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
Vvi3g0113 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0114 . . . . . Adu03g00759 . . Aev04g3559 . Ahy13g0968 . Aip03g01052 . . . Amo13g1116 . . . . Arst3g00967 . . . . Bva13g01598 . Car06g02120 . . . . . Dod03g3351 . . . . Glsi01g0120 . . . Gma12g00226 . . . . . Lal2g0061 Lal9g0056 . . . . . . . . . . Lapu11g00931 . Lasa7g02405 . . . . . . . . . . Mal7g2841 . . Mepo2g02583 . Mesa13g02423 . . Mtr4g2337 . . Phac11g00357 . Phco9g00309 . . . . . . . . . . . Pumo10g00838 . Pvu11g0266 . Rops3g00331 . . . Spst2g02737 . . . Sto10g0100 Tpr3g2578 . . Trre7g02472 Tsu02g02733 . . Vian5g01659 . Vifa6g01415 . Vimu5g02577 . Viun11g00543 . Vivi5g03095 . .
Vvi3g0115 Acco10g2376 Acco01g2119 Accr4g00400 Accr1g01830 Adu08g00627 Adu03g00756 . Aed9g0061 Aev04g3558 . Ahy13g0967 . Aip03g01051 . Alju08g0419 Alju02g1917 Amo13g1115 . . Apr5g1830 Arst8g00812 Arst3g00963 Bach12g00817 . Bisa09g1636 Bisa01g4073 Bva13g01597 . Car06g02121 . . Cca07g00070 Dere04g0993 Dere06g0124 Dod03g3350 . Enph1g1678 Enph12g0621 Glsi08g1175 Glsi01g0118 Gma04g00060 Gma06g00052 . . Gso4g0052 Gso4g0052 . . Lal1g0108 Lal2g0062 . . . . Lan13g0128 Lan13g0128 . . . . Lapu9g01525 Lapu11g00930 Lasa5g01798 Lasa7g02404 Lele01g0335 Lele02g0328 Lele03g0342 Lele04g0338 Lele45g1333 Lele46g1430 Lele47g0078 Lele48g0083 Lja1g2365 . Mal7g2840 . Mepo3g05642 Mepo2g02582 Mesa9g03016 Mesa13g02424 Mibi05g0365 Mibi01g1791 Mtr4g2336 . Phac9g00824 Phac11g00358 Phco7g01215 Phco9g00310 Prci15g0514 Prci14g0147 . . Pste2g02976 Pste1g01056 . . . . Pumo10g01216 Pumo11g02043 Pvu9g1256 Pvu11g0267 Rops10g01864 Rops3g00332 Seca4g02250 Seca6g00534 Spst9g01260 Spst2g02736 . . Sto2g0904 Sto10g0099 Tpr3g2573 . Trre5g02220 Trre7g02473 Tsu02g02729 . Vian4g01574 Vian5g01658 Vifa2g01787 Vifa6g01416 Vimu10g02202 Vimu5g02576 Viun9g02463 Viun11g02694 . Vivi5g03094 . Vra5g1831
Vvi3g0116 . . . . Adu08g00298 . . Aed9g0060 . . . . . . . . . . . Apr5g1831 Arst8g00360 . . . . . . Bva14g02293 Car06g02122 . . Cca07g00069 . . . . . . . . Gma04g00059 Gma06g00051 . Gma12g00227 Gso4g0051 Gso4g0051 . Gso4g0051 . . . . . . . . . . . . Lapu9g02467 . Lasa5g04724 . . . . . . . . . Lja1g2366 . Mal7g2839 . Mepo3g08025 . Mesa9g05693 . . . Mtr4g2335 . . . Phco7g00083 . . . . . . . . . . . . . Pvu9g0004 . Rops10g02667 . Seca4g00099 . Spst9g00069 . . . . . Tpr3g2572 . Trre5g05942 . Tsu02g02727 . . . . . Vimu10g03700 . Viun9g03935 . Vivi3g01011 . . Vra5g1832
Vvi3g0117 . . . . . . . . . . Ahy13g1111 . Aip03g01220 . . . Amo13g1171 . . . . . . . . . . Bva14g02294 . . . . . . . . . . . . . . . . . . . . Lal1g0109 . . . . . Lan13g0129 . . . . . . . . . . . . . . . . . . . Mal7g2838 . . . . . . . Mtr4g2334 . . . . . . . Psa7g4096 . . . . . . . . . . . . . . . . . . . . Sto10g0096 . . . . Tsu02g02725 . . . . . . . . . . . . .
