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
Vvi18g0246 . . . . . . . Aed10g0351 Aev08g0908 . Ahy17g2786 . Aip07g03041 . . . Amo17g2697 . . Apr1g0218 . . . . . . . Bva12g02063 Car05g02186 . . Cca03g01091 . . . . . . . . Gma04g02348 Gma06g01048 . . Gso4g2055 Gso4g2055 . . . Lal17g0494 . . . . . . . . . . . . . . . . . . . . . . Lja1g4999 . . Mal2g1936 . . . . . . . Mtr3g2991 . . . . . . . Psa5g1983 . . . . . . . . . . . . . . . . . Ssu1g2958 Sto5g0367 Sto9g2871 . Tpr2g5015 . . . . . . . . . . . . . . . Vra5g0750
Vvi18g0247 . . . . Adu08g02596 . . . . . . . . . . . . . . . Arst8g03589 . . . . . . . . Car05g02528 . . . . . . . . . . Gma04g02026 Gma06g01391 . . Gso4g1766 Gso4g1766 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal2g1468 . . . . . . . Mtr3g3383 . . Phco7g01764 . . . . Psa5g1409 Pste2g00020 . . . . . . . Pvu9g1593 . . . . . Spst9g01891 . . . . . . Tpr3g3188 . . . Tsu07g01278 . . . . . . . . . . . .
Vvi18g0248 Acco10g2428 . Accr4g00340 . . . . Aed10g0350 Aev08g0910 . Ahy17g2787 . Aip07g03043 . Alju08g0358 . Amo17g2699 . . Apr1g0217 Arst8g00717 . Bach12g00875 . Bisa09g1718 . Bva06g02869 . Car05g02185 . . Cca03g01092 Dere04g1075 . . . Enph1g1733 . Glsi08g1094 . . Gma06g01047 . . . . . . . Lal17g0493 . . . . . . . . . . Lapu9g01452 . Lasa5g02837 . . Lele02g0274 . Lele04g0281 . . . . Lja1g5001 . . Mal2g1937 Mepo3g06418 . Mesa9g03924 . Mibi05g0303 . . Mtr3g2990 Phac9g00935 . Phco7g01292 . Prci15g0446 . . Psa5g1985 Pste2g03188 . . . . . Pumo10g01285 . Pvu9g1337 . Rops10g01944 . Seca4g02375 . Spst9g01340 . . Ssu1g2960 . Sto9g2872 . Tpr2g5012 Trre5g03565 . . . Vian4g01495 . Vifa2g02680 . Vimu10g02306 . Viun9g02338 . Vivi3g03063 . . Vra5g0751
Vvi18g0249 . . . . Adu08g00557 . . . . . . . . . . . . . . . Arst8g00719 . Bach12g00874 . Bisa09g1717 . Bva06g02868 . Car05g02184 . . . Dere04g1073 . . . . . Glsi08g1095 . Gma04g02349 . . . . . . . . Lal17g0492 . . . . . . . . . . . . Lasa5g02836 . Lele01g0288 Lele02g0275 . Lele04g0283 . . . . Lja1g5002 . . . . . . . Mibi05g0304 . . . Phac9g00933 . Phco7g01291 . . . . Psa5g1986 Pste2g03187 . . . . . . . Pvu9g1336 . . . . . . . . . . Sto9g2874 . . . . . . . . . . Vimu10g02305 . . . Vivi3g03065 . . .
Vvi18g0250 . . . . . . . Aed10g0347 . . . . . . . . . . . Apr1g0215 Arst4g01145 . Bach12g00873 . . . Bva06g02867 . Car05g02182 . Cca05g00347 Cca03g01094 . . . . . . . . . Gma06g01045 . . . . . . . . . . . . . . . . . . Lapu9g01454 . . . . . . . . . . . Lja1g5004 . . Mal2g1939 Mepo3g06413 . Mesa9g03921 . . . . Mtr3g2988 . . . . . . . Psa5g1988 . . . . . . Pumo10g01282 . Pvu9g1335 . Rops10g01939 . Seca4g02372 . Spst9g01338 . . Ssu1g2962 Sto5g0368 . . Tpr2g5010 Trre5g03554 . . . Vian4g01497 . Vifa2g02678 . . . Viun9g02343 . Vivi3g03068 . . Vra5g0753
Vvi18g0251 . . . . . . . . . . . . . . . . . . Apr9g0798 . . . . . . . Bva06g02865 . Car04g02932 . Cca05g00923 . . . . . . . . . . . . Gma13g00187 . . . . . . . . . Lal22g0498 . . . . . . . . . . . . . . . . . . . Lja1g5828 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g2875 . . . . . . . . . . . . . . . . . .
