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
Vvi3g0173 . . . . . . . Aed9g0045 . . . . . . . . . . . Apr5g1845 . . . . . . . Bva14g02325 Car06g02206 . . Cca07g00051 . . . . . . . . Gma04g00043 Gma06g00039 . Gma12g00299 Gso4g0037 Gso4g0037 . Gso4g0037 Lal1g0153 . Lal9g0116 . . Lal24g0215 Lan13g0176 . Lan13g0176 . . Lan13g0176 . . . . . . . . . . . . . . . . . . . . . . . . . . Phco7g00065 . . . . . . . . . . . . . Pvu9g1234 . . . . . Spst9g00051 . . . Sto2g0953 . . . . . . . . . . . Vimu10g03721 . . . . . . Vra5g1851
Vvi3g0174 . . . . . . . . . . . . . . . . . . . Apr5g1846 . . . . . . . Bva14g02326 Car06g02208 . . . . . . . . . . . Gma04g00042 . . Gma12g00300 Gso4g0036 . . Gso4g0036 Lal1g0154 . . . . . Lan13g0177 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g0956 Sto10g0075 . . . . . . . . . . . . . . . . . .
Vvi3g0175 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0176 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g2413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0177 . . . . . . . . . . . . . Aip05g00391 . . . . . . . . . . . . . Bva14g02327 Car06g02209 . . . . . . . . . . . . . . Gma12g00301 . . . . . Lal2g0095 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g3173 Psa2g3482 . . . . . . . . . . . . . . . . . . Sto2g0958 . . . . . . . . . . . . . . . . . . .
Vvi3g0178 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car06g02210 . . . . . . . . . . . . . . Gma12g00302 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g3172 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0179 . . . . Adu09g02819 . Aed1g1797 . . . Ahy19g3099 . Aip09g03561 . . . Amo19g3966 . Apr8g2619 . Arst9g03762 . . . . . . . . . Cca02g02718 . . . Dod06g0264 . . . . . . . . . . . . . . . . Lal13g0225 Lal12g0257 . . . . . . . Lapu7g02476 . Lasa6g04741 . . . . . . . . . . . . Mal1g0257 Mepo4g04815 . . . . . . Mtr1g4283 Phac7g00336 . Phco6g03017 . . . Psa6g5297 . Pste4g00504 . . Pte9g00692 . . Pumo3g00223 . Pvu7g0212 . Rops6g03381 . Seca8g07963 . Spst10g01518 . Ssu7g0254 . . . . Tpr1g0224 Trre1g06125 . . Tsu01g04959 . . Vifa3g03666 . Vimu3g03627 . Viun7g03926 . . . Vra8g2616 .
Vvi3g0180 . . . . . . . Aed9g0043 . . . . . . . . . . . Apr5g1847 . . . . . . . Bva14g02329 Car06g02211 . . Cca07g00050 . . . . . . . . Gma04g00041 Gma06g00038 . Gma12g00303 Gso4g0035 Gso4g0035 . Gso4g0035 Lal1g0157 Lal2g0097 Lal9g0117 . . . Lan13g0178 Lan13g0178 Lan13g0178 . . . . . . . . . . . . . . . Lja1g2374 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto2g0960 Sto10g0074 . . . . . . . . . . . . . . . . . Vra5g1853
Vvi3g0181 . . . . . . . . . Aev05g0410 . Ahy15g0397 . Aip05g00389 . . . . . . . . . . . . . Bva14g02330 Car06g02212 . . . . . . Dod02g0433 . . . . . . . Gma12g00304 . . . . Lal1g0158 . Lal9g0118 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa2g3479 . . . . . . . . . . . . . . . . . . Sto2g0961 . . . . . . . . . . . . . . . . . . .