Vvi3g0118 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0119 . . . . . . . . . . Ahy13g1111 . Aip03g01220 . . . Amo13g1171 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g3506 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0120 . . . . . . . . . . Ahy13g1110 . Aip03g01219 . . . Amo13g1172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0121 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g4020 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0122 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0113 Chr3 1004686 1005093 +
Vvi Vvi3g0114 Chr3 1006320 1007936 +
Adu Adu03g00759 Chr03 7077098 7078822 -
Aev Aev04g3559 Chr04 33589054 33590360 -
Ahy Ahy13g0968 Chr13 10576083 10579525 -
Aip Aip03g01052 Chr03 10243961 10245512 -
Amo Amo13g1116 Chr13 14136094 14137860 -
Arst Arst3g00967 Chr3 7070904 7083249 -
Bva Bva13g01598 Chr13 9568478 9570226 -
Car Car06g02120 Chr06 21645113 21646618 +
Dod Dod03g3351 Chr03 66165564 66168815 -
Glsi Glsi01g0120 Chr01 993118 995280 -
Gma Gma12g00226 Chr12 1766425 1769447 +
Lal Lal2g0061 Chr2 346916 348423 +
Lal Lal9g0056 Chr9 344426 346541 +
Lapu Lapu11g00931 Chr11 11812424 11814067 -
Lasa Lasa7g02405 Chr7 521375622 521376902 -
Mal Mal7g2841 Chr7 90961705 90963063 -
Mepo Mepo2g02583 Chr2 35508420 35509876 -
Mesa Mesa13g02423 Chr13 28403801 28405082 +
Mtr Mtr4g2337 Chr4 36850896 36852494 -
Phac Phac11g00357 Chr11 2217843 2219489 +
Phco Phco9g00309 Chr9 2102522 2104095 +
Pumo Pumo10g00838 Chr10 10405704 10406966 -
Pvu Pvu11g0266 Chr11 2140672 2142301 +
Rops Rops3g00331 Chr3 4152810 4154243 +
Spst Spst2g02737 Chr2 27139272 27140759 -
Sto Sto10g0100 Chr10 756890 758422 -
Tpr Tpr3g2578 Chr3 24930133 24932126 -
Trre Trre7g02472 Chr7 20369117 20370549 +
Tsu Tsu02g02733 Chr02 28946165 28948868 -
Vian Vian5g01659 Chr5 39049323 39050877 -
Vifa Vifa6g01415 Chr6 516099651 516100937 +
Vimu Vimu5g02577 Chr5 36061418 36062974 -
Viun Viun11g00543 Chr11 5531684 5533157 -
Vivi Vivi5g03095 Chr5 119657265 119658594 -
Vvi Vvi3g0115 Chr3 1009993 1014481 -
Acco Acco10g2376 Chr10 35413986 35419242 +
Acco Acco01g2119 Chr01 37081642 37084258 -
Accr Accr4g00400 Chr4 3849922 3852049 -
Accr Accr1g01830 Chr1 48667706 48670357 -
Adu Adu08g00627 Chr08 11274635 11278206 -
Adu Adu03g00756 Chr03 7063023 7065838 +
Aed Aed9g0061 Chr9 410680 413371 +
Aev Aev04g3558 Chr04 33586558 33588597 +
Ahy Ahy13g0967 Chr13 10573373 10575986 +
