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
Vvi3g0183 Acco10g2234 . Accr4g00546 . . . . Aed9g0041 . . . . . . Alju08g0568 . . . . . . . . . Bisa09g1456 . . . Car06g02214 . . Cca07g00047 Dere04g0808 . . . Enph1g1559 . Glsi08g1346 . Gma04g00040 Gma06g00036 . Gma12g00306 Gso4g0034 Gso4g0034 . Gso4g0034 Lal1g0160 Lal2g0099 Lal9g0120 . . . Lan13g0179 Lan13g0179 Lan13g0179 . . . Lapu9g02489 . Lasa5g04763 . Lele01g0459 Lele02g0449 Lele03g0472 Lele04g0465 . . . . Lja1g2376 . . . . . . . Mibi05g0507 . . . . . Phco7g00060 . Prci15g0710 . Psa7g4047 . . . . . . . . . Pvu9g1230 . . . . . Spst9g00045 . . . Sto2g0975 . . . . . . . . . . . Vimu10g03726 . . . Vivi3g01071 . . Vra5g1855
Vvi3g0184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0185 . . . . . . . Aed9g0040 . Aev05g0405 Ahy13g0073 Ahy15g0392 Aip03g00077 Aip05g00384 . . Amo13g5761 . . Apr5g1849 . . . . . . . Bva14g02333 Car06g02215 . . Cca07g00046 . . . Dod02g0427 . . . . Gma04g00039 . . Gma12g00307 Gso4g0033 . . Gso4g0033 Lal1g0166 . Lal9g0121 . . . Lan13g0180 . Lan13g0180 . . . Lapu9g02491 . Lasa5g04760 . . . . . . . . . Lja1g2379 . . . Mepo3g08032 . . . . . . . . . Phco7g00059 . . . . Psa2g3473 . . . . . . . . Pvu9g1229 . . . . . Spst9g00043 . . . Sto2g0977 Sto10g0072 . . . . . . . . . . Vimu10g03727 . . . Vivi3g01078 . . Vra5g1856
Vvi3g0186 . . . . . . . Aed9g0039 . . . . . . . . . . . . . . . . . . . Bva14g02334 . . . Cca07g00045 . . . . . . . . Gma04g00038 . . . Gso4g0032 . . . . . . . . . . . . . . . Lapu9g02492 . Lasa5g04759 . . . . . . . . . Lja1g2381 . . . Mepo3g08033 . Mesa9g05703 . . . . . Phac9g02130 . Phco7g00057 . . . . . . . . . . . . . Pvu9g1228 . . . . . Spst9g00042 . . . Sto2g0983 . . . Trre5g05955 . . . . . . . Vimu10g03728 . . . Vivi3g01079 . . Vra5g1857
Vvi3g0187 . . . . . . . . . Aev05g0404 . Ahy15g0391 . Aip05g00383 . . . . . . . . . . . . . . Car06g02216 . . . . . . Dod02g0426 . . . . . . . Gma12g00308 . . . . Lal1g0167 Lal2g0100 Lal9g0122 . . . Lan13g0181 Lan13g0181 Lan13g0181 . . . . . . . . . . . . . . . Lja1g2382 . . . . . . . . . . . . . . . . . Psa7g4042 Psa2g3472 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0188 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g02335 Car06g02217 . . . . . . . . . . . . . . Gma12g00309 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g4041 . . . . . . . . . . . . . . . . . . . . Sto10g0070 . . . . . . . . . . . . . . . . . .
Vvi3g0189 . . . . . . . . . . . . . . . . . . . Apr5g1853 . . . . . . . Bva14g02336 Car06g02218 . . . . . . . . . . . . . . Gma12g00310 . . . . Lal1g0168 . Lal9g0123 . . . . . . . . . . . . . . . . . . . . . Lja1g2383 . . . . . . . . . . . . . . . . . Psa7g4040 . . . . . . . . . . . . . . . . . . . . Sto10g0069 . . . . . . . . . . . . . . . . . .
Vvi3g0190 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0191 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g02337 Car06g02220 . . . . . . . . . . . . . . . . . . . Lal1g0169 Lal2g0101 Lal9g0124 . . . Lan13g0184 Lan13g0184 Lan13g0184 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g4039 . . . . . . . . . . . . . . . . . . . Sto2g0991 Sto10g0068 . . . . . . . . . . . . . . . . . .