Vvi3g0182 . . . . Adu08g00278 . . Aed9g0042 . . . . . . . . . . . . Arst8g00342 . . . . . . Bva14g02331 Car06g02213 . . Cca07g00048 . . . . . . . . . Gma06g00037 . Gma12g00305 . . . . . Lal2g0098 Lal9g0119 . . . . . . . . . Lapu9g02488 . Lasa5g04764 . . . . . . . . . Lja1g2375 . . . . . . . . . . . . . Phco7g00061 . . . . . . . . . . . . . Pvu9g1231 . . . . . Spst9g00046 . . . Sto2g0962 Sto10g0073 . . . . . . . . . . Vimu10g03724 . . . Vivi3g01069 . . Vra5g1854
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0173 Chr3 1527977 1528708 +
Aed Aed9g0045 Chr9 328742 330291 -
Apr Apr5g1845 Chr5 21594755 21595753 +
Bva Bva14g02325 Chr14 20058783 20059813 +
Car Car06g02206 Chr06 22615722 22616765 +
Cca Cca07g00051 Chr07 724337 725151 -
Gma Gma04g00043 Chr04 382393 383563 -
Gma Gma06g00039 Chr06 361774 362907 -
Gma Gma12g00299 Chr12 2400234 2401562 +
Gso Gso4g0037 Chr4 377789 379008 -
Gso Gso4g0037 Chr4 377789 379008 -
Gso Gso4g0037 Chr4 377789 379008 -
Lal Lal1g0153 Chr1 983524 984851 +
Lal Lal9g0116 Chr9 763272 764456 +
Lal Lal24g0215 Chr24 1560625 1565585 +
Lan Lan13g0176 Chr13 1067335 1068602 +
Lan Lan13g0176 Chr13 1067335 1068602 +
Lan Lan13g0176 Chr13 1067335 1068602 +
Phco Phco7g00065 Chr7 436398 437170 -
Pvu Pvu9g1234 Chr9 17835044 17836080 -
Spst Spst9g00051 Chr9 425772 426610 -
Sto Sto2g0953 Chr2 8216814 8219246 +
Vimu Vimu10g03721 Chr10 46108360 46109849 +
Vra Vra5g1851 Chr5 24364560 24365716 +
Vvi Vvi3g0174 Chr3 1535585 1537909 +
Apr Apr5g1846 Chr5 21600100 21602424 +
Bva Bva14g02326 Chr14 20066671 20069514 +
Car Car06g02208 Chr06 22643219 22646242 +
Gma Gma04g00042 Chr04 373383 375716 -
Gma Gma12g00300 Chr12 2413451 2416202 +
Gso Gso4g0036 Chr4 368462 371313 -
Gso Gso4g0036 Chr4 368462 371313 -
Lal Lal1g0154 Chr1 995639 997978 +
Lan Lan13g0177 Chr13 1075106 1077774 +
Sto Sto2g0956 Chr2 8261200 8262825 +
Sto Sto10g0075 Chr10 571451 573070 -
Vvi Vvi3g0175 Chr3 1543989 1546853 -
Vvi Vvi3g0176 Chr3 1549919 1551967 -
Lja Lja1g2413 Chr1 27831291 27833553 -
Vvi Vvi3g0177 Chr3 1560187 1564616 +
Aip Aip05g00391 Chr05 4401742 4404459 -
Bva Bva14g02327 Chr14 20072282 20075256 +
Car Car06g02209 Chr06 22654734 22656651 +
Gma Gma12g00301 Chr12 2416697 2417470 +
Lal Lal2g0095 Chr2 589386 591376 +
Psa Psa7g3173 Chr7 236259457 236261008 -
Psa Psa2g3482 Chr2 383583738 383590087 -
Sto Sto2g0958 Chr2 8275718 8278070 +
Vvi Vvi3g0178 Chr3 1565251 1567724 -
Car Car06g02210 Chr06 22657760 22660809 -
Gma Gma12g00302 Chr12 2417993 2421906 -
Psa Psa7g3172 Chr7 236256939 236259135 +
Vvi Vvi3g0179 Chr3 1570696 1574690 +
Adu Adu09g02819 Chr09 115891530 115895236 +
Aed Aed1g1797 Chr1 15437830 15442990 -
Ahy Ahy19g3099 Chr19 153859348 153863260 -
Aip Aip09g03561 Chr09 142352243 142356089 -
Amo Amo19g3966 Chr19 155568160 155571901 -
Apr Apr8g2619 Chr8 36035737 36041719 -
Arst Arst9g03762 Chr9 113787910 113791528 +
Cca Cca02g02718 Chr02 48585448 48590983 +
Dod Dod06g0264 Chr06 3597589 3601773 +
Lal Lal13g0225 Chr13 1426657 1431337 +
Lal Lal12g0257 Chr12 1828232 1832597 +
Lapu Lapu7g02476 Chr7 41172437 41179119 +
Lasa Lasa6g04741 Chr6 666490164 666494526 +
Mal Mal1g0257 Chr1 2805800 2810043 -
Mepo Mepo4g04815 Chr4 57528228 57533000 +
Mtr Mtr1g4283 Chr1 54467638 54472276 +
