cca06g01246 . . . . . . . . . . Gma01g01682 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3947 . . . . . . . . . . . . . . . . . . .
Vvi4g1336 . . . . . . Aed11g1194 . Aev05g0409 . Ahy15g0396 . Aip05g00388 . . . . . . Apr7g1116 . Arst5g00516 . Bach4g00757 . . Bva08g00880 . . . Cca06g01245 . . . Dod02g0431 . . . . . Gma11g00714 Gma01g01681 . Gma16g01171 Gso11g0663 Gso11g0663 . Gso11g0663 . . Lal23g1476 . . . . . . . . . . Lapu2g00772 . Lasa2g03445 . . . . . . . . Lja2g0567 . Mal6g1001 . . Mepo5g01010 . . . . Mtr5g0895 . . Phac2g01677 . Phco4g00843 . . Psa2g3478 . . Pste1g03114 . . . . . . . Pvu2g1103 . . . . . Spst2g00928 Ssu2g2239 . Sto6g3967 Sto11g1460 Tpr2g1129 . . Trre9g01256 Tsu05g00863 . . . . . . Vimu7g03090 . . . . Vra11g0795 .
Vvi4g1337 . Acco11g2401 . Accr9g00088 . . Aed11g1193 . Aev05g0408 . Ahy15g0395 . Aip05g00387 . . Alju09g2406 . . . Apr7g1117 . Arst5g00515 . Bach4g00758 . Bisa11g1818 Bva08g00881 . . . Cca06g01244 . . Dere09g1087 Dod02g0430 . . Enph13g0830 . Glsi05g1324 Gma11g00715 Gma01g01680 . . Gso11g0664 Gso11g0664 . . . . . . . . . . . . . . . Lapu2g00773 . Lasa2g03448 . . . . Lele49g0065 Lele50g0075 . Lele52g0074 Lja2g0568 . Mal6g0999 . . . . Mesa17g01059 . Mibi12g2097 Mtr5g0897 . . Phac2g01673 . Phco4g00842 . Prci10g0136 Psa2g3476 . . Pste1g03116 . . . . . . . Pvu2g1102 . . . . . . Ssu2g2238 . . . Tpr2g1131 . . Trre9g01258 Tsu05g00865 . . . . . . Vimu7g03091 . . . . Vra11g0796 .
Vvi4g1338 Acco12g1339 . . . Adu01g00789 . . . . . . . . . Alju12g0794 . . . Apr3g0370 . Arst1g01066 . . . . . Bva08g00882 . . . . . Dere13g0756 . . . Enph14g0053 . Glsi09g0660 . . . . Gma16g01170 . . . . . Lal15g1523 . . . . . . . . . . . . Lasa4g02199 . . Lele54g0539 Lele55g0972 Lele56g0894 . . . . . Lja4g3110 . Mal5g3306 Mepo1g02158 . Mesa29g02321 . Mibi10g0703 . . Mtr8g2387 Phac3g04143 . Phco8g00380 . . . . Psa4g2376 Pste7g01750 . . . . . Pumo4g02237 . Pvu3g2727 . Rops2g03231 . Seca12g02961 . Spst3g03773 . . . . Sto11g1459 . Tpr4g4304 . . . Tsu04g03540 Vian1g01859 . Vifa4g02303 . Vimu11g00769 . Viun3g03542 . . . . .
Vvi4g1339 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1340 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1341 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1342 . . . . . . Aed11g1192 . Aev05g0406 . Ahy15g0393 . Aip05g00385 . . . . . . Apr7g1118 . Arst5g00513 . . . . Bva08g00883 . . . Cca06g01243 . . . Dod02g0428 . . . . . Gma11g00716 . . . Gso11g0667 . . . . . Lal23g1477 . . . . . . . . . . Lapu2g00774 . Lasa2g03449 . . . . . . . . Lja2g0571 . Mal6g0998 . . Mepo5g01012 . Mesa17g01060 . . Mtr5g0898 . . Phac2g01671 . Phco4g00841 . . Psa2g3474 . . Pste1g03117 . . . . . . . Pvu2g1101 . . . . . . Ssu2g2234 . . Sto11g1458 Tpr2g1132 . . Trre9g01260 Tsu05g00866 . . . . . . Vimu7g03092 . . . . Vra11g0797 .