Vvi18g0252 . . . . . . . . Aev08g0912 . Ahy17g2789 . Aip07g03045 . . . . . . Apr1g0214 . . . . . . . Bva12g02064 Car05g02181 . . . . . . . . . . . Gma04g02023 Gma06g01394 . . Gso4g1763 Gso4g1763 . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g5005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g2877 . . . . . . . . . . . . . . . . . .
Vvi18g0253 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0254 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0255 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Psa Psa5g1409 Chr5 109128820 109131373 +
Apr Apr1g0215 Chr1 2336905 2340100 +
Bach Bach12g00873 Chr12 6151361 6152803 +
Vvi Vvi18g0246 Chr18 2347198 2348427 -
Aed Aed10g0351 Chr10 2834027 2835967 +
Aev Aev08g0908 Chr08 5365298 5366593 -
Ahy Ahy17g2786 Chr17 126330528 126332422 -
Aip Aip07g03041 Chr07 117393386 117395380 -
Amo Amo17g2697 Chr17 127336757 127337381 -
Apr Apr1g0218 Chr1 2387878 2389673 +
Bva Bva12g02063 Chr12 16145279 16146492 -
Car Car05g02186 Chr05 67107736 67109910 +
Cca Cca03g01091 Chr03 26527537 26529421 -
Gma Gma04g02348 Chr04 53914357 53916246 -
Gma Gma06g01048 Chr06 9824154 9826113 +
Gso Gso4g2055 Chr4 50989509 50991412 -
Gso Gso4g2055 Chr4 50989509 50991412 -
Lal Lal17g0494 Chr17 3428286 3430054 +
Lja Lja1g4999 Chr1 70114082 70115835 -
Mal Mal2g1936 Chr2 23412464 23414059 -
Mtr Mtr3g2991 Chr3 43743748 43745669 +
Psa Psa5g1983 Chr5 153246178 153248193 -
Ssu Ssu1g2958 Chr1 77772301 77773758 -
Sto Sto5g0367 Chr5 2247824 2249194 -
Sto Sto9g2871 Chr9 30133879 30135121 -
Tpr Tpr2g5015 Chr2 55974913 55976791 +
Vra Vra5g0750 Chr5 12780508 12782400 -
Vvi Vvi18g0247 Chr18 2352063 2359074 +
Adu Adu08g02596 Chr08 42057657 42061674 +
Arst Arst8g03589 Chr8 46430279 46434375 +
Car Car05g02528 Chr05 70363466 70368779 +
Gma Gma04g02026 Chr04 50700259 50705864 -
Gma Gma06g01391 Chr06 13144569 13147963 +
Gso Gso4g1766 Chr4 47788371 47792034 -
Gso Gso4g1766 Chr4 47788371 47792034 -
Mal Mal2g1468 Chr2 17598452 17601835 -
Mtr Mtr3g3383 Chr3 47726564 47730415 +
Phco Phco7g01764 Chr7 17933808 17937293 -
Psa Psa5g1409 Chr5 109128820 109131373 +
Pste Pste2g00020 Chr2 91714 95996 -
Pvu Pvu9g1593 Chr9 22392742 22396207 -
Spst Spst9g01891 Chr9 25341731 25344789 +
Tpr Tpr3g3188 Chr3 35080169 35084550 +
Tsu Tsu07g01278 Chr07 11147165 11150370 -
Vvi Vvi18g0248 Chr18 2359940 2405390 -
Acco Acco10g2428 Chr10 35797392 35808996 +
Accr Accr4g00340 Chr4 3284523 3304475 -
Aed Aed10g0350 Chr10 2808529 2824413 +
Aev Aev08g0910 Chr08 5382394 5385689 -
Ahy Ahy17g2787 Chr17 126384225 126402909 -
Aip Aip07g03043 Chr07 117443726 117461562 -
