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
Vvi2g0612 . . . . Adu05g01014 . Aed11g1628 . . . Ahy15g0994 . Aip05g01022 . . . . . Apr7g0685 . Arst5g01267 . . . . . . Bva11g01985 Car08g00302 . Cca06g01699 . . . Dod02g0979 . . . . . Gma01g02113 Gma11g00297 . . Gso1g1785 Gso1g1785 . . . Lal16g0327 . . . . . . . . . . . . . . . . . . . . . . Lja2g0111 . Mal6g1578 . Mepo5g00477 . Mesa17g00493 . . . Mtr5g0416 . . . . . . . Psa2g4043 . . . . . . . Pumo8g02205 . Pvu2g0650 . Rops1g02053 . Seca10g00466 . . . Ssu2g2750 . . . Tpr2g3775 . Trre9g00517 . Tsu05g00380 . Vian10g00370 . Vifa1g07726 . Vimu7g02558 . Viun2g02428 . Vivi2g03699 . Vra11g0365 .
Vvi2g0613 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0614 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0615 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0616 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0617 . . . . Adu05g01016 . Aed11g1625 . Aev05g0874 . Ahy15g0999 . Aip05g01028 . . . . . Apr7g0687 . Arst5g01269 . . Bach10g00240 . . Bva08g00319 Bva11g01981 Car08g00304 . Cca06g01695 Cca11g01602 . . Dod02g0975 . . . . . Gma01g02110 Gma11g00300 . Gma17g01306 Gso1g1784 Gso1g1784 . Gso1g1784 . . Lal23g0724 . . . . . . . . . . . . Lasa2g02902 . . . . . . . . . . Mal6g1575 . Mepo5g00479 . Mesa17g00495 . . . Mtr5g0419 . Phac2g00956 . . Phco8g00775 . . . . . Pste7g00485 . . Pte3g02164 . Pumo8g02202 Pumo4g01672 Pvu2g0653 Pvu3g2271 Rops1g02051 Rops2g04267 . . . Spst3g04301 Ssu2g2747 Ssu6g1619 Sto6g3388 . Tpr2g3773 . . . . . Vian10g00373 Vian1g01411 Vifa1g07722 . Vimu7g02563 Vimu7g02563 Viun2g02426 Viun3g04163 . . Vra11g0367 Vra7g1381
Vvi2g0618 . . . . . Adu01g01424 . Aed6g0551 . . . . . . . . . . . Apr10g1600 . Arst1g01909 . Bach10g00241 . . Bva08g00320 Bva11g01980 . Car07g01245 . Cca11g01601 . . . . . . . . . . Gma05g00563 Gma17g01307 . . . . . . Lal23g0725 . . . . . . . . . . Lapu3g01328 . Lasa4g02828 . . . . . . . . . Lja4g2556 . Mal5g3860 . Mepo1g01624 . . . . . Mtr4g3587 . Phac3g03421 . Phco8g00777 . . . Psa4g1688 . Pste7g00486 . . Pte14g01179 Pte12g00167 . Pumo4g01673 . Pvu3g2272 . Rops2g04268 . Seca12g01975 . Spst3g04300 . Ssu6g1620 . . . Tpr5g2636 . Trre15g03294 . Tsu04g02374 . Vian1g01412 . Vifa4g02924 . Vimu11g00151 . Viun3g04162 . . . Vra7g1380
Vvi2g0619 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0620 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g0621 . . . . . . Aed11g1595 . . . . . . . . . . . Apr7g0712 . . . . . . . Bva08g00351 Bva11g01945 Car08g00321 . Cca06g01668 . . . . . . . . . Gma01g02089 Gma11g00324 . . Gso1g1763 Gso1g1763 . . Lal15g0250 . . . . . Lan18g0917 . . . . . . . . . . . . . . . . . Lja2g0128 . Mal6g1543 . . . . . . . Mtr5g0442 . . . . . . . Psa2g4040 . . . . . . . . . . . . . . . . . Ssu2g2719 . . . Tpr2g5537 . . . Tsu05g00409 . . . . . . . . . . . Vra11g0397 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g0612 Chr2 5297318 5325864 -
Adu Adu05g01014 Chr05 13455492 13461999 -
Aed Aed11g1628 Chr11 20225309 20235270 +
Ahy Ahy15g0994 Chr15 15207615 15215101 -