Vvi4g1343 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi4g1334 Chr4 20279074 20280781 +
Adu Adu01g00788 Chr01 10637077 10639596 +
Arst Arst1g01065 Chr1 10634297 10636791 +
Bva Bva08g00878 Chr08 4504620 4506661 +
Gma Gma02g00420 Chr02 4290948 4293235 -
Gma Gma16g01093 Chr16 27660656 27665645 +
Lal Lal15g1521 Chr15 17346693 17349515 +
Lasa Lasa4g02200 Chr4 440718060 440719980 -
Mal Mal5g3307 Chr5 96477656 96480096 -
Mepo Mepo1g02157 Chr1 22179337 22181909 +
Mesa Mesa29g02320 Chr29 31832486 31834759 +
Mtr Mtr8g2388 Chr8 34284368 34286961 -
Phac Phac3g04142 Chr3 40589350 40591613 +
Phco Phco8g00381 Chr8 3475271 3478992 -
Psa Psa4g2375 Chr4 191591660 191593867 +
Pste Pste7g01742 Chr7 16192706 16195362 +
Pumo Pumo4g02235 Chr4 33032811 33035158 +
Pvu Pvu3g2726 Chr3 49202715 49204868 +
Rops Rops2g03233 Chr2 59091589 59093611 -
Seca Seca12g02956 Chr12 56450770 56452977 +
Tpr Tpr4g4303 Chr4 50248956 50251520 +
Tsu Tsu04g03539 Chr04 44593152 44595614 +
Vian Vian1g01858 Chr1 22044751 22046732 +
Vifa Vifa4g02304 Chr4 695241029 695242856 -
Vimu Vimu11g00768 Chr11 8040009 8041986 +
Viun Viun3g03543 Chr3 42265592 42267946 -
Vvi Vvi4g1335 Chr4 20281250 20283702 -
Bva Bva08g00879 Chr08 4506898 4508770 -
Cca Cca06g01246 Chr06 26937426 26939866 +
Gma Gma01g01682 Chr01 52485248 52490083 +
Sto Sto6g3947 Chr6 43560856 43562622 -
Vvi Vvi4g1336 Chr4 20287801 20291182 +
Aed Aed11g1194 Chr11 17251328 17255153 -
Aev Aev05g0409 Chr05 2818305 2821647 -
Ahy Ahy15g0396 Chr15 4616614 4620709 -
Aip Aip05g00388 Chr05 4356778 4363916 -
Apr Apr7g1116 Chr7 18131300 18151150 +
Arst Arst5g00516 Chr5 4326745 4329778 -
Bach Bach4g00757 Chr4 5057131 5060591 +
Bva Bva08g00880 Chr08 4510937 4515030 +
Cca Cca06g01245 Chr06 26931595 26936021 -
Dod Dod02g0431 Chr02 5701035 5705783 -
Gma Gma11g00714 Chr11 6006832 6010626 +
Gma Gma01g01681 Chr01 52481429 52485109 -
Gma Gma16g01171 Chr16 28958890 28961850 -
Gso Gso11g0663 Chr11 5954200 5958709 +
Gso Gso11g0663 Chr11 5954200 5958709 +
Gso Gso11g0663 Chr11 5954200 5958709 +
Lal Lal23g1476 Chr23 15089244 15094538 +
Lapu Lapu2g00772 Chr2 6922411 6926691 +
Lasa Lasa2g03445 Chr2 536288737 536292811 +
Lja Lja2g0567 Chr2 5122316 5125832 +
Mal Mal6g1001 Chr6 14945612 14949573 -
Mepo Mepo5g01010 Chr5 9971311 9976280 +
Mtr Mtr5g0895 Chr5 8908496 8913637 +
Phac Phac2g01677 Chr2 17154095 17158442 -
Phco Phco4g00843 Chr4 6509799 6513445 -
Psa Psa2g3478 Chr2 383427821 383432953 -
Pste Pste1g03114 Chr1 14033512 14037381 +
Pvu Pvu2g1103 Chr2 21526081 21530585 -
Spst Spst2g00928 Chr2 7991273 7994948 -