Alju Alju08g0358 Chr08 2590626 2601332 -
Amo Amo17g2699 Chr17 127403895 127407709 -
Apr Apr1g0217 Chr1 2345505 2375432 +
Arst Arst8g00717 Chr8 10018189 10027597 -
Bach Bach12g00875 Chr12 6160299 6169568 +
Bisa Bisa09g1718 Chr09 25837115 25848979 +
Bva Bva06g02869 Chr06 17933281 17943726 +
Car Car05g02185 Chr05 67082022 67096323 +
Cca Cca03g01092 Chr03 26584049 26618625 -
Dere Dere04g1075 Chr04 11531797 11543132 +
Enph Enph1g1733 Chr1 42397851 42426433 +
Glsi Glsi08g1094 Chr08 8057758 8075914 -
Gma Gma06g01047 Chr06 9782247 9804377 +
Lal Lal17g0493 Chr17 3410284 3422774 +
Lapu Lapu9g01452 Chr9 28878264 28909049 -
Lasa Lasa5g02837 Chr5 512326943 512347481 +
Lele Lele02g0274 Chr02 1554444 1569744 -
Lele Lele04g0281 Chr04 1654502 1664999 -
Lja Lja1g5001 Chr1 70159096 70180715 -
Mal Mal2g1937 Chr2 23437669 23467296 -
Mepo Mepo3g06418 Chr3 78180421 78205281 +
Mesa Mesa9g03924 Chr9 71442360 71476692 +
Mibi Mibi05g0303 Chr05 2997397 3007455 -
Mtr Mtr3g2990 Chr3 43694696 43723170 +
Phac Phac9g00935 Chr9 7104210 7116113 +
Phco Phco7g01292 Chr7 11521057 11540953 +
Prci Prci15g0446 Chr15 2865224 2884490 -
Psa Psa5g1985 Chr5 153717763 153737740 -
Pste Pste2g03188 Chr2 31760665 31776311 +
Pumo Pumo10g01285 Chr10 16842065 16857151 +
Pvu Pvu9g1337 Chr9 19047225 19068103 +
Rops Rops10g01944 Chr10 35553639 35559019 +
Seca Seca4g02375 Chr4 40311163 40314026 +
Spst Spst9g01340 Chr9 13015718 13038019 +
Ssu Ssu1g2960 Chr1 77849608 77852295 -
Sto Sto9g2872 Chr9 30147884 30148559 -
Tpr Tpr2g5012 Chr2 55900359 55936940 +
Trre Trre5g03565 Chr5 33793495 33819761 +
Vian Vian4g01495 Chr4 29996043 30000440 -
Vifa Vifa2g02680 Chr2 716799111 716804146 +
Vimu Vimu10g02306 Chr10 33699649 33709511 +
Viun Viun9g02338 Chr9 32920949 32960407 -
Vivi Vivi3g03063 Chr3 51781989 51803494 -
Vra Vra5g0751 Chr5 12815436 12856288 -
Vvi Vvi18g0249 Chr18 2406583 2411502 -
Adu Adu08g00557 Chr08 10047444 10068390 -
Arst Arst8g00719 Chr8 10036753 10039398 -
Bach Bach12g00874 Chr12 6153940 6158588 +
Bisa Bisa09g1717 Chr09 25831645 25836800 +
Bva Bva06g02868 Chr06 17928257 17932649 +
Car Car05g02184 Chr05 67072636 67081207 +
Dere Dere04g1073 Chr04 11522694 11527379 +
Glsi Glsi08g1095 Chr08 8077150 8082290 -
Gma Gma04g02349 Chr04 53932552 53933499 -
Lal Lal17g0492 Chr17 3404380 3409383 +
Lasa Lasa5g02836 Chr5 512100629 512105818 +
Lele Lele01g0288 Chr01 1633359 1637246 -
Lele Lele02g0275 Chr02 1570532 1571245 -
Lele Lele04g0283 Chr04 1670559 1671095 -
Lja Lja1g5002 Chr1 70226212 70230611 -
Mibi Mibi05g0304 Chr05 3010997 3015171 -
Phac Phac9g00933 Chr9 7097417 7103040 +