Aip Aip05g01022 Chr05 14707202 14714914 -
Apr Apr7g0685 Chr7 13667829 13677327 -
Arst Arst5g01267 Chr5 13498958 13505883 -
Bva Bva11g01985 Chr11 16886765 16892675 +
Car Car08g00302 Chr08 2382402 2390081 -
Cca Cca06g01699 Chr06 32270987 32280286 +
Dod Dod02g0979 Chr02 12383139 12398221 +
Gma Gma01g02113 Chr01 56469443 56478574 +
Gma Gma11g00297 Chr11 2393455 2401896 -
Gso Gso1g1785 Chr1 54655713 54664645 +
Gso Gso1g1785 Chr1 54655713 54664645 +
Lal Lal16g0327 Chr16 1960006 1969312 +
Lja Lja2g0111 Chr2 872410 882787 +
Mal Mal6g1578 Chr6 29067321 29078989 +
Mepo Mepo5g00477 Chr5 4142517 4153213 -
Mesa Mesa17g00493 Chr17 5743568 5753374 -
Mtr Mtr5g0416 Chr5 3782484 3793507 -
Psa Psa2g4043 Chr2 417043606 417052800 +
Pumo Pumo8g02205 Chr8 59109479 59118055 +
Pvu Pvu2g0650 Chr2 6969004 6980044 -
Rops Rops1g02053 Chr1 41333746 41346002 +
Seca Seca10g00466 Chr10 4085449 4099784 -
Ssu Ssu2g2750 Chr2 88056183 88078679 +
Tpr Tpr2g3775 Chr2 40698735 40707508 +
Trre Trre9g00517 Chr9 3711106 3719232 -
Tsu Tsu05g00380 Chr05 2835939 2844255 -
Vian Vian10g00370 Chr10 3307717 3319318 -
Vifa Vifa1g07726 Chr1 1201970302 1201979111 +
Vimu Vimu7g02558 Chr7 21710894 21720171 -
Viun Viun2g02428 Chr2 31057958 31068004 +
Vivi Vivi2g03699 Chr2 147102768 147111112 +
Vra Vra11g0365 Chr11 2644446 2654224 -
Vvi Vvi2g0613 Chr2 5332501 5332851 +
Vvi Vvi2g0614 Chr2 5340221 5340355 -
Vvi Vvi2g0615 Chr2 5352851 5353186 +
Vvi Vvi2g0616 Chr2 5365660 5365995 +
Vvi Vvi2g0617 Chr2 5378602 5380748 +
Adu Adu05g01016 Chr05 13561480 13565306 +
Aed Aed11g1625 Chr11 20202905 20204457 -
Aev Aev05g0874 Chr05 6125934 6128919 -
Ahy Ahy15g0999 Chr15 15334398 15338313 +
Aip Aip05g01028 Chr05 14819524 14823355 +
Apr Apr7g0687 Chr7 13721778 13725752 +
Arst Arst5g01269 Chr5 13605024 13608955 +
Bach Bach10g00240 Chr10 1696432 1698778 +
Bva Bva08g00319 Chr08 1561970 1564498 +
Bva Bva11g01981 Chr11 16869496 16871935 -
Car Car08g00304 Chr08 2400405 2402916 +
Cca Cca06g01695 Chr06 32211483 32215301 -
Cca Cca11g01602 Chr11 39777010 39780623 -
Dod Dod02g0975 Chr02 12333925 12346531 -
Gma Gma01g02110 Chr01 56445484 56449163 -
Gma Gma11g00300 Chr11 2415042 2418011 +
Gma Gma17g01306 Chr17 11747189 11750283 +
Gso Gso1g1784 Chr1 54633433 54637284 -
Gso Gso1g1784 Chr1 54633433 54637284 -
Gso Gso1g1784 Chr1 54633433 54637284 -
Lal Lal23g0724 Chr23 9869003 9872791 +
Lasa Lasa2g02902 Chr2 513841643 513843435 +
Mal Mal6g1575 Chr6 28980647 28983181 -
Mepo Mepo5g00479 Chr5 4168802 4171262 +
Mesa Mesa17g00495 Chr17 5775669 5778667 +
Mtr Mtr5g0419 Chr5 3831822 3834602 +
Phac Phac2g00956 Chr2 6052987 6056065 -
Phco Phco8g00775 Chr8 7776047 7779963 +
Pste Pste7g00485 Chr7 4598692 4602581 +
Pte Pte3g02164 Chr3 37909955 37911651 +
Pumo Pumo8g02202 Chr8 59075532 59079168 -
Pumo Pumo4g01672 Chr4 21223455 21228378 +
Pvu Pvu2g0653 Chr2 7024916 7027439 +
Pvu Pvu3g2271 Chr3 43767814 43772398 +
Rops Rops1g02051 Chr1 41279609 41283827 -
Rops Rops2g04267 Chr2 77803262 77808688 +
Spst Spst3g04301 Chr3 94600912 94605132 -
Ssu Ssu2g2747 Chr2 88003682 88008374 -
