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
Vvi2g0392 Acco11g1653 . Accr9g00787 . Adu03g02821 . Aed11g1705 . . Aev03g3053 Ahy15g1026 Ahy13g2870 Aip05g01059 Aip03g03236 Alju09g1650 . . Amo13g3523 . Apr2g1181 Arst3g03737 . Bach4g00153 . Bisa11g0981 . . Bva11g02104 . Car06g00541 Cca06g01787 . Dere09g0261 . Dod02g1082 Dod04g2702 Enph13g1373 . Glsi05g2066 . Gma01g02187 . Gma05g02019 Gma08g00124 Gso1g1853 . Gso1g1853 Gso1g1853 Lal15g0070 . . Lal15g1381 Lal16g1224 . Lan18g1104 . . Lan18g1104 Lan18g1104 . Lapu3g03570 . Lasa7g04704 . Lele49g0627 Lele50g0656 Lele51g0647 Lele52g0648 . . . . Lja4g0439 . . Mal7g4903 Mepo2g04595 . Mesa13g00500 . Mibi12g1412 . . Mtr8g3437 . . Phco4g03273 . Prci10g1004 . . Psa7g0796 Pste3g01096 . Pte14g01265 Pte12g00098 . . Pumo6g00515 . Pvu2g2963 . Rops2g00579 . Seca12g06462 . Spst3g01118 . Ssu2g2848 . . Sto11g2085 . Tpr3g0663 Trre7g05413 . . Tsu02g00481 Vian1g03810 . Vifa6g03494 . Vimu11g04388 . Viun3g00603 . Vivi5g05860 . Vra11g0292 .
Vvi2g0393 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr8g3436 . . . . . . . Psa7g0798 . . . . . . . . . . . . . . . . . . . . . Tpr3g0664 . . . Tsu02g00483 . . . . . . . . . . . .
Vvi2g0394 Acco11g1654 . Accr9g00785 . Adu03g02822 . Aed11g1704 . Aev05g0962 Aev03g3052 Ahy15g1025 Ahy13g2871 Aip05g01058 Aip03g03238 Alju09g1651 . . Amo13g3525 Apr7g0603 Apr2g1180 Arst3g03738 . Bach4g00154 . Bisa11g0982 . Bva08g00183 Bva11g02103 Car08g00229 Car06g00542 Cca06g01786 . Dere09g0262 . Dod02g1081 Dod04g2701 Enph13g1372 . Glsi05g2064 . Gma01g02186 Gma11g00230 Gma05g02018 Gma08g00123 Gso1g1852 Gso1g1852 Gso1g1852 Gso1g1852 . . . Lal15g1380 Lal16g1225 Lal23g1520 . . . . . . Lapu3g03569 . Lasa7g04702 . Lele49g0626 Lele50g0655 Lele51g0646 Lele52g0647 . . . . Lja4g0440 . Mal6g0195 Mal7g4902 Mepo2g04594 . . . Mibi12g1413 . Mtr5g0306 Mtr8g3435 Phac2g00466 . Phco4g03272 . Prci10g1002 . . . Pste3g01102 . Pte14g01264 Pte12g00097 . . Pumo6g00516 . Pvu2g2962 . Rops2g00580 . Seca12g06461 . Spst3g01120 . Ssu2g2847 . Sto6g3262 Sto11g2084 Tpr2g3865 Tpr3g0665 Trre7g05410 . Tsu05g00283 Tsu02g00484 Vian1g03809 . Vifa6g03490 . Vimu11g04380 . Viun3g00604 . Vivi5g05857 . Vra11g0293 .
Vvi2g0395 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva08g00184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto6g3263 Sto11g2079 . . . . . . . . . . . . . . . . . .
Vvi2g0396 . . . . . . Aed11g1703 . . Aev03g3050 Ahy15g1024 Ahy13g2872 Aip05g01053 Aip03g03239 . . . . Apr7g0604 Apr2g1179 . . . . . . Bva08g00185 Bva11g02102 . Car06g00543 Cca06g01785 . . . Dod02g1080 Dod04g2700 . . . . Gma01g02185 Gma11g00231 . . Gso1g1851 Gso1g1851 . . . . . . Lal16g1227 . . . . . . . . . . . . . . . . . . . Lja4g0442 . Mal6g0193 Mal7g4901 . . . . . . Mtr5g0309 Mtr8g3434 . . . . . . Psa2g4151 Psa7g0800 . . . . . . . . . . . . . . . . Ssu2g2846 . Sto6g3264 . Tpr2g3862 Tpr3g0666 . . Tsu05g00285 Tsu02g00485 . . . . . . . . . . Vra11g0295 .