Phco Phco7g01291 Chr7 11514807 11518810 +
Psa Psa5g1986 Chr5 153763546 153769113 -
Pste Pste2g03187 Chr2 31751262 31757208 +
Pvu Pvu9g1336 Chr9 19041215 19045877 +
Sto Sto9g2874 Chr9 30152658 30156705 -
Vimu Vimu10g02305 Chr10 33693097 33697355 +
Vivi Vivi3g03065 Chr3 51811047 51815185 -
Vvi Vvi18g0250 Chr18 2413199 2414689 +
Aed Aed10g0347 Chr10 2797018 2797447 +
Apr Apr1g0215 Chr1 2336905 2340100 +
Arst Arst4g01145 Chr4 10304707 10308269 +
Bach Bach12g00873 Chr12 6151361 6152803 +
Bva Bva06g02867 Chr06 17924875 17927455 +
Car Car05g02182 Chr05 67064998 67067155 +
Cca Cca05g00347 Chr05 7583585 7592959 +
Cca Cca03g01094 Chr03 26624177 26627708 -
Gma Gma06g01045 Chr06 9774240 9776658 +
Lapu Lapu9g01454 Chr9 28913548 28917446 -
Lja Lja1g5004 Chr1 70235527 70238443 -
Mal Mal2g1939 Chr2 23473552 23474994 -
Mepo Mepo3g06413 Chr3 78150240 78153342 +
Mesa Mesa9g03921 Chr9 71423988 71425430 +
Mtr Mtr3g2988 Chr3 43677129 43685273 +
Psa Psa5g1988 Chr5 153774402 153777361 -
Pumo Pumo10g01282 Chr10 16826149 16828021 +
Pvu Pvu9g1335 Chr9 19034521 19037644 -
Rops Rops10g01939 Chr10 35526522 35530237 +
Seca Seca4g02372 Chr4 40284206 40285588 +
Spst Spst9g01338 Chr9 13008682 13010064 +
Ssu Ssu1g2962 Chr1 77872318 77873292 -
Sto Sto5g0368 Chr5 2257737 2259119 -
Tpr Tpr2g5010 Chr2 55889460 55894818 +
Trre Trre5g03554 Chr5 33334242 33335387 +
Vian Vian4g01497 Chr4 30050000 30051382 -
Vifa Vifa2g02678 Chr2 716790383 716791825 +
Viun Viun9g02343 Chr9 32973737 32977237 -
Vivi Vivi3g03068 Chr3 51823172 51826563 -
Vra Vra5g0753 Chr5 12861233 12864040 -
Vvi Vvi18g0251 Chr18 2415377 2417215 -
Apr Apr9g0798 Chr9 15324385 15328250 -
Bva Bva06g02865 Chr06 17922233 17924053 +
Car Car04g02932 Chr04 56478710 56480762 -
Cca Cca05g00923 Chr05 24817366 24819165 -
Gma Gma13g00187 Chr13 10760795 10762841 +
Lal Lal22g0498 Chr22 3289881 3291713 +
Lja Lja1g5828 Chr1 104703824 104706013 -
Sto Sto9g2875 Chr9 30158054 30162221 -
Vvi Vvi18g0252 Chr18 2419128 2422510 +
Aev Aev08g0912 Chr08 5390378 5394036 +
Ahy Ahy17g2789 Chr17 126406581 126411947 +
Aip Aip07g03045 Chr07 117465599 117470873 +
Apr Apr1g0214 Chr1 2331275 2336006 -
Bva Bva12g02064 Chr12 16153096 16158792 +
Car Car05g02181 Chr05 67054645 67060074 -
Gma Gma04g02023 Chr04 50661188 50670067 -
Gma Gma06g01394 Chr06 13175496 13183524 +
Gso Gso4g1763 Chr4 47744890 47753650 -
Gso Gso4g1763 Chr4 47744890 47753650 -
Lja Lja1g5005 Chr1 70241124 70247226 +
Sto Sto9g2877 Chr9 30164858 30169319 +
Vvi Vvi18g0253 Chr18 2435143 2435965 +
Vvi Vvi18g0254 Chr18 2438554 2440490 +
Vvi Vvi18g0255 Chr18 2443023 2443205 +