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
Vvi3g0103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0104 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g2361 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0106 . Acco01g2116 . Accr1g01826 . Adu03g00766 . Aed9g0064 Aev04g3562 . Ahy13g0974 . Aip03g01059 . . Alju02g1920 Amo13g1123 . . Apr5g1827 . Arst3g00983 . . . Bisa01g4070 Bva13g01603 . Car06g02118 . . Cca07g00074 . Dere06g0130 Dod03g3355 . . Enph12g0616 . Glsi01g0123 Gma04g00063 Gma06g00055 . Gma12g00223 Gso4g0056 Gso4g0056 . Gso4g0056 . . Lal9g0084 . . . . . . . . . Lapu9g02463 . Lasa5g04777 Lasa7g02410 . . . . Lele45g1330 Lele46g1426 Lele47g0081 Lele48g0085 Lja1g2362 . Mal7g2848 . Mepo3g08022 Mepo2g02588 Mesa9g05688 Mesa13g02418 . Mibi01g1794 Mtr4g2342 . Phac9g02086 Phac11g01830 Phco7g00087 Phco9g00305 . Prci14g0150 . . . Pste1g01047 . . . . . Pumo11g02047 Pvu9g0010 Pvu11g0262 Rops10g02663 Rops3g00327 Seca4g00108 Seca6g00522 Spst9g00074 Spst2g02743 . . Sto2g0898 Sto10g0103 Tpr3g2581 . Trre5g05939 Trre7g02467 Tsu02g02737 . . Vian5g01663 . Vifa6g01411 Vimu10g03695 Vimu5g02581 Viun9g03927 Viun11g02699 . Vivi5g03115 . Vra5g1827
Vvi3g0107 . . . . . . . . Aev04g3561 . Ahy13g0973 . Aip03g01058 . . . Amo13g1121 . . . . . . . . . Bva13g01602 . Car06g02119 . . . . Dere06g0128 Dod03g3354 . . Enph12g0617 . . . . . Gma12g00224 . . . . Lal1g0106 . . . . . Lan13g0126 . . . . . . Lapu11g00933 . . . . . . . . . . . . Mal7g2845 . . Mepo2g02586 . Mesa13g02420 . . Mtr4g2340 . . Phac11g00355 . Phco9g00306 . . . . . . . . . . . . . Pvu11g0263 . . . . . Spst2g02742 . . . . . . . Trre7g02469 . . . . . . . Vimu5g02580 . . . Vivi5g03108 . .
Vvi3g0108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma12g00225 . . . . Lal1g0107 . . . . . Lan13g0127 . . . . . . . . . . . . . . . . . . . Mal7g2843 . . . . . . . Mtr4g2338 . . . . Phco9g00307 . . . . . . . . . . . Pumo11g02046 . Pvu11g0264 . Rops3g00329 . Seca6g00530 . . . . Sto2g0899 Sto10g0102 Tpr3g2579 . . . Tsu02g02734 . . Vian5g01662 . Vifa6g01412 . . . Viun11g02697 . Vivi5g03107 . .
Vvi3g0110 . . . . . . . Aed9g0063 . . . . . . . . . . . Apr5g1828 . . . . . . Bva13g01601 . . . . Cca07g00073 . . . . . . . . Gma04g00062 Gma06g00054 . . Gso4g0055 Gso4g0055 . . . . . . . . . . . . . . Lapu9g02464 . Lasa5g04776 . . . . . . . . . . . . . Mepo3g08023 . Mesa9g05691 . . . . . Phac9g02087 . Phco7g00086 . . . . . . . . . . . . . Pvu9g0009 . Rops10g02664 . Seca4g00107 . Spst9g00073 . . . . . . . Trre5g05940 . . . . . . . Vimu10g03696 . Viun9g03928 . Vivi3g01007 . . Vra5g1828
Vvi3g0111 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g2363 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g0901 . . . . . . . . . . . . . . . . . . .
