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
Vvi4g0494 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g02416 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g3290 . . . . . . . . . . . . . . . . . .
Vvi4g0495 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0496 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0497 . Acco05g2284 . . . . Aed4g1811 . . . Ahy16g3099 . Aip06g03329 . . Alju07g2250 . . . . . Arst6g03634 . . . . Bva10g00352 . Car05g02977 Car04g03168 Cca03g01548 Cca05g00543 . . Dod08g1663 . . Enph7g0978 . Glsi10g0722 Gma14g01106 . Gma04g00635 Gma06g00624 Gso14g1018 . Gso14g1018 Gso14g1018 Lal21g0347 Lal4g0225 Lal17g0241 . Lal8g1560 . Lan3g1061 Lan3g1061 Lan3g1061 . Lan3g1061 . . . . . . . . . . . . . Lja1g3860 . Mal2g0858 Mal1g5509 . Mepo4g00646 . Mesa1g00678 . . Mtr3g3935 Mtr1g0204 . . . Phco2g00610 . Prci2g0990 . . . . . . . . . . . Pvu1g0541 . . . . . Spst8g01567 Ssu1g3437 . Sto5g0829 . Tpr7g0612 Tpr1g3384 . Trre1g00712 Tsu07g00625 Tsu01g00703 . . . . . Vimu1g02580 . . . Vivi4g05074 Vra3g1209 Vra6g1555
Vvi4g0498 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g0499 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva10g00353 . Car05g02976 . Cca03g01549 . . . . . . . . . . . . Gma06g00623 . . . . . . . . . . . . . . . . Lapu9g01872 . Lasa5g04092 . . . . . . . . . Lja1g3861 . Mal2g0859 . Mepo3g07453 . Mesa9g05062 . . . Mtr3g3934 . . . Phco7g00779 . . . . . . . . . . . Pumo10g00059 . Pvu9g0975 . Rops10g01422 . Seca4g00949 . . . Ssu1g3438 . Sto5g0831 . Tpr7g0613 . Trre5g05247 . Tsu07g00626 . Vian4g01949 . . . . . . . Vivi3g01309 . . .
Vvi4g0500 . . . . Adu08g02505 . . . . Aev08g2627 . Ahy18g2651 . Aip08g03045 . . . . . . Arst8g03455 . Bach12g00514 . . . Bva10g00354 Bva06g02414 Car05g02975 . Cca03g01550 . . . . Dod09g0930 . . . . . . Gma04g00634 Gma06g00622 . . . . . Lal4g0224 Lal17g0240 . . . . . . . . . Lapu9g01873 . Lasa5g04091 . . . . . . . . . Lja1g3862 . Mal2g0860 . Mepo3g07452 . Mesa9g05061 . . . Mtr3g3933 . . . Phco7g00778 . . . . . Pste2g01801 . Pte3g01112 Pte1g02362 . . Pumo10g00060 . Pvu9g0974 . Rops10g01421 . Seca4g00951 . . . Ssu1g3439 . Sto5g0832 . Tpr7g0614 . Trre5g05246 . Tsu07g00627 . Vian4g01951 . . . Vimu10g02927 . . . Vivi3g01311 . Vra3g1192 .
Vvi4g0501 . Acco05g2281 . Accr3g00727 . Adu06g02801 . . . . . . . . . Alju07g2246 . . Apr5g1122 Apr7g0415 . Arst6g03636 . Bach3g01939 . . . . . . . . . Dere05g2146 . . . Enph7g0975 . Glsi10g0719 Gma14g01105 Gma17g01980 . . . . . . . . . Lal25g1069 Lal8g1562 . . . . . . . . Lapu8g00600 . . . . . . Lele25g0611 Lele26g0623 Lele27g1476 Lele28g0607 . . . . . Mepo4g00645 . Mesa1g00677 . Mibi08g1972 . . . . . Phco2g00607 . Prci2g0995 . . . Pste8g01041 . . Pte3g01113 . . . . Pvu1g0537 . Rops9g01892 . Seca8g03118 . . . . . . . . . Trre1g00711 . . . . . . . Vimu1g02588 . . . Vivi4g05076 . .
Vvi4g0502 . . . . . . . Aed6g1135 Aev07g1180 . Ahy16g3100 . Aip06g03330 . . . . . . . . . . . . . Bva10g00355 Bva06g02413 . Car04g03171 . Cca05g00539 . . Dod08g1665 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja5g2833 . Mal1g5510 . . . . . . . Mtr1g0206 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g0587 Sto5g0833 . . Tpr1g3385 . . . Tsu01g00702 . . . . . . . . . . . .
Vvi4g0503 . . . . Adu08g02507 . . . . Aev08g2625 . Ahy18g2653 . Aip08g03047 . . . . . . Arst8g03457 . . . . . Bva10g00356 . . . . . . . . Dod09g0929 . . . . . . Gma04g00633 . . . . . . Lal4g0223 Lal17g0239 . . . . . . . . . Lapu9g01874 . Lasa5g04087 . . . . . . . . . Lja1g3864 . Mal2g0861 . Mepo3g07451 . Mesa9g05060 . . . Mtr3g3932 . . . Phco7g00777 . . . . . Pste2g01792 . . . . . . . Pvu9g0973 . . . . . Spst9g00807 . . . Sto5g0834 . Tpr7g0615 . Trre5g05244 . . . . . . . Vimu10g02929 . . . Vivi3g01315 . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Bva Bva10g00356 Chr10 4144592 4145248 +
Apr Apr5g1122 Chr5 15827965 15832461 +
Bva Bva10g00355 Chr10 4136842 4141546 -
Sto Sto5g0833 Chr5 5612578 5617362 -
Vvi Vvi4g0494 Chr4 4545482 4550148 -
Bva Bva06g02416 Chr06 15497922 15501324 +
Sto Sto9g3290 Chr9 32988863 32992391 -
Vvi Vvi4g0495 Chr4 4553793 4556216 -
Vvi Vvi4g0496 Chr4 4560587 4562817 +
Vvi Vvi4g0497 Chr4 4566088 4576275 +
Acco Acco05g2284 Chr05 38789269 38794812 -
Aed Aed4g1