Ssu Ssu2g2239 Chr2 78876178 78879522 -
Sto Sto6g3967 Chr6 43669789 43675550 +
Sto Sto11g1460 Chr11 13867703 13870998 -
Tpr Tpr2g1129 Chr2 13225093 13229826 +
Trre Trre9g01256 Chr9 10631405 10635523 +
Tsu Tsu05g00863 Chr05 7471166 7476020 +
Vimu Vimu7g03090 Chr7 26212849 26216825 +
Vra Vra11g0795 Chr11 6552849 6556663 +
Vvi Vvi4g1337 Chr4 20292022 20293244 -
Acco Acco11g2401 Chr11 37275680 37277756 -
Accr Accr9g00088 Chr9 1034023 1035611 +
Aed Aed11g1193 Chr11 17247685 17250249 +
Aev Aev05g0408 Chr05 2816462 2817653 +
Ahy Ahy15g0395 Chr15 4614840 4616541 +
Aip Aip05g00387 Chr05 4355007 4356631 +
Alju Alju09g2406 Chr09 46987212 46988741 -
Apr Apr7g1117 Chr7 18138019 18140576 -
Arst Arst5g00515 Chr5 4324877 4326576 +
Bach Bach4g00758 Chr4 5061168 5062300 -
Bisa Bisa11g1818 Chr11 40074471 40075655 -
Bva Bva08g00881 Chr08 4515480 4517464 -
Cca Cca06g01244 Chr06 26927075 26930067 +
Dere Dere09g1087 Chr09 14320764 14322198 -
Dod Dod02g0430 Chr02 5698811 5700851 +
Enph Enph13g0830 Chr13 14580105 14583341 +
Glsi Glsi05g1324 Chr05 62408864 62410421 +
Gma Gma11g00715 Chr11 6012762 6015847 -
Gma Gma01g01680 Chr01 52475509 52477556 +
Gso Gso11g0664 Chr11 5960580 5963631 -
Gso Gso11g0664 Chr11 5960580 5963631 -
Lapu Lapu2g00773 Chr2 6927734 6931131 -
Lasa Lasa2g03448 Chr2 536343030 536344086 -
Lele Lele49g0065 Chr49 408943 411905 +
Lele Lele50g0075 Chr50 496489 498060 +
Lele Lele52g0074 Chr52 470504 472066 +
Lja Lja2g0568 Chr2 5126612 5129577 -
Mal Mal6g0999 Chr6 14938908 14940403 +
Mesa Mesa17g01059 Chr17 13538567 13539815 -
Mibi Mibi12g2097 Chr12 37435363 37439040 -
Mtr Mtr5g0897 Chr5 8920605 8923246 -
Phac Phac2g01673 Chr2 17149920 17153493 +
Phco Phco4g00842 Chr4 6506152 6508709 +
Prci Prci10g0136 Chr10 825554 829304 +
Psa Psa2g3476 Chr2 383413134 383415723 -
Pste Pste1g03116 Chr1 14039371 14044152 -
Pvu Pvu2g1102 Chr2 21521806 21525244 +
Ssu Ssu2g2238 Chr2 78869895 78871925 +
Tpr Tpr2g1131 Chr2 13235994 13238986 -
Trre Trre9g01258 Chr9 10643010 10644151 -
Tsu Tsu05g00865 Chr05 7479210 7480870 -
Vimu Vimu7g03091 Chr7 26218091 26220873 -
Vra Vra11g0796 Chr11 6557580 6561013 -
Vvi Vvi4g1338 Chr4 20299787 20306280 -
Acco Acco12g1339 Chr12 18896318 18900886 +
Adu Adu01g00789 Chr01 10639868 10643884 -
Alju Alju12g0794 Chr12 23064123 23069545 -
Apr Apr3g0370 Chr3 7317661 7324881 -
Arst Arst1g01066 Chr1 10636922 10641141 -
Bva Bva08g00882 Chr08 4517999 4523165 -
Dere Dere13g0756 Chr13 9463620 9468510 -
Enph Enph14g0053 Chr14 1770246 1776096 +
Glsi Glsi09g0660 Chr09 4558233 4563219 -
Gma Gma16g01170 Chr16 28950877 28956781 +