Phac Phac7g00336 Chr7 1620386 1626120 -
Phco Phco6g03017 Chr6 51266973 51273359 +
Psa Psa6g5297 Chr6 465259669 465264590 +
Pste Pste4g00504 Chr4 3814118 3823525 -
Pte Pte9g00692 Chr9 14888239 14892994 -
Pumo Pumo3g00223 Chr3 2882897 2886849 -
Pvu Pvu7g0212 Chr7 1465263 1470676 -
Rops Rops6g03381 Chr6 58337405 58349503 +
Seca Seca8g07963 Chr8 177261579 177265973 +
Spst Spst10g01518 Chr10 15835548 15840072 +
Ssu Ssu7g0254 Chr7 4272188 4276801 -
Tpr Tpr1g0224 Chr1 1862194 1866346 -
Trre Trre1g06125 Chr1 65232042 65235702 +
Tsu Tsu01g04959 Chr01 56453506 56457994 +
Vifa Vifa3g03666 Chr3 1073046243 1073050124 +
Vimu Vimu3g03627 Chr3 48984554 48990029 +
Viun Viun7g03926 Chr7 39113082 39119008 +
Vra Vra8g2616 Chr8 44050880 44056503 +
Vvi Vvi3g0180 Chr3 1584232 1585073 -
Aed Aed9g0043 Chr9 302093 303887 +
Apr Apr5g1847 Chr5 21612372 21613516 -
Bva Bva14g02329 Chr14 20096819 20098006 -
Car Car06g02211 Chr06 22689147 22690543 -
Cca Cca07g00050 Chr07 698495 700018 +
Gma Gma04g00041 Chr04 359626 360591 +
Gma Gma06g00038 Chr06 344991 346029 +
Gma Gma12g00303 Chr12 2443087 2444532 -
Gso Gso4g0035 Chr4 354942 355906 +
Gso Gso4g0035 Chr4 354942 355906 +
Gso Gso4g0035 Chr4 354942 355906 +
Lal Lal1g0157 Chr1 1008605 1010137 -
Lal Lal2g0097 Chr2 598344 599771 -
Lal Lal9g0117 Chr9 768831 770267 -
Lan Lan13g0178 Chr13 1086793 1088091 -
Lan Lan13g0178 Chr13 1086793 1088091 -
Lan Lan13g0178 Chr13 1086793 1088091 -
Lja Lja1g2374 Chr1 27421879 27423153 -
Sto Sto2g0960 Chr2 8320217 8322302 -
Sto Sto10g0074 Chr10 557803 558719 +
Vra Vra5g1853 Chr5 24377429 24378634 -
Vvi Vvi3g0181 Chr3 1587828 1594603 -
Aev Aev05g0410 Chr05 2824837 2828115 +
Ahy Ahy15g0397 Chr15 4636315 4641094 +
Aip Aip05g00389 Chr05 4383285 4386439 +
Bva Bva14g02330 Chr14 20104510 20108493 -
Car Car06g02212 Chr06 22693726 22699259 -
Dod Dod02g0433 Chr02 5723399 5726903 +
Gma Gma12g00304 Chr12 2447477 2453297 -
Lal Lal1g0158 Chr1 1012706 1015199 -
Lal Lal9g0118 Chr9 773130 776856 -
Psa Psa2g3479 Chr2 383459970 383462058 +
Sto Sto2g0961 Chr2 8331937 8336531 -
Vvi Vvi3g0182 Chr3 1595399 1600077 -
Adu Adu08g00278 Chr08 4854108 4856749 +
Aed Aed9g0042 Chr9 281154 290122 +
Arst Arst8g00342 Chr8 4865405 4868309 +
Bva Bva14g02331 Chr14 20109623 20115566 -
Car Car06g02213 Chr06 22704118 22711167 -
Cca Cca07g00048 Chr07 661883 671351 +
Gma Gma06g00037 Chr06 324128 330504 +
Gma Gma12g00305 Chr12 2455499 2466777 -
Lal Lal2g0098 Chr2 603222 613751 -
Lal Lal9g0119 Chr9 778027 783179 -
Lapu Lapu9g02488 Chr9 39166389 39170022 -
Lasa Lasa5g04764 Chr5 694759328 694762557 +
Lja Lja1g2375 Chr1 27432870 27437314 -
Phco Phco7g00061 Chr7 397198 400819 +
Pvu Pvu9g1231 Chr9 17778175 17783906 +
Spst Spst9g00046 Chr9 381159 384668 +
Sto Sto2g0962 Chr2 8350752 8355286 -
Sto Sto10g0073 Chr10 543709 547883 +
Vimu Vimu10g03724 Chr10 46130466 46135471 -
Vivi Vivi3g01069 Chr3 17897463 17900890 -
Vra Vra5g1854 Chr5 24381974 24386981 -
Lja Lja1g2413 Chr1 27831291 27833553 -
Psa Psa2g3482 Chr2 383583738 383590087 -
Aev Aev05g0410 Chr05 2824837 2828115 +
Ahy Ahy15g0397 Chr15 4636315 4641094 +
Aip Aip05g00389 Chr05 4383285 4386439 +
Dod Dod02g0433 Chr02 5723399 5726903 +
Psa Psa2g3479 Chr2 383459970 383462058 +
Lal Lal24g0215 Chr24 1560625 1565585 +