Vvi2g0397 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0399 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0400 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0401 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0392 Chr2 3242225 3242957 +
Acco Acco11g1653 Chr11 30969528 30970320 +
Accr Accr9g00787 Chr9 9197411 9198231 -
Adu Adu03g02821 Chr03 106580250 106581113 +
Aed Aed11g1705 Chr11 20710159 20711007 -
Aev Aev03g3053 Chr03 29395300 29396267 -
Ahy Ahy15g1026 Chr15 15678388 15679453 -
Ahy Ahy13g2870 Chr13 114943436 114947313 +
Aip Aip05g01059 Chr05 15136153 15136918 -
Aip Aip03g03236 Chr03 105571903 105572824 +
Alju Alju09g1650 Chr09 40368124 40369349 +
Amo Amo13g3523 Chr13 119481846 119482770 +
Apr Apr2g1181 Chr2 18059725 18060843 -
Arst Arst3g03737 Chr3 105307256 105308083 +
Bach Bach4g00153 Chr4 1045549 1046344 +
Bisa Bisa11g0981 Chr11 26505060 26505926 +
Bva Bva11g02104 Chr11 17463000 17463715 -
Car Car06g00541 Chr06 5484211 5485413 +
Cca Cca06g01787 Chr06 33202196 33203212 -
Dere Dere09g0261 Chr09 5394947 5395762 +
Dod Dod02g1082 Chr02 13503199 13504440 -
Dod Dod04g2702 Chr04 50974561 50975468 -
Enph Enph13g1373 Chr13 19378587 19379716 -
Glsi Glsi05g2066 Chr05 67408583 67409344 -
Gma Gma01g02187 Chr01 57142074 57143290 -
Gma Gma05g02019 Chr05 41520526 41524731 -
Gma Gma08g00124 Chr08 1054760 1055476 -
Gso Gso1g1853 Chr1 55308444 55309662 -
Gso Gso1g1853 Chr1 55308444 55309662 -
Gso Gso1g1853 Chr1 55308444 55309662 -
Lal Lal15g0070 Chr15 490295 491297 +
Lal Lal15g1381 Chr15 15976651 15978470 -
Lal Lal16g1224 Chr16 8532192 8533428 +
Lan Lan18g1104 Chr18 16093518 16094511 -
Lan Lan18g1104 Chr18 16093518 16094511 -
Lan Lan18g1104 Chr18 16093518 16094511 -
Lapu Lapu3g03570 Chr3 59120480 59121815 -
Lasa Lasa7g04704 Chr7 681109430 681110035 -
Lele Lele49g0627 Chr49 3805774 3806500 -
Lele Lele50g0656 Chr50 4022727 4023364 -
Lele Lele51g0647 Chr51 3910311 3911438 -
Lele Lele52g0648 Chr52 4110947 4111588 -
Lja Lja4g0439 Chr4 3581628 3582942 +
Mal Mal7g4903 Chr7 117710697 117711397 -
Mepo Mepo2g04595 Chr2 54357892 54359054 -
Mesa Mesa13g00500 Chr13 5912637 5913251 -
Mibi Mibi12g1412 Chr12 29755403 29756249 +
Mtr Mtr8g3437 Chr8 44942960 44943992 -
Phco Phco4g03273 Chr4 53314436 53315392 -
Prci Prci10g1004 Chr10 6822105 6826231 -
Psa Psa7g0796 Chr7 57958452 57959699 +
Pste Pste3g01096 Chr3 7031951 7033130 +
Pte Pte14g01265 Chr14 33831947 33832759 -
Pte Pte12g00098 Chr12 836159 837073 -
Pumo Pumo6g00515 Chr6 6375717 6376775 +
Pvu Pvu2g2963 Chr2 45141417 45142609 -
Rops Rops2g00579 Chr2 8362865 8363912 +
Seca Seca12g06462 Chr12 156680236 156685095 -
Spst Spst3g01118 Chr3 14558178 14559513 +
Ssu Ssu2g2848 Chr2 89551666 89552535 -
Sto Sto11g2085 Chr11 19693006 19694495 -
Tpr Tpr3g0663 Chr3 6438439 6439387 +
Trre Trre7g05413 Chr7 60143005 60143613 -
