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
Vvi3g0313 . . . . . Adu05g01227 . . Aev04g3563 . Ahy13g0975 . Aip03g01060 . . . Amo13g1330 . . . . . . . . . . . Car06g02116 . Cca04g00245 . . . Dod03g3356 . . . . . . . . . . . . . Lal1g0105 . . . . . Lan13g0124 . . . . . . . . Lasa2g02626 . . . . . . . . . . Mal7g2851 . . Mepo5g00165 . Mesa17g00168 . . Mtr4g2343 . . Phac2g00194 . . . . . . . Pste1g01364 . . . . . Pumo8g02495 . Pvu2g0426 . . . . . Spst2g00149 Ssu3g3063 . . . Tpr3g2583 . . Trre9g00168 Tsu02g02738 . . . . . . . . . . Vivi2g04093 Vra2g0253 .
Vvi3g0314 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0315 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g02423 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g0021 . . . . . . . . . . . . . . . . . .
Vvi3g0316 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0317 . . . . . Adu03g04523 . . . . . . . . . . . . . . . Arst3g05983 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu3g02587 . Lasa7g03923 . . . . . . . . . . . . . Mepo2g03851 . . . . . . . Phac2g02739 . Phco4g02037 . . . . . Pste3g02723 . . . . . Pumo6g01244 . Pvu2g1801 . Rops2g01362 . Seca12g05694 . Spst3g00139 . . . . . . . Trre7g04511 . . . Vian1g02691 . Vifa2g02464 . Vimu11g01840 . Viun3g02275 . Vivi5g05586 . .
Vvi3g0318 Acco10g2366 . Accr4g00412 . . . . Aed9g0010 . . . . . . Alju08g0432 . . . . Apr5g1882 . . . . Bisa09g1618 . . Bva14g02424 . . . Cca07g00015 Dere04g0978 . . . Enph1g1668 . Glsi08g1192 . Gma04g00011 Gma06g00008 . . Gso4g0009 Gso4g0009 . . . . . . . . . . . . . . Lapu9g02518 . Lasa5g04841 . Lele01g0343 Lele02g0338 Lele03g0351 Lele04g0347 . . . . . . . . Mepo3g08065 . Mesa9g05733 . Mibi05g0376 . . . Phac9g02175 . Phco7g00023 . Prci15g0529 . . . . . . . . . . . Pvu9g1192 . . . . . . . . . . . . . Trre5g05995 . . . . . . . Vimu10g03767 . . . Vivi3g01115 . . Vra5g1887
Vvi3g0319 . . . . . Adu01g00843 . . . . Ahy20g0098 . Aip10g00086 . . Alju12g1790 . . . . . Arst1g01143 . Bach10g00696 . Bisa01g2915 . . . . . . . Dere13g0807 . . . Enph14g0815 . Glsi09g0711 . . . . . . . . . . . . . . . . . . . . . . . Lasa4g02016 . . . . Lele53g1249 Lele54g1222 . Lele56g0225 . . . . . Mepo1g02219 . . . Mibi10g1724 . . . Phac3g04220 . Phco8g00335 . Prci5g2169 . Psa2g3396 . Pste7g01905 . . Pte14g00819 Pte12g00551 . . . Pvu3g2771 . . . . . Spst3g03730 . . . . . . . Trre15g02525 . . . . . . . Vimu7g03167 . . . Vivi1g03226 . .