Vvi3g0112 . . . . . . . . . . . . . . . . . . . Apr5g1829 . . . . . . Bva13g01599 Bva14g02291 . . . Cca07g00071 . . . . . . . . Gma04g00061 Gma06g00053 . . Gso4g0054 Gso4g0054 . . . . . . . . . . . . . . Lapu9g02465 . . . . . . . . . . . Lja1g2364 . . . Mepo3g08024 . Mesa9g05692 . . . . . . . . . . . . . . . . . . . . . Pvu9g0006 . Rops10g02665 . . . Spst9g00071 . . . Sto2g0902 . . . Trre5g05941 . . . . . . . Vimu10g03698 . Viun9g03932 . Vivi3g01010 . . Vra5g1830
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0103 Chr3 955152 956441 -
Vvi Vvi3g0104 Chr3 964896 965980 +
Vvi Vvi3g0105 Chr3 967780 969830 +
Lja Lja1g2361 Chr1 27329581 27330829 +
Vvi Vvi3g0106 Chr3 973574 975272 +
Acco Acco01g2116 Chr01 37046569 37050132 +
Accr Accr1g01826 Chr1 48642205 48645762 +
Adu Adu03g00766 Chr03 7159408 7163034 -
Aed Aed9g0064 Chr9 423894 429029 -
Aev Aev04g3562 Chr04 33597629 33601497 -
Ahy Ahy13g0974 Chr13 10693068 10696594 -
Aip Aip03g01059 Chr03 10370553 10374140 -
Alju Alju02g1920 Chr02 18427334 18430918 -
Amo Amo13g1123 Chr13 14221577 14223348 -
Apr Apr5g1827 Chr5 21495953 21499481 +
Arst Arst3g00983 Chr3 7164553 7166723 -
Bisa Bisa01g4070 Chr01 97869036 97872675 +
Bva Bva13g01603 Chr13 9606246 9610359 -
Car Car06g02118 Chr06 21628216 21633375 +
Cca Cca07g00074 Chr07 949982 952915 -
Dere Dere06g0130 Chr06 1520523 1526253 -
Dod Dod03g3355 Chr03 66183494 66188683 -
Enph Enph12g0616 Chr12 12639506 12644057 +
Glsi Glsi01g0123 Chr01 1001059 1005700 -
Gma Gma04g00063 Chr04 502030 508280 -
Gma Gma06g00055 Chr06 483055 486779 -
Gma Gma12g00223 Chr12 1755804 1759656 +
Gso Gso4g0056 Chr4 494963 501465 -
Gso Gso4g0056 Chr4 494963 501465 -
Gso Gso4g0056 Chr4 494963 501465 -
Lal Lal9g0084 Chr9 548939 552135 +
Lapu Lapu9g02463 Chr9 38997425 39001462 +
Lasa Lasa5g04777 Chr5 695410164 695412074 -
Lasa Lasa7g02410 Chr7 521495817 521501321 -
Lele Lele45g1330 Chr45 23048503 23051800 +
Lele Lele46g1426 Chr46 21092279 21096156 +
Lele Lele47g0081 Chr47 547059 550490 -
Lele Lele48g0085 Chr48 1275293 1278802 -
Lja Lja1g2362 Chr1 27332655 27336768 +
Mal Mal7g2848 Chr7 90990939 90994806 -
Mepo Mepo3g08022 Chr3 93081507 93086300 +
Mepo Mepo2g02588 Chr2 35535226 35539286 -
Mesa Mesa9g05688 Chr9 92573661 92578038 +
Mesa Mesa13g02418 Chr13 28360989 28365163 +
Mibi Mibi01g1794 Chr01 26229417 26233129 -
Mtr Mtr4g2342 Chr4 36872210 36876168 -
Phac Phac9g02086 Chr9 19603677 19607823 +
Phac Phac11g01830 Chr11 24427621 24428752 -