Tsu Tsu02g00481 Chr02 4000118 4000993 +
Vian Vian1g03810 Chr1 61179961 61180801 -
Vifa Vifa6g03494 Chr6 1151423568 1151424143 -
Vimu Vimu11g04388 Chr11 65097994 65098834 -
Viun Viun3g00603 Chr3 3706739 3707877 +
Vivi Vivi5g05860 Chr5 162714424 162715590 -
Vra Vra11g0292 Chr11 2072680 2073570 +
Vvi Vvi2g0393 Chr2 3248584 3249811 +
Mtr Mtr8g3436 Chr8 44937803 44938917 -
Psa Psa7g0798 Chr7 58023245 58024457 +
Tpr Tpr3g0664 Chr3 6442197 6443124 +
Tsu Tsu02g00483 Chr02 4005351 4006266 +
Vvi Vvi2g0394 Chr2 3250592 3255459 -
Acco Acco11g1654 Chr11 30973417 30978014 -
Accr Accr9g00785 Chr9 9187408 9191977 +
Adu Adu03g02822 Chr03 106631957 106637889 -
Aed Aed11g1704 Chr11 20702615 20707873 +
Aev Aev05g0962 Chr05 6786318 6790624 +
Aev Aev03g3052 Chr03 29387025 29392148 +
Ahy Ahy15g1025 Chr15 15673727 15678463 +
Ahy Ahy13g2871 Chr13 115012226 115018188 -
Aip Aip05g01058 Chr05 15131839 15136094 +
Aip Aip03g03238 Chr03 105636642 105642582 -
Alju Alju09g1651 Chr09 40374022 40378622 -
Amo Amo13g3525 Chr13 119541074 119548782 -
Apr Apr7g0603 Chr7 12612818 12617474 -
Apr Apr2g1180 Chr2 18036182 18041422 +
Arst Arst3g03738 Chr3 105358948 105364918 -
Bach Bach4g00154 Chr4 1047080 1053369 -
Bisa Bisa11g0982 Chr11 26514606 26519387 -
Bva Bva08g00183 Chr08 901547 906925 -
Bva Bva11g02103 Chr11 17455928 17461394 +
Car Car08g00229 Chr08 1823467 1829056 -
Car Car06g00542 Chr06 5489802 5494491 -
Cca Cca06g01786 Chr06 33182005 33186857 +
Dere Dere09g0262 Chr09 5406339 5411351 -
Dod Dod02g1081 Chr02 13492941 13498421 +
Dod Dod04g2701 Chr04 50963196 50969131 +
Enph Enph13g1372 Chr13 19371055 19376953 +
Glsi Glsi05g2064 Chr05 67395047 67399168 +
Gma Gma01g02186 Chr01 57132339 57137359 +
Gma Gma11g00230 Chr11 1790030 1795029 -
Gma Gma05g02018 Chr05 41505850 41510727 +
Gma Gma08g00123 Chr08 1043885 1049265 +
Gso Gso1g1852 Chr1 55298581 55304037 +
Gso Gso1g1852 Chr1 55298581 55304037 +
Gso Gso1g1852 Chr1 55298581 55304037 +
Gso Gso1g1852 Chr1 55298581 55304037 +
Lal Lal15g1380 Chr15 15969672 15974883 +
Lal Lal16g1225 Chr16 8537292 8542331 -
Lal Lal23g1520 Chr23 15370003 15375275 +
Lapu Lapu3g03569 Chr3 59110297 59115929 +
Lasa Lasa7g04702 Chr7 680711738 680716162 +
Lele Lele49g0626 Chr49 3799060 3803511 +
Lele Lele50g0655 Chr50 4017148 4021682 +
Lele Lele51g0646 Chr51 3904152 3908596 +
Lele Lele52g0647 Chr52 4103743 4108210 +
Lja Lja4g0440 Chr4 3586573 3592556 -
Mal Mal6g0195 Chr6 2812178 2816736 +
Mal Mal7g4902 Chr7 117703756 117708398 +
Mepo Mepo2g04594 Chr2 54350254 54355429 +
Mibi Mibi12g1413 Chr12 29763902 29768369 -
Mtr Mtr5g0306 Chr5 2844358 2849424 -
Mtr Mtr8g3435 Chr8 44928151 44933243 +
Phac Phac2g00466 Chr2 2357104 2362415 -
Phco Phco4g03272 Chr4 53302637 53307459 +
Prci Prci10g1002 Chr10 6813640 6818967 +
Pste Pste3g01102 Chr3 7064578 7069855 -
Pte Pte14g01264 Chr14 33826790 33832072 +
