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
Vvi1g1511 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1512 Acco04g0112 . Accr8g02437 . . . . . . . . . . . Alju06g0133 . . . . . . . . . Bisa08g0212 . . . . . . . Dere03g1832 . . . Enph6g0928 . Glsi12g2758 . . . Gma08g01003 . . . . . . . . . . . . . . . . . Lapu6g00036 . Lasa5g02553 . Lele21g0095 Lele22g0102 Lele23g1957 Lele24g0091 . . . . . Lja4g1002 Mal2g2009 Mal7g4252 Mepo3g06167 . Mesa9g03433 . Mibi09g2345 . Mtr3g2761 Mtr8g2847 . . Phco2g03032 . Prci4g0178 . Psa5g2319 . . . . . . . Pumo1g00498 . Pvu1g2741 . Rops11g03671 . Seca6g01569 . Spst1g01843 . . . . . Tpr2g4625 Tpr3g1262 Trre5g03006 . Tsu07g02517 Tsu02g01150 Vian2g03226 . Vifa2g02394 . Vimu6g01455 . Viun1g03505 . . . . .
Vvi1g1513 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1514 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1515 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1516 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1517 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g1518 . . . . . Adu04g03200 . . . . . . . . . . . . . . . Arst4g04189 . . . . . . . . Cca07g02391 . . . . . . . . . Gma02g00877 . . . Gso2g0804 . . . Lal6g1663 . . . . . Lan8g0110 . . . . . . . . Lasa3g00501 . . . . . . . . . . . . . Mepo3g00515 . Mesa25g04255 . . . . . . . Phco3g03082 . . . . . Pste5g00374 . . . . . Pumo5g00567 . Pvu8g0173 . Rops8g00266 . Seca2g00271 . Spst1g01575 Ssu3g0211 . . . . . . Trre13g00467 . . . Vian2g00170 . Vifa1g00740 . Vimu6g01192 . Viun5g00258 . . . .
Vvi1g1519 . . . . Adu03g02848 . . . . . . . . . . . . . . . Arst3g03768 . . . . . . . . . . . . . . . . . . . . . Gma08g02416 . . . . . . . . . . . . . . . . . Lapu3g03548 . . . . . . . . . . . . . . Mal7g4881 Mepo2g04566 . . . . . . Mtr8g3412 Phac2g04301 . Phco4g03244 . . . . Psa7g0840 Pste3g01163 . Pte2g02476 Pte3g00151 . . Pumo6g00539 . Pvu2g2940 . Rops2g00607 . Seca12g06427 . Spst3g01145 . . . Sto3g1879 Sto4g0144 . Tpr3g0687 Trre7g05382 . . Tsu02g00510 Vian1g03790 . Vifa2g03423 . Vimu11g04354 . Viun3g00636 . Vivi5g05781 . . .
Vvi1g1520 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g01712 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto3g2017 . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Phac Phac2g04301 Chr2 41482396 41484785 -
Lal Lal6g1663 Chr6 19412989 19416122 +
Lan Lan8g0110 Chr8 1795070 1798454 -
Vvi Vvi1g1511 Chr1 21696243 21698956 +
Vvi Vvi1g1512 Chr1 21705632 21715753 +
Acco Acco04g0112 Chr04 950381 960411 +
Accr Accr8g02437 Chr8 47988079 47999349 -
Alju Alju06g0133 Chr06 1028394 1038256 +
Bisa Bisa08g0212 Chr08 3945169 3966780 +
Dere Dere03g1832 Chr03 30131098 30142556 +
Enph Enph6g0928 Chr6 12168686 12180095 +
Glsi Glsi12g2758 Chr12 40876201 40888802 -
Gma Gma08g01003 Chr08 8460321 8471404 -
Lapu Lapu6g00036 Chr6 327040 335153 +
Lasa Lasa5g02553 Chr5 489051367 489058231 +
Lele Lele21g0095 Chr21 610670 618922 +
Lele Lele22g0102 Chr22 572625 580978 +
Lele Lele23g1957 Chr23 22536246 22544825 -
Lele Lele24g0091 Chr24 583970 592436 +
Lja Lja4g1002 Chr4 8521494 8533325 +
Mal Mal2g2009 Chr2 24657433 24665652 -
Mal Mal7g4252 Chr7 109400919 109411151 -
Mepo Mepo3g06167 Chr3 75900599 75907950 +
Mesa Mesa9g03433 Chr9 65259646 65270326 -
Mibi Mibi09g2345 Chr09 42941905 42950236 -
Mtr Mtr3g2761 Chr3 41594257 41601802 +
Mtr Mtr8g2847 Chr8 39160733 39173626 -
Phco Phco2g03032 Chr2 58887112 58893585 -
Prci Prci4g0178 Chr4 1167147 1178326 +
Psa Psa5g2319 Chr5 179827003 179834814 +