Aip Aip03g01051 Chr03 10241092 10243848 +
Alju Alju08g0419 Chr08 3011450 3014759 -
Alju Alju02g1917 Chr02 18416263 18418944 +
Amo Amo13g1115 Chr13 14122784 14125791 +
Apr Apr5g1830 Chr5 21507045 21514069 -
Arst Arst8g00812 Chr8 11244827 11248414 -
Arst Arst3g00963 Chr3 7068200 7081695 +
Bach Bach12g00817 Chr12 5751330 5753490 +
Bisa Bisa09g1636 Chr09 24413139 24414202 +
Bisa Bisa01g4073 Chr01 97885374 97889098 -
Bva Bva13g01597 Chr13 9565156 9568201 +
Car Car06g02121 Chr06 21646714 21649879 -
Cca Cca07g00070 Chr07 923349 926050 +
Dere Dere04g0993 Chr04 10509421 10514513 +
Dere Dere06g0124 Chr06 1402273 1405714 +
Dod Dod03g3350 Chr03 66162456 66165353 +
Enph Enph1g1678 Chr1 41988264 41991301 +
Enph Enph12g0621 Chr12 12659853 12663367 -
Glsi Glsi08g1175 Chr08 8567149 8569501 -
Glsi Glsi01g0118 Chr01 988780 992158 +
Gma Gma04g00060 Chr04 478413 480834 +
Gma Gma06g00052 Chr06 460109 462318 +
Gso Gso4g0052 Chr4 471895 474303 +
Gso Gso4g0052 Chr4 471895 474303 +
Lal Lal1g0108 Chr1 722134 725465 -
Lal Lal2g0062 Chr2 347115 351741 -
Lan Lan13g0128 Chr13 747113 749894 -
Lan Lan13g0128 Chr13 747113 749894 -
Lapu Lapu9g01525 Chr9 29663243 29667145 -
Lapu Lapu11g00930 Chr11 11808184 11812397 +
Lasa Lasa5g01798 Chr5 413771789 413774021 +
Lasa Lasa7g02404 Chr7 521373242 521375335 +
Lele Lele01g0335 Chr01 1928802 1930920 -
Lele Lele02g0328 Chr02 1851786 1853951 -
Lele Lele03g0342 Chr03 1920179 1922317 -
Lele Lele04g0338 Chr04 1972089 1974254 -
Lele Lele45g1333 Chr45 23059122 23061648 -
Lele Lele46g1430 Chr46 21113182 21115845 -
Lele Lele47g0078 Chr47 537720 540315 +
Lele Lele48g0083 Chr48 1265532 1268125 +
Lja Lja1g2365 Chr1 27349442 27351397 -
Mal Mal7g2840 Chr7 90958279 90961222 +
Mepo Mepo3g05642 Chr3 70394980 70398508 -
Mepo Mepo2g02582 Chr2 35505034 35508275 +
Mesa Mesa9g03016 Chr9 59642949 59645898 -
Mesa Mesa13g02424 Chr13 28405569 28408317 -
Mibi Mibi05g0365 Chr05 3568414 3570911 -
Mibi Mibi01g1791 Chr01 26211139 26211848 +
Mtr Mtr4g2336 Chr4 36847742 36850791 +
Phac Phac9g00824 Chr9 6103487 6107527 +
Phac Phac11g00358 Chr11 2219951 2223230 -
Phco Phco7g01215 Chr7 10609711 10612058 +
Phco Phco9g00310 Chr9 2105544 2108148 -
Prci Prci15g0514 Chr15 3319227 3321758 -
Prci Prci14g0147 Chr14 1236996 1240163 +
Pste Pste2g02976 Chr2 29691662 29694595 +
Pste Pste1g01056 Chr1 3420860 3424086 +
Pumo Pumo10g01216 Chr10 15888268 15891267 +