Vvi3g0320 . . . . . . . Aed9g0007 . . . . . . . . . . . Apr5g1886 . . . . . . . Bva14g02428 . . . Cca07g00012 . . . . . . . . Gma04g00008 Gma06g00005 . . Gso4g0006 Gso4g0006 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0321 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g02429 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0322 . . . . . . . Aed9g0006 . . . . . . . . . . . . . . . . . . . . . . . Cca07g00011 . . . . . . . . Gma04g00007 Gma06g00004 . . Gso4g0005 Gso4g0005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco7g00020 Phco9g02244 . . . . . Pste1g04267 . . . . . Pumo10g02650 Pvu9g1189 Pvu11g2213 . Rops3g02732 . Seca4g09909 Spst9g00006 Spst11g00209 . . . . . . . . . . . Vian5g00062 . . Vimu10g03770 Vimu5g00094 . Viun11g00066 . . . Vra5g1892
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vifa Vifa2g02464 Chr2 645115098 645118194 +
Aev Aev04g3563 Chr04 33605574 33608378 -
Ahy Ahy13g0975 Chr13 10704966 10708093 -
Aip Aip03g01060 Chr03 10388939 10392104 -
Amo Amo13g1330 Chr13 17718240 17721426 +
Dod Dod03g3356 Chr03 66192562 66194628 -
Mal Mal7g2851 Chr7 91018666 91021469 -
Mtr Mtr4g2343 Chr4 36884211 36887805 -
Tpr Tpr3g2583 Chr3 24962092 24966670 -
Tsu Tsu02g02738 Chr02 29029511 29033344 -
Vvi Vvi3g0313 Chr3 2604678 2608928 +
Adu Adu05g01227 Chr05 17733940 17739378 -
Aev Aev04g3563 Chr04 33605574 33608378 -
Ahy Ahy13g0975 Chr13 10704966 10708093 -
Aip Aip03g01060 Chr03 10388939 10392104 -
Amo Amo13g1330 Chr13 17718240 17721426 +
Car Car06g02116 Chr06 21621447 21625740 +
Cca Cca04g00245 Chr04 2408367 2411692 +
Dod Dod03g3356 Chr03 66192562 66194628 -
Lal Lal1g0105 Chr1 707265 710421 +
Lan Lan13g0124 Chr13 730729 733769 +
Lasa Lasa2g02626 Chr2 506636089 506639525 +
Mal Mal7g2851 Chr7 91018666 91021469 -
Mepo Mepo5g00165 Chr5 1499550 1504745 +
Mesa Mesa17g00168 Chr17 1769236 1773584 +
Mtr Mtr4g2343 Chr4 36884211 36887805 -
Phac Phac2g00194 Chr2 1015449 1020351 +
Pste Pste1g01364 Chr1 4315774 4320552 +
Pumo Pumo8g02495 Chr8 62119476 62123522 -
Pvu Pvu2g0426 Chr2 3937079 3941627 -
Spst Spst2g00149 Chr2 1145766 1159707 +
Ssu Ssu3g3063 Chr3 86149956 86152868 -
Tpr Tpr3g2583 Chr3 24962092 24966670 -
Trre Trre9g00168 Chr9 1307381 1309960 +
Tsu Tsu02g02738 Chr02 29029511 29033344 -
Vivi Vivi2g04093 Chr2 153967085 153972451 -
Vra Vra2g0253 Chr2 1962231 1965487 +
Vvi Vvi3g0314 Chr3 2611323 2612072 -
Vvi Vvi3g0315 Chr3 2613704 2616819 +
Bva Bva14g02423 Chr14 20705332 20706862 +
Sto Sto10g0021 Chr10 227239 230303 -
Vvi Vvi3g0316 Chr3 2618017 2619617 +
Vvi Vvi3g0317 Chr3 2620579 2622895 -
Adu Adu03g04523 Chr03 134582049 134586581 -
Arst Arst3g05983 Chr3 133345444 133348967 -
Lapu Lapu3g02587 Chr3 48208661 48213854 +
Lasa Lasa7g03923 Chr7 625764281 625768216 -
Mepo Mepo2g03851 Chr2 47740214 47745282 -
Phac Phac2g02739 Chr2 28929001 28933891 +
Phco Phco4g02037 Chr4 40492806 40496382 +
Pste Pste3g02723 Chr3 20020600 20025334 -
Pumo Pumo6g01244 Chr6 16521606 16526274 +
Pvu Pvu2g1801 Chr2 32534123 32538811 +