Pumo Pumo1g00498 Chr1 6583173 6594409 -
Pvu Pvu1g2741 Chr1 51867571 51874451 -
Rops Rops11g03671 Chr11 70253239 70261878 +
Seca Seca6g01569 Chr6 67513142 67533559 +
Spst Spst1g01843 Chr1 26604369 26610178 +
Tpr Tpr2g4625 Chr2 51454575 51462557 +
Tpr Tpr3g1262 Chr3 11237859 11250097 +
Trre Trre5g03006 Chr5 24384043 24389896 +
Tsu Tsu07g02517 Chr07 28854794 28862043 -
Tsu Tsu02g01150 Chr02 9506121 9516726 +
Vian Vian2g03226 Chr2 52563426 52569097 -
Vifa Vifa2g02394 Chr2 619423800 619435568 +
Vimu Vimu6g01455 Chr6 13971156 13977958 +
Viun Viun1g03505 Chr1 41746337 41752509 -
Vvi Vvi1g1513 Chr1 21718229 21724065 -
Vvi Vvi1g1514 Chr1 21736728 21739613 +
Vvi Vvi1g1515 Chr1 21739999 21740604 -
Vvi Vvi1g1516 Chr1 21747587 21750226 -
Vvi Vvi1g1517 Chr1 21761882 21762070 +
Vvi Vvi1g1518 Chr1 21767073 21769808 -
Adu Adu04g03200 Chr04 120107842 120110899 +
Arst Arst4g04189 Chr4 120070890 120073627 +
Cca Cca07g02391 Chr07 52612966 52618682 +
Gma Gma02g00877 Chr02 8823408 8826485 -
Gso Gso2g0804 Chr2 8627520 8630591 -
Lal Lal6g1663 Chr6 19412989 19416122 +
Lan Lan8g0110 Chr8 1795070 1798454 -
Lasa Lasa3g00501 Chr3 35327559 35330116 +
Mepo Mepo3g00515 Chr3 7385523 7388625 +
Mesa Mesa25g04255 Chr25 76519264 76522029 -
Phco Phco3g03082 Chr3 56943365 56945766 +
Pste Pste5g00374 Chr5 2478521 2481728 -
Pumo Pumo5g00567 Chr5 11399949 11403162 -
Pvu Pvu8g0173 Chr8 1443790 1446746 -
Rops Rops8g00266 Chr8 5355573 5358541 -
Seca Seca2g00271 Chr2 3826712 3829742 -
Spst Spst1g01575 Chr1 19624315 19626709 +
Ssu Ssu3g0211 Chr3 3768259 3770457 -
Trre Trre13g00467 Chr13 3675291 3677382 +
Vian Vian2g00170 Chr2 1622503 1624888 -
Vifa Vifa1g00740 Chr1 124229336 124231713 +
Vimu Vimu6g01192 Chr6 12154263 12154616 +
Viun Viun5g00258 Chr5 1480216 1483436 -
Vvi Vvi1g1519 Chr1 21774426 21777127 -
Adu Adu03g02848 Chr03 107662895 107664955 +
Arst Arst3g03768 Chr3 106389102 106390810 +
Gma Gma08g02416 Chr08 23981216 23989179 +
Lapu Lapu3g03548 Chr3 58938833 58940895 -
Mal Mal7g4881 Chr7 117395175 117396828 -
Mepo Mepo2g04566 Chr2 54115737 54117801 -
Mtr Mtr8g3412 Chr8 44707527 44709357 -
Phac Phac2g04301 Chr2 41482396 41484785 -
Phco Phco4g03244 Chr4 53112834 53116926 -
Psa Psa7g0840 Chr7 61444949 61446455 +
Pste Pste3g01163 Chr3 7399071 7400540 +
Pte Pte2g02476 Chr2 43992702 43993576 +
Pte Pte3g00151 Chr3 1498188 1500360 -
Pumo Pumo6g00539 Chr6 6707872 6709979 +
Pvu Pvu2g2940 Chr2 44944635 44946573 -
Rops Rops2g00607 Chr2 8636658 8638573 +
Seca Seca12g06427 Chr12 156337813 156339701 -
Spst Spst3g01145 Chr3 14815344 14821648 +
Sto Sto3g1879 Chr3 15060540 15075258 +
Sto Sto4g0144 Chr4 1111098 1112296 +
Tpr Tpr3g0687 Chr3 6616054 6617957 +
Trre Trre7g05382 Chr7 59893050 59894666 -
Tsu Tsu02g00510 Chr02 4260388 4262281 +
Vian Vian1g03790 Chr1 60922368 60923891 -
Vifa Vifa2g03423 Chr2 988385775 988387107 -
Vimu Vimu11g04354 Chr11 64879414 64881439 -
Viun Viun3g00636 Chr3 3876803 3878609 +
Vivi Vivi5g05781 Chr5 161641745 161643618 -
Vvi Vvi1g1520 Chr1 21822871 21823245 +
Bva Bva06g01712 Chr06 11949641 11953276 -
Sto Sto3g2017 Chr3 16688476 16691012 +
Mesa Mesa9g03433 Chr9 65259646 65270326 -
Arst Arst3g03768 Chr3 106389102 106390810 +
Mal Mal7g4881 Chr7 117395175 117396828 -
Mtr Mtr8g3412 Chr8 44707527 44709357 -
Psa Psa7g0840 Chr7 61444949 61446455 +
Pte Pte3g00151 Chr3 1498188 1500360 -
Sto Sto4g0144 Chr4 1111098 1112296 +
Tpr Tpr3g0687 Chr3 6616054 6617957 +
Tsu Tsu02g00510 Chr02 4260388 4262281 +
Vifa Vifa2g03423 Chr2 988385775 988387107 -