Ssu Ssu6g1619 Chr6 26949949 26954077 +
Sto Sto6g3388 Chr6 39846943 39848443 +
Tpr Tpr2g3773 Chr2 40680275 40683503 -
Vian Vian10g00373 Chr10 3340968 3344978 +
Vian Vian1g01411 Chr1 15463917 15467131 +
Vifa Vifa1g07722 Chr1 1201302753 1201304523 -
Vimu Vimu7g02563 Chr7 21740306 21741593 +
Vimu Vimu7g02563 Chr7 21740306 21741593 +
Viun Viun2g02426 Chr2 31032957 31035682 -
Viun Viun3g04163 Chr3 49279165 49282809 -
Vra Vra11g0367 Chr11 2685805 2689223 +
Vra Vra7g1381 Chr7 30904563 30908687 -
Vvi Vvi2g0618 Chr2 5382165 5389914 -
Adu Adu01g01424 Chr01 36678518 36678835 +
Aed Aed6g0551 Chr6 4662836 4666405 -
Apr Apr10g1600 Chr10 28546753 28550936 -
Arst Arst1g01909 Chr1 37118151 37140641 +
Bach Bach10g00241 Chr10 1699226 1702185 -
Bva Bva08g00320 Chr08 1564499 1568237 -
Bva Bva11g01980 Chr11 16866121 16869226 +
Car Car07g01245 Chr07 11283763 11286520 -
Cca Cca11g01601 Chr11 39773006 39776707 +
Gma Gma05g00563 Chr05 5574596 5578169 -
Gma Gma17g01307 Chr17 11752724 11756821 -
Lal Lal23g0725 Chr23 9872046 9877080 -
Lapu Lapu3g01328 Chr3 14589141 14593940 -
Lasa Lasa4g02828 Chr4 532145137 532148084 +
Lja Lja4g2556 Chr4 32664702 32668793 -
Mal Mal5g3860 Chr5 107610321 107613144 +
Mepo Mepo1g01624 Chr1 15978053 15981378 -
Mtr Mtr4g3587 Chr4 49610598 49614112 +
Phac Phac3g03421 Chr3 34671143 34675289 -
Phco Phco8g00777 Chr8 7780693 7784278 -
Psa Psa4g1688 Chr4 118942516 118945828 -
Pste Pste7g00486 Chr7 4604019 4607989 -
Pte Pte14g01179 Chr14 33160747 33163468 -
Pte Pte12g00167 Chr12 1421820 1425743 +
Pumo Pumo4g01673 Chr4 21228505 21231824 -
Pvu Pvu3g2272 Chr3 43772574 43776559 -
Rops Rops2g04268 Chr2 77809146 77812502 -
Seca Seca12g01975 Chr12 23741725 23742385 -
Spst Spst3g04300 Chr3 94596334 94600205 +
Ssu Ssu6g1620 Chr6 26955255 26959735 -
Tpr Tpr5g2636 Chr5 48576725 48580082 +
Trre Trre15g03294 Chr15 32283170 32285692 -
Tsu Tsu04g02374 Chr04 26575317 26577976 +
Vian Vian1g01412 Chr1 15467873 15471816 -
Vifa Vifa4g02924 Chr4 938374514 938376925 +
Vimu Vimu11g00151 Chr11 1355432 1358677 -
Viun Viun3g04162 Chr3 49273868 49279101 +
Vra Vra7g1380 Chr7 30899939 30904239 +
Vvi Vvi2g0619 Chr2 5390641 5391471 -
Vvi Vvi2g0620 Chr2 5395019 5396372 -
Vvi Vvi2g0621 Chr2 5401696 5409155 +
Aed Aed11g1595 Chr11 20027938 20032284 +
Apr Apr7g0712 Chr7 13992785 14012063 -
Bva Bva08g00351 Chr08 1739231 1744785 -
Bva Bva11g01945 Chr11 16677175 16683906 +
Car Car08g00321 Chr08 2556193 2561329 -
Cca Cca06g01668 Chr06 31927000 31931940 +
Gma Gma01g02089 Chr01 56251133 56257082 +
Gma Gma11g00324 Chr11 2628509 2633602 -
Gso Gso1g1763 Chr1 54441361 54447363 +
Gso Gso1g1763 Chr1 54441361 54447363 +
Lal Lal15g0250 Chr15 1701047 1707178 +
Lan Lan18g0917 Chr18 14436620 14442002 -
Lja Lja2g0128 Chr2 1084699 1091599 -
Mal Mal6g1543 Chr6 28596207 28614768 +
Mtr Mtr5g0442 Chr5 4076871 4082003 -
Psa Psa2g4040 Chr2 416922753 416927043 +
Ssu Ssu2g2719 Chr2 87543611 87549595 +
Tpr Tpr2g5537 Chr2 64145768 64149270 -
Tsu Tsu05g00409 Chr05 3091128 3097082 -
Vra Vra11g0397 Chr11 2902174 2906653 -