Rops Rops2g01362 Chr2 19530101 19535217 +
Seca Seca12g05694 Chr12 148511596 148517120 -
Spst Spst3g00139 Chr3 2514498 2518072 -
Trre Trre7g04511 Chr7 53096997 53100848 -
Vian Vian1g02691 Chr1 40562636 40566124 +
Vifa Vifa2g02464 Chr2 645115098 645118194 +
Vimu Vimu11g01840 Chr11 25771463 25774466 -
Viun Viun3g02275 Chr3 20052670 20057491 +
Vivi Vivi5g05586 Chr5 159069461 159073775 +
Vvi Vvi3g0318 Chr3 2631520 2638651 +
Acco Acco10g2366 Chr10 35332478 35338629 +
Accr Accr4g00412 Chr4 3945573 3952248 -
Aed Aed9g0010 Chr9 86258 91944 +
Alju Alju08g0432 Chr08 3104177 3111003 -
Apr Apr5g1882 Chr5 21853510 21858680 -
Bisa Bisa09g1618 Chr09 24113256 24121446 +
Bva Bva14g02424 Chr14 20707161 20713770 -
Cca Cca07g00015 Chr07 279633 284885 +
Dere Dere04g0978 Chr04 10386302 10392062 +
Enph Enph1g1668 Chr1 41894443 41902122 +
Glsi Glsi08g1192 Chr08 8661595 8668719 -
Gma Gma04g00011 Chr04 114533 119486 +
Gma Gma06g00008 Chr06 101663 106885 +
Gso Gso4g0009 Chr4 113344 118108 +
Gso Gso4g0009 Chr4 113344 118108 +
Lapu Lapu9g02518 Chr9 39417863 39423384 -
Lasa Lasa5g04841 Chr5 699305940 699309901 -
Lele Lele01g0343 Chr01 1995217 2001278 -
Lele Lele02g0338 Chr02 1930713 1936536 -
Lele Lele03g0351 Chr03 1989201 1995193 -
Lele Lele04g0347 Chr04 2041742 2047635 -
Mepo Mepo3g08065 Chr3 93410950 93417632 -
Mesa Mesa9g05733 Chr9 93025770 93032357 -
Mibi Mibi05g0376 Chr05 3669981 3676372 -
Phac Phac9g02175 Chr9 20864640 20869036 -
Phco Phco7g00023 Chr7 167413 171795 +
Prci Prci15g0529 Chr15 3423392 3430406 -
Pvu Pvu9g1192 Chr9 17398629 17403843 +
Trre Trre5g05995 Chr5 59201159 59206893 -
Vimu Vimu10g03767 Chr10 46356620 46359397 -
Vivi Vivi3g01115 Chr3 18641543 18647565 -
Vra Vra5g1887 Chr5 24602385 24607495 -
Vvi Vvi3g0319 Chr3 2641633 2645487 +
Adu Adu01g00843 Chr01 11283979 11288389 +
Ahy Ahy20g0098 Chr20 786878 791268 -
Aip Aip10g00086 Chr10 797432 801867 -
Alju Alju12g1790 Chr12 38978550 38980794 -
Arst Arst1g01143 Chr1 11281205 11285603 +
Bach Bach10g00696 Chr10 4907432 4911433 -
Bisa Bisa01g2915 Chr01 60224075 60232042 +
Dere Dere13g0807 Chr13 10004000 10009032 +
Enph Enph14g0815 Chr14 10091284 10096756 +
Glsi Glsi09g0711 Chr09 4891273 4897909 +
Lasa Lasa4g02016 Chr4 412405439 412411115 +
Lele Lele53g1249 Chr53 21096988 21101468 -
Lele Lele54g1222 Chr54 17727771 17728237 -
Lele Lele56g0225 Chr56 1819773 1823218 +
Mepo Mepo1g02219 Chr1 22850055 22856261 +
Mibi Mibi10g1724 Chr10 38543454 38544985 -
Phac Phac3g04220 Chr3 40961985 40969910 +
Phco Phco8g00335 Chr8 3114025 3122974 -
Prci Prci5g2169 Chr5 39015506 39020561 -
Psa Psa2g3396 Chr2 380280823 380287203 +
Pste Pste7g01905 Chr7 17421826 17424170 +
Pte Pte14g00819 Chr14 29712641 29717499 -
Pte Pte12g00551 Chr12 4942069 4947050 +
Pvu Pvu3g2771 Chr3 49537900 49545539 +
Spst Spst3g03730 Chr3 87310228 87344797 -
Trre Trre15g02525 Chr15 21194260 21199040 -
Vimu Vimu7g03167 Chr7 26852240 26853239 +
Vivi Vivi1g03226 Chr1 70155098 70160696 +
Vvi Vvi3g0320 Chr3 2657553 2659541 +