Pumo Pumo11g02043 Chr11 52471357 52474442 +
Pvu Pvu9g1256 Chr9 18154882 18157737 +
Pvu Pvu11g0267 Chr11 2142887 2146099 -
Rops Rops10g01864 Chr10 34554047 34556756 +
Rops Rops3g00332 Chr3 4154597 4157655 -
Seca Seca4g02250 Chr4 38335540 38338677 -
Seca Seca6g00534 Chr6 16296319 16299228 -
Spst Spst9g01260 Chr9 11964170 11966536 +
Spst Spst2g02736 Chr2 27135586 27137954 +
Sto Sto2g0904 Chr2 7836454 7840203 -
Sto Sto10g0099 Chr10 753444 756237 +
Tpr Tpr3g2573 Chr3 24912335 24915428 +
Trre Trre5g02220 Chr5 16709575 16712713 -
Trre Trre7g02473 Chr7 20371017 20374628 -
Tsu Tsu02g02729 Chr02 28925832 28929088 +
Vian Vian4g01574 Chr4 31216248 31218503 -
Vian Vian5g01658 Chr5 39045482 39048040 +
Vifa Vifa2g01787 Chr2 462854879 462857174 -
Vifa Vifa6g01416 Chr6 516101233 516103356 -
Vimu Vimu10g02202 Chr10 32346811 32349056 -
Vimu Vimu5g02576 Chr5 36057534 36060096 +
Viun Viun9g02463 Chr9 33860024 33862794 -
Viun Viun11g02694 Chr11 39671427 39674382 +
Vivi Vivi5g03094 Chr5 119654703 119657192 +
Vra Vra5g1831 Chr5 24254261 24256597 -
Vvi Vvi3g0116 Chr3 1015486 1018723 -
Adu Adu08g00298 Chr08 5276860 5277657 -
Aed Aed9g0060 Chr9 407651 410354 +
Apr Apr5g1831 Chr5 21515641 21519573 -
Arst Arst8g00360 Chr8 5249360 5252069 -
Bva Bva14g02293 Chr14 19821911 19826502 -
Car Car06g02122 Chr06 21654262 21659274 -
Cca Cca07g00069 Chr07 917558 920810 +
Gma Gma04g00059 Chr04 474077 476718 +
Gma Gma06g00051 Chr06 454744 458163 +
Gma Gma12g00227 Chr12 1770396 1777689 -
Gso Gso4g0051 Chr4 466860 470280 +
Gso Gso4g0051 Chr4 466860 470280 +
Gso Gso4g0051 Chr4 466860 470280 +
Lapu Lapu9g02467 Chr9 39018584 39020984 -
Lasa Lasa5g04724 Chr5 691781045 691782197 -
Lja Lja1g2366 Chr1 27352493 27355706 -
Mal Mal7g2839 Chr7 90953059 90955359 +
Mepo Mepo3g08025 Chr3 93101548 93105458 -
Mesa Mesa9g05693 Chr9 92629318 92631980 -
Mtr Mtr4g2335 Chr4 36840590 36843825 +
Phco Phco7g00083 Chr7 523922 526174 +
Pvu Pvu9g0004 Chr9 253995 257697 +
Rops Rops10g02667 Chr10 46145548 46149231 -
Seca Seca4g00099 Chr4 1442324 1446896 +
Spst Spst9g00069 Chr9 544908 547379 +
Tpr Tpr3g2572 Chr3 24907181 24908492 +
Trre Trre5g05942 Chr5 58873166 58875886 -
Tsu Tsu02g02727 Chr02 28918822 28922188 +
Vimu Vimu10g03700 Chr10 46001402 46004327 -
Viun Viun9g03935 Chr9 43404092 43407450 -
Vivi Vivi3g01011 Chr3 16922023 16925924 -
Vra Vra5g1832 Chr5 24257879 24261472 -
Vvi Vvi3g0117 Chr3 1025537 1039605 +