Phco Phco7g00087 Chr7 547710 551117 -
Phco Phco9g00305 Chr9 2091474 2094915 +
Prci Prci14g0150 Chr14 1254919 1259104 -
Pste Pste1g01047 Chr1 3374186 3377602 +
Pumo Pumo11g02047 Chr11 52491370 52495615 -
Pvu Pvu9g0010 Chr9 322750 326672 -
Pvu Pvu11g0262 Chr11 2128424 2132260 +
Rops Rops10g02663 Chr10 46083159 46090381 +
Rops Rops3g00327 Chr3 4127601 4131414 +
Seca Seca4g00108 Chr4 1556524 1561533 -
Seca Seca6g00522 Chr6 15742944 15747128 +
Spst Spst9g00074 Chr9 587840 591397 -
Spst Spst2g02743 Chr2 27189426 27192760 -
Sto Sto2g0898 Chr2 7788223 7793379 +
Sto Sto10g0103 Chr10 764202 768479 -
Tpr Tpr3g2581 Chr3 24944080 24948927 -
Trre Trre5g05939 Chr5 58859056 58861759 +
Trre Trre7g02467 Chr7 20344115 20348940 +
Tsu Tsu02g02737 Chr02 28995560 29000267 -
Vian Vian5g01663 Chr5 39058097 39061112 -
Vifa Vifa6g01411 Chr6 515589556 515596882 +
Vimu Vimu10g03695 Chr10 45974508 45977897 +
Vimu Vimu5g02581 Chr5 36069800 36072789 -
Viun Viun9g03927 Chr9 43377725 43381698 +
Viun Viun11g02699 Chr11 39681143 39685943 -
Vivi Vivi5g03115 Chr5 119942407 119947341 +
Vra Vra5g1827 Chr5 24228353 24232225 +
Vvi Vvi3g0107 Chr3 976131 977121 -
Aev Aev04g3561 Chr04 33593238 33596881 +
Ahy Ahy13g0973 Chr13 10666236 10668307 -
Aip Aip03g01058 Chr03 10330296 10332606 -
Amo Amo13g1121 Chr13 14204000 14210898 -
Bva Bva13g01602 Chr13 9603802 9604606 +
Car Car06g02119 Chr06 21640266 21642203 -
Dere Dere06g0128 Chr06 1510892 1512326 +
Dod Dod03g3354 Chr03 66182212 66183057 +
Enph Enph12g0617 Chr12 12647542 12648897 -
Gma Gma12g00224 Chr12 1760160 1761653 -
Lal Lal1g0106 Chr1 715616 716660 -
Lan Lan13g0126 Chr13 740607 742085 -
Lapu Lapu11g00933 Chr11 11819514 11822916 +
Mal Mal7g2845 Chr7 90985865 90986874 +
Mepo Mepo2g02586 Chr2 35528223 35531723 +
Mesa Mesa13g02420 Chr13 28386675 28388203 -
Mtr Mtr4g2340 Chr4 36864742 36866175 +
Phac Phac11g00355 Chr11 2211868 2212782 -
Phco Phco9g00306 Chr9 2095471 2096555 -
Pvu Pvu11g0263 Chr11 2132584 2134170 -
Spst Spst2g02742 Chr2 27184760 27188878 +
Trre Trre7g02469 Chr7 20358679 20360178 -
Vimu Vimu5g02580 Chr5 36065435 36069413 +
Vivi Vivi5g03108 Chr5 119857233 119865735 +
Vvi Vvi3g0108 Chr3 979763 981975 +
Vvi Vvi3g0109 Chr3 984267 985423 -
Gma Gma12g00225 Chr12 1762618 1763277 -
Lal Lal1g0107 Chr1 717721 718883 -
Lan Lan13g0127 Chr13 744317 745721 -
Mal Mal7g2843 Chr7 90977317 90978383 +
Mtr Mtr4g2338 Chr4 36859889 36861228 +
Phco Phco9g00307 Chr9 2097315 2099304 -