Pte Pte12g00097 Chr12 830837 836062 +
Pumo Pumo6g00516 Chr6 6382585 6388211 -
Pvu Pvu2g2962 Chr2 45129328 45134717 +
Rops Rops2g00580 Chr2 8377004 8382568 -
Seca Seca12g06461 Chr12 156670811 156676563 +
Spst Spst3g01120 Chr3 14565098 14569956 -
Ssu Ssu2g2847 Chr2 89532446 89537430 +
Sto Sto6g3262 Chr6 38977364 38982196 -
Sto Sto11g2084 Chr11 19685698 19690898 +
Tpr Tpr2g3865 Chr2 41432894 41438077 +
Tpr Tpr3g0665 Chr3 6449948 6455125 -
Trre Trre7g05410 Chr7 60119470 60124017 +
Tsu Tsu05g00283 Chr05 2099941 2111632 -
Tsu Tsu02g00484 Chr02 4015185 4020328 -
Vian Vian1g03809 Chr1 61168920 61173649 +
Vifa Vifa6g03490 Chr6 1149647283 1149651669 +
Vimu Vimu11g04380 Chr11 65043635 65048371 +
Viun Viun3g00604 Chr3 3713966 3718980 -
Vivi Vivi5g05857 Chr5 162655829 162660768 +
Vra Vra11g0293 Chr11 2078794 2083928 -
Vvi Vvi2g0395 Chr2 3263715 3264065 +
Bva Bva08g00184 Chr08 913184 913558 +
Sto Sto6g3263 Chr6 38991676 38992989 +
Sto Sto11g2079 Chr11 19638807 19639172 -
Vvi Vvi2g0396 Chr2 3274791 3275789 +
Aed Aed11g1703 Chr11 20693364 20694965 -
Aev Aev03g3050 Chr03 29373160 29374344 -
Ahy Ahy15g1024 Chr15 15650612 15653102 -
Ahy Ahy13g2872 Chr13 115030852 115032131 +
Aip Aip05g01053 Chr05 15108299 15110713 -
Aip Aip03g03239 Chr03 105653521 105654786 +
Apr Apr7g0604 Chr7 12629879 12632499 +
Apr Apr2g1179 Chr2 18016110 18017978 -
Bva Bva08g00185 Chr08 918015 919397 +
Bva Bva11g02102 Chr11 17448639 17450536 -
Car Car06g00543 Chr06 5512525 5515061 +
Cca Cca06g01785 Chr06 33161642 33164540 -
Dod Dod02g1080 Chr02 13465352 13469116 -
Dod Dod04g2700 Chr04 50939127 50942045 -
Gma Gma01g02185 Chr01 57115461 57117903 -
Gma Gma11g00231 Chr11 1808347 1811898 +
Gso Gso1g1851 Chr1 55282187 55285107 -
Gso Gso1g1851 Chr1 55282187 55285107 -
Lal Lal16g1227 Chr16 8568780 8569215 +
Lja Lja4g0442 Chr4 3610584 3612246 +
Mal Mal6g0193 Chr6 2744369 2749497 -
Mal Mal7g4901 Chr7 117672726 117675012 -
Mtr Mtr5g0309 Chr5 2885080 2887328 +
Mtr Mtr8g3434 Chr8 44900999 44903841 -
Psa Psa2g4151 Chr2 421367883 421369248 -
Psa Psa7g0800 Chr7 58262821 58264432 -
Ssu Ssu2g2846 Chr2 89491470 89494073 -
Sto Sto6g3264 Chr6 38998083 38999507 +
Tpr Tpr2g3862 Chr2 41404818 41407035 -
Tpr Tpr3g0666 Chr3 6471028 6473075 +
Tsu Tsu05g00285 Chr05 2134334 2136635 +
Tsu Tsu02g00485 Chr02 4041353 4043585 +
Vra Vra11g0295 Chr11 2097831 2100411 +
Vvi Vvi2g0397 Chr2 3284195 3292998 -
Vvi Vvi2g0398 Chr2 3301703 3302335 +
Vvi Vvi2g0399 Chr2 3319407 3319565 -
Vvi Vvi2g0400 Chr2 3329622 3330104 +
Vvi Vvi2g0401 Chr2 3340580 3344292 +
Aed Aed11g1703 Chr11 20693364 20694965 -
Cca Cca06g01785 Chr06 33161642 33164540 -
Ssu Ssu2g2846 Chr2 89491470 89494073 -
Vra Vra11g0295 Chr11 2097831 2100411 +
Aed Aed11g1704 Chr11 20702615 20707873 +
Cca Cca06g01786 Chr06 33182005 33186857 +
Ssu Ssu2g2847 Chr2 89532446 89537430 +
Vra Vra11g0293 Chr11 2078794 2083928 -