Ahy Ahy13g1111 Chr13 12532815 12536569 -
Aip Aip03g01220 Chr03 12097088 12099916 -
Amo Amo13g1171 Chr13 15242328 15245703 +
Bva Bva14g02294 Chr14 19832773 19842528 +
Lal Lal1g0109 Chr1 723923 734820 +
Lan Lan13g0129 Chr13 751156 761129 +
Mal Mal7g2838 Chr7 90941413 90951258 -
Mtr Mtr4g2334 Chr4 36826132 36835906 -
Psa Psa7g4096 Chr7 335389870 335399622 -
Sto Sto10g0096 Chr10 731467 740800 -
Tsu Tsu02g02725 Chr02 28902411 28913734 -
Vvi Vvi3g0118 Chr3 1041643 1041810 +
Vvi Vvi3g0119 Chr3 1044353 1047456 -
Ahy Ahy13g1111 Chr13 12532815 12536569 -
Aip Aip03g01220 Chr03 12097088 12099916 -
Amo Amo13g1171 Chr13 15242328 15245703 +
Psa Psa2g3506 Chr2 384763713 384766547 -
Vvi Vvi3g0120 Chr3 1050448 1058022 -
Ahy Ahy13g1110 Chr13 12527249 12530513 -
Aip Aip03g01219 Chr03 12086293 12094560 -
Amo Amo13g1172 Chr13 15247381 15250602 +
Vvi Vvi3g0121 Chr3 1062491 1063732 -
Psa Psa7g4020 Chr7 331186601 331190720 +
Vvi Vvi3g0122 Chr3 1066258 1068897 -
Vimu Vimu10g02202 Chr10 32346811 32349056 -
Acco Acco10g2376 Chr10 35413986 35419242 +
Accr Accr4g00400 Chr4 3849922 3852049 -
Adu Adu08g00627 Chr08 11274635 11278206 -
Alju Alju08g0419 Chr08 3011450 3014759 -
Arst Arst8g00812 Chr8 11244827 11248414 -
Bach Bach12g00817 Chr12 5751330 5753490 +
Bisa Bisa09g1636 Chr09 24413139 24414202 +
Dere Dere04g0993 Chr04 10509421 10514513 +
Enph Enph1g1678 Chr1 41988264 41991301 +
Glsi Glsi08g1175 Chr08 8567149 8569501 -
Lapu Lapu9g01525 Chr9 29663243 29667145 -
Lasa Lasa5g01798 Chr5 413771789 413774021 +
Lele Lele01g0335 Chr01 1928802 1930920 -
Lele Lele02g0328 Chr02 1851786 1853951 -
Lele Lele03g0342 Chr03 1920179 1922317 -
Lele Lele04g0338 Chr04 1972089 1974254 -
Mepo Mepo3g05642 Chr3 70394980 70398508 -
Mesa Mesa9g03016 Chr9 59642949 59645898 -
Mibi Mibi05g0365 Chr05 3568414 3570911 -
Phac Phac9g00824 Chr9 6103487 6107527 +
Phco Phco7g01215 Chr7 10609711 10612058 +
Prci Prci15g0514 Chr15 3319227 3321758 -
Pste Pste2g02976 Chr2 29691662 29694595 +
Pumo Pumo10g01216 Chr10 15888268 15891267 +
Pvu Pvu9g1256 Chr9 18154882 18157737 +
Rops Rops10g01864 Chr10 34554047 34556756 +
Seca Seca4g02250 Chr4 38335540 38338677 -
Spst Spst9g01260 Chr9 11964170 11966536 +
Trre Trre5g02220 Chr5 16709575 16712713 -
Vian Vian4g01574 Chr4 31216248 31218503 -
Vifa Vifa2g01787 Chr2 462854879 462857174 -
Vimu Vimu10g02202 Chr10 32346811 32349056 -
Viun Viun9g02463 Chr9 33860024 33862794 -