Pumo Pumo11g02046 Chr11 52488111 52488764 +
Pvu Pvu11g0264 Chr11 2134437 2135279 -
Rops Rops3g00329 Chr3 4143857 4144654 -
Seca Seca6g00530 Chr6 16172033 16173078 -
Sto Sto2g0899 Chr2 7795652 7797149 -
Sto Sto10g0102 Chr10 761773 763368 +
Tpr Tpr3g2579 Chr3 24935160 24937018 +
Tsu Tsu02g02734 Chr02 28956007 28956822 +
Vian Vian5g01662 Chr5 39056655 39057725 +
Vifa Vifa6g01412 Chr6 515945223 515947244 -
Viun Viun11g02697 Chr11 39678935 39681096 +
Vivi Vivi5g03107 Chr5 119835890 119837956 +
Vvi Vvi3g0110 Chr3 991431 993320 +
Aed Aed9g0063 Chr9 419772 421478 -
Apr Apr5g1828 Chr5 21502415 21504668 +
Bva Bva13g01601 Chr13 9588320 9589953 -
Cca Cca07g00073 Chr07 943716 946100 -
Gma Gma04g00062 Chr04 488212 496594 -
Gma Gma06g00054 Chr06 469198 477982 -
Gso Gso4g0055 Chr4 486353 489314 -
Gso Gso4g0055 Chr4 486353 489314 -
Lapu Lapu9g02464 Chr9 39002925 39005085 +
Lasa Lasa5g04776 Chr5 695407646 695409354 -
Mepo Mepo3g08023 Chr3 93088406 93091165 +
Mesa Mesa9g05691 Chr9 92603148 92605648 +
Phac Phac9g02087 Chr9 19608873 19611876 +
Phco Phco7g00086 Chr7 543582 547593 -
Pvu Pvu9g0009 Chr9 318742 321004 -
Rops Rops10g02664 Chr10 46097620 46107442 +
Seca Seca4g00107 Chr4 1542081 1551185 -
Spst Spst9g00073 Chr9 583268 586787 -
Trre Trre5g05940 Chr5 58863219 58865392 +
Vimu Vimu10g03696 Chr10 45979900 45982168 +
Viun Viun9g03928 Chr9 43383323 43385376 +
Vivi Vivi3g01007 Chr3 16868730 16871168 -
Vra Vra5g1828 Chr5 24234036 24236231 +
Vvi Vvi3g0111 Chr3 993362 994100 +
Lja Lja1g2363 Chr1 27338968 27341592 +
Sto Sto2g0901 Chr2 7810072 7812460 +
Vvi Vvi3g0112 Chr3 996346 1004637 +
Apr Apr5g1829 Chr5 21506306 21510199 +
Bva Bva13g01599 Chr13 9570699 9575660 -
Bva Bva14g02291 Chr14 19808670 19812425 +
Cca Cca07g00071 Chr07 927194 932035 -
Gma Gma04g00061 Chr04 482034 486049 -
Gma Gma06g00053 Chr06 463716 467378 -
Gso Gso4g0054 Chr4 481257 483483 -
Gso Gso4g0054 Chr4 481257 483483 -
Lapu Lapu9g02465 Chr9 39008137 39012494 +
Lja Lja1g2364 Chr1 27344040 27348342 +
Mepo Mepo3g08024 Chr3 93095483 93099523 +
Mesa Mesa9g05692 Chr9 92623561 92627590 +
Pvu Pvu9g0006 Chr9 289209 293094 -
Rops Rops10g02665 Chr10 46128834 46134689 +
Spst Spst9g00071 Chr9 553303 557240 -
Sto Sto2g0902 Chr2 7824392 7828612 +
Trre Trre5g05941 Chr5 58866652 58870747 +
Vimu Vimu10g03698 Chr10 45991285 45995132 +
Viun Viun9g03932 Chr9 43394377 43398706 +
Vivi Vivi3g01010 Chr3 16912444 16917063 +
Vra Vra5g1830 Chr5 24248367 24252735 +