Vvi3g0192 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva14g02338 Car06g02221 . . . . . . . . . . . . . . Gma12g00311 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa7g4038 . . . . . . . . . . . . . . . . . . . Sto2g0993 . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0183 Chr3 1612834 1639214 +
Acco Acco10g2234 Chr10 34305084 34320084 +
Accr Accr4g00546 Chr4 5284181 5299165 -
Aed Aed9g0041 Chr9 268952 279720 -
Alju Alju08g0568 Chr08 4142122 4157190 -
Bisa Bisa09g1456 Chr09 21132089 21147713 +
Car Car06g02214 Chr06 22717715 22728794 +
Cca Cca07g00047 Chr07 648006 659333 -
Dere Dere04g0808 Chr04 8277625 8293522 +
Enph Enph1g1559 Chr1 40906826 40923968 +
Glsi Glsi08g1346 Chr08 9789851 9806626 -
Gma Gma04g00040 Chr04 336301 346162 -
Gma Gma06g00036 Chr06 313201 322500 -
Gma Gma12g00306 Chr12 2474802 2485777 +
Gso Gso4g0034 Chr4 331442 341760 -
Gso Gso4g0034 Chr4 331442 341760 -
Gso Gso4g0034 Chr4 331442 341760 -
Lal Lal1g0160 Chr1 1021452 1032494 +
Lal Lal2g0099 Chr2 622895 632154 +
Lal Lal9g0120 Chr9 784730 795721 +
Lan Lan13g0179 Chr13 1097824 1108718 +
Lan Lan13g0179 Chr13 1097824 1108718 +
Lan Lan13g0179 Chr13 1097824 1108718 +
Lapu Lapu9g02489 Chr9 39171409 39182559 +
Lasa Lasa5g04763 Chr5 694598533 694622875 -
Lele Lele01g0459 Chr01 2691313 2706592 -
Lele Lele02g0449 Chr02 2642578 2655418 -
Lele Lele03g0472 Chr03 2697510 2712452 -
Lele Lele04g0465 Chr04 2769019 2783950 -
Lja Lja1g2376 Chr1 27441199 27452112 +
Mibi Mibi05g0507 Chr05 4840749 4856599 -
Phco Phco7g00060 Chr7 385789 395164 -
Prci Prci15g0710 Chr15 4603136 4619786 -
Psa Psa7g4047 Chr7 333187249 333198024 +
Pvu Pvu9g1230 Chr9 17765694 17776046 -
Spst Spst9g00045 Chr9 374816 379029 -
Sto Sto2g0975 Chr2 8494049 8504416 +
Vimu Vimu10g03726 Chr10 46137258 46146740 +
Vivi Vivi3g01071 Chr3 18006464 18032073 +
Vra Vra5g1855 Chr5 24388241 24398284 +
Vvi Vvi3g0184 Chr3 1639344 1639651 +
Vvi Vvi3g0185 Chr3 1641239 1645417 -
Aed Aed9g0040 Chr9 264878 268031 +
Aev Aev05g0405 Chr05 2803171 2808124 +
Ahy Ahy13g0073 Chr13 725873 738702 -
Ahy Ahy15g0392 Chr15 4599606 4605595 +
Aip Aip03g00077 Chr03 704527 721303 -
Aip Aip05g00384 Chr05 4336180 4340873 +
Amo Amo13g5761 Chr13 159686543 159698681 -
Apr Apr5g1849 Chr5 21623483 21627344 +
Bva Bva14g02333 Chr14 20133667 20142874 -
Car Car06g02215 Chr06 22759273 22765550 -
Cca Cca07g00046 Chr07 636485 640079 +
Dod Dod02g0427 Chr02 5683686 5688710 +
Gma Gma04g00039 Chr04 330180 333032 +
Gma Gma12g00307 Chr12 2488225 2493456 -
Gso Gso4g0033 Chr4 325619 328670 +
Gso Gso4g0033 Chr4 325619 328670 +
Lal Lal1g0166 Chr1 1046420 1052725 -
Lal Lal9g0121 Chr9 796140 801467 -
Lan Lan13g0180 Chr13 1109736 1130777 -
Lan Lan13g0180 Chr13 1109736 1130777 -
Lapu Lapu9g02491 Chr9 39193648 39197977 -
Lasa Lasa5g04760 Chr5 694413799 694417248 +
Lja Lja1g2379 Chr1 27486082 27490196 -
Mepo Mepo3g08032 Chr3 93180214 93184001 -
Phco Phco7g00059 Chr7 377247 381237 +
Psa Psa2g3473 Chr2 383325421 383330578 +
Pvu Pvu9g1229 Chr9 17749493 17753666 +
Spst Spst9g00043 Chr9 344691 347502 +
Sto Sto2g0977 Chr2 8539708 8544382 -
Sto Sto10g0072 Chr10 535911 539912 +
Vimu Vimu10g03727 Chr10 46150183 46154220 -
Vivi Vivi3g01078 Chr3 18096960 18100871 -
Vra Vra5g1856 Chr5 24400898 24405092 -
Vvi Vvi3g0186 Chr3 1647090 1651227 +