Aed Aed9g0007 Chr9 72357 75770 -
Apr Apr5g1886 Chr5 21887371 21893786 +
Bva Bva14g02428 Chr14 20740378 20745418 +
Cca Cca07g00012 Chr07 253535 258727 -
Gma Gma04g00008 Chr04 95232 96575 -
Gma Gma06g00005 Chr06 72935 78139 -
Gso Gso4g0006 Chr4 94363 99800 -
Gso Gso4g0006 Chr4 94363 99800 -
Vvi Vvi3g0321 Chr3 2660982 2661950 +
Bva Bva14g02429 Chr14 20745880 20747305 +
Vvi Vvi3g0322 Chr3 2668403 2673028 +
Aed Aed9g0006 Chr9 51785 54220 -
Cca Cca07g00011 Chr07 223852 226740 -
Gma Gma04g00007 Chr04 74065 76794 -
Gma Gma06g00004 Chr06 46146 48711 -
Gso Gso4g0005 Chr4 74419 77875 -
Gso Gso4g0005 Chr4 74419 77875 -
Phco Phco7g00020 Chr7 132803 135570 -
Phco Phco9g02244 Chr9 47778548 47780238 -
Pste Pste1g04267 Chr1 27202570 27204580 +
Pumo Pumo10g02650 Chr10 49187924 49190327 -
Pvu Pvu9g1189 Chr9 17341245 17344727 -
Pvu Pvu11g2213 Chr11 49730523 49732695 -
Rops Rops3g02732 Chr3 58055172 58068096 +
Seca Seca4g09909 Chr4 231868922 231870252 -
Spst Spst9g00006 Chr9 69283 72376 -
Spst Spst11g00209 Chr11 7573967 7576252 -
Vian Vian5g00062 Chr5 1047036 1048040 +
Vimu Vimu10g03770 Chr10 46393405 46396012 +
Vimu Vimu5g00094 Chr5 708715 715416 +
Viun Viun11g00066 Chr11 384507 387141 +
Vra Vra5g1892 Chr5 24677902 24680551 +
Adu Adu01g00843 Chr01 11283979 11288389 +
Alju Alju12g1790 Chr12 38978550 38980794 -
Arst Arst1g01143 Chr1 11281205 11285603 +
Bach Bach10g00696 Chr10 4907432 4911433 -
Bisa Bisa01g2915 Chr01 60224075 60232042 +
Dere Dere13g0807 Chr13 10004000 10009032 +
Enph Enph14g0815 Chr14 10091284 10096756 +
Glsi Glsi09g0711 Chr09 4891273 4897909 +
Lasa Lasa4g02016 Chr4 412405439 412411115 +
Lele Lele53g1249 Chr53 21096988 21101468 -
Lele Lele54g1222 Chr54 17727771 17728237 -
Lele Lele56g0225 Chr56 1819773 1823218 +
Mepo Mepo1g02219 Chr1 22850055 22856261 +
Mibi Mibi10g1724 Chr10 38543454 38544985 -
Phac Phac3g04220 Chr3 40961985 40969910 +
Phco Phco8g00335 Chr8 3114025 3122974 -
Prci Prci5g2169 Chr5 39015506 39020561 -
Pste Pste7g01905 Chr7 17421826 17424170 +
Pte Pte14g00819 Chr14 29712641 29717499 -
Pte Pte12g00551 Chr12 4942069 4947050 +
Pte Pte14g00819 Chr14 29712641 29717499 -
Pte Pte12g00551 Chr12 4942069 4947050 +
Pvu Pvu3g2771 Chr3 49537900 49545539 +
Spst Spst3g03730 Chr3 87310228 87344797 -
Spst Spst3g03730 Chr3 87310228 87344797 -
Trre Trre15g02525 Chr15 21194260 21199040 -
Vimu Vimu7g03167 Chr7 26852240 26853239 +
Vimu Vimu7g03167 Chr7 26852240 26853239 +
Vivi Vivi1g03226 Chr1 70155098 70160696 +
Acco Acco10g2366 Chr10 35332478 35338629 +
Accr Accr4g00412 Chr4 3945573 3952248 -
Alju Alju08g0432 Chr08 3104177 3111003 -
Bisa Bisa09g1618 Chr09 24113256 24121446 +
Dere Dere04g0978 Chr04 10386302 10392062 +
Enph Enph1g1668 Chr1 41894443 41902122 +
Glsi Glsi08g1192 Chr08 8661595 8668719 -
Lele Lele01g0343 Chr01 1995217 2001278 -
Lele Lele02g0338 Chr02 1930713 1936536 -
Lele Lele03g0351 Chr03 1989201 1995193 -
Lele Lele04g0347 Chr04 2041742 2047635 -
Mibi Mibi05g0376 Chr05 3669981 3676372 -
Prci Prci15g0529 Chr15 3423392 3430406 -