Lal Lal15g1523 Chr15 17355859 17362167 -
Lasa Lasa4g02199 Chr4 440710193 440715840 +
Lele Lele54g0539 Chr54 11823976 11829279 +
Lele Lele55g0972 Chr55 7351591 7356692 -
Lele Lele56g0894 Chr56 7534600 7540155 -
Lja Lja4g3110 Chr4 58847251 58852436 +
Mal Mal5g3306 Chr5 96468950 96476627 +
Mepo Mepo1g02158 Chr1 22182393 22189631 -
Mesa Mesa29g02321 Chr29 31835813 31842616 -
Mibi Mibi10g0703 Chr10 17509818 17515395 -
Mtr Mtr8g2387 Chr8 34277477 34284032 +
Phac Phac3g04143 Chr3 40593274 40597880 -
Phco Phco8g00380 Chr8 3468405 3472856 +
Psa Psa4g2376 Chr4 191600238 191606996 -
Pste Pste7g01750 Chr7 16260177 16269139 -
Pumo Pumo4g02237 Chr4 33051786 33053211 -
Pvu Pvu3g2727 Chr3 49206047 49209912 -
Rops Rops2g03231 Chr2 59073497 59078810 +
Seca Seca12g02961 Chr12 56542308 56548659 -
Spst Spst3g03773 Chr3 87785170 87789659 +
Sto Sto11g1459 Chr11 13861121 13866091 +
Tpr Tpr4g4304 Chr4 50251765 50257627 -
Tsu Tsu04g03540 Chr04 44595954 44601617 -
Vian Vian1g01859 Chr1 22051664 22056030 -
Vifa Vifa4g02303 Chr4 695227109 695232914 +
Vimu Vimu11g00769 Chr11 8044474 8050380 -
Viun Viun3g03542 Chr3 42253710 42258696 +
Vvi Vvi4g1339 Chr4 20310407 20310911 +
Vvi Vvi4g1340 Chr4 20311023 20311549 +
Vvi Vvi4g1341 Chr4 20315481 20318581 +
Vvi Vvi4g1342 Chr4 20321604 20326106 +
Aed Aed11g1192 Chr11 17243566 17247175 -
Aev Aev05g0406 Chr05 2808733 2811923 -
Ahy Ahy15g0393 Chr15 4605471 4608701 -
Aip Aip05g00385 Chr05 4341328 4344068 -
Apr Apr7g1118 Chr7 18142359 18146280 +
Arst Arst5g00513 Chr5 4315738 4318882 -
Bva Bva08g00883 Chr08 4524726 4525663 +
Cca Cca06g01243 Chr06 26917218 26920479 -
Dod Dod02g0428 Chr02 5689073 5693019 -
Gma Gma11g00716 Chr11 6018533 6030240 +
Gso Gso11g0667 Chr11 5973902 5976896 +
Lal Lal23g1477 Chr23 15095295 15098766 +
Lapu Lapu2g00774 Chr2 6931922 6935510 +
Lasa Lasa2g03449 Chr2 536385120 536387791 +
Lja Lja2g0571 Chr2 5138069 5142061 +
Mal Mal6g0998 Chr6 14931175 14935296 -
Mepo Mepo5g01012 Chr5 9982888 9987981 +
Mesa Mesa17g01060 Chr17 13541458 13546210 +
Mtr Mtr5g0898 Chr5 8923366 8927779 +
Phac Phac2g01671 Chr2 17144993 17148610 -
Phco Phco4g00841 Chr4 6500642 6503800 -
Psa Psa2g3474 Chr2 383330558 383334688 -
Pste Pste1g03117 Chr1 14058457 14063251 +
Pvu Pvu2g1101 Chr2 21516894 21520358 -
Ssu Ssu2g2234 Chr2 78786065 78788544 -
Sto Sto11g1458 Chr11 13853345 13856420 -
Tpr Tpr2g1132 Chr2 13240123 13244019 +
Trre Trre9g01260 Chr9 10664442 10667875 +
Tsu Tsu05g00866 Chr05 7484762 7488557 +
Vimu Vimu7g03092 Chr7 26222350 26226756 +
Vra Vra11g0797 Chr11 6561499 6567069 +
Vvi Vvi4g1343 Chr4 20328659 20338746 +