Aed Aed9g0039 Chr9 261305 266550 -
Bva Bva14g02334 Chr14 20149076 20153049 +
Cca Cca07g00045 Chr07 632147 635389 -
Gma Gma04g00038 Chr04 326137 329276 -
Gso Gso4g0032 Chr4 321654 324780 -
Lapu Lapu9g02492 Chr9 39199144 39204226 +
Lasa Lasa5g04759 Chr5 694395787 694399714 -
Lja Lja1g2381 Chr1 27526275 27528968 +
Mepo Mepo3g08033 Chr3 93185976 93189024 +
Mesa Mesa9g05703 Chr9 92725777 92728637 -
Phac Phac9g02130 Chr9 20244337 20248256 +
Phco Phco7g00057 Chr7 366046 368940 -
Pvu Pvu9g1228 Chr9 17744775 17748140 -
Spst Spst9g00042 Chr9 340783 343566 -
Sto Sto2g0983 Chr2 8632183 8635630 +
Trre Trre5g05955 Chr5 58953801 58956303 +
Vimu Vimu10g03728 Chr10 46155664 46158637 +
Vivi Vivi3g01079 Chr3 18106234 18110704 +
Vra Vra5g1857 Chr5 24406356 24409785 +
Vvi Vvi3g0187 Chr3 1656165 1659987 +
Aev Aev05g0404 Chr05 2798901 2800822 -
Ahy Ahy15g0391 Chr15 4596138 4598572 -
Aip Aip05g00383 Chr05 4325640 4328217 -
Car Car06g02216 Chr06 22774347 22777431 +
Dod Dod02g0426 Chr02 5679517 5682669 -
Gma Gma12g00308 Chr12 2504371 2507814 +
Lal Lal1g0167 Chr1 1055570 1061735 +
Lal Lal2g0100 Chr2 633582 636372 +
Lal Lal9g0122 Chr9 802761 811959 +
Lan Lan13g0181 Chr13 1123455 1126874 +
Lan Lan13g0181 Chr13 1123455 1126874 +
Lan Lan13g0181 Chr13 1123455 1126874 +
Lja Lja1g2382 Chr1 27532885 27535073 +
Psa Psa7g4042 Chr7 332679087 332684660 -
Psa Psa2g3472 Chr2 383278995 383280923 -
Vvi Vvi3g0188 Chr3 1661295 1662143 +
Bva Bva14g02335 Chr14 20156742 20157929 +
Car Car06g02217 Chr06 22778524 22780752 +
Gma Gma12g00309 Chr12 2508236 2509933 +
Psa Psa7g4041 Chr7 332676959 332678908 -
Sto Sto10g0070 Chr10 515593 521254 -
Vvi Vvi3g0189 Chr3 1671220 1673841 +
Apr Apr5g1853 Chr5 21654908 21658022 +
Bva Bva14g02336 Chr14 20162420 20165949 +
Car Car06g02218 Chr06 22789658 22794268 +
Gma Gma12g00310 Chr12 2516327 2519945 +
Lal Lal1g0168 Chr1 1063443 1066113 +
Lal Lal9g0123 Chr9 812890 819414 +
Lja Lja1g2383 Chr1 27537223 27541826 +
Psa Psa7g4040 Chr7 332604769 332608936 -
Sto Sto10g0069 Chr10 506809 510940 -
Vvi Vvi3g0190 Chr3 1674326 1676892 -
Vvi Vvi3g0191 Chr3 1680123 1682840 +
Bva Bva14g02337 Chr14 20168137 20170961 +
Car Car06g02220 Chr06 22797955 22800641 +
Lal Lal1g0169 Chr1 1066178 1073056 +
Lal Lal2g0101 Chr2 637295 638053 +
Lal Lal9g0124 Chr9 819518 822238 +
Lan Lan13g0184 Chr13 1137364 1139710 +
Lan Lan13g0184 Chr13 1137364 1139710 +
Lan Lan13g0184 Chr13 1137364 1139710 +
Psa Psa7g4039 Chr7 332601218 332604419 -
Sto Sto2g0991 Chr2 8740815 8742469 +
Sto Sto10g0068 Chr10 498115 505328 -
Vvi Vvi3g0192 Chr3 1684485 1690368 -
Bva Bva14g02338 Chr14 20171591 20175079 -
Car Car06g02221 Chr06 22802791 22805474 -
Gma Gma12g00311 Chr12 2526604 2529452 -
Psa Psa7g4038 Chr7 332589125 332591811 +
Sto Sto2g0993 Chr2 8746874 8750049 -
Apr Apr5g1853 Chr5 21654908 21658022 +
Gma Gma12g00310 Chr12 2516327 2519945 +
Lja Lja1g2383 Chr1 27537223 27541826 +
Aev Aev05g0405 Chr05 2803171 2808124 +
Ahy Ahy15g0392 Chr15 4599606 4605595 +
Aip Aip05g00384 Chr05 4336180 4340873 +
Dod Dod02g0427 Chr02 5683686 5688710 +
Psa Psa2g3473 Chr2 383325421 383330578 +
Aev Aev05g0404 Chr05 2798901 2800822 -
Ahy Ahy15g0391 Chr15 4596138 4598572 -
Aip Aip05g00383 Chr05 4325640 4328217 -
Dod Dod02g0426 Chr02 5679517 5682669 -
Psa Psa2g3472 Chr2 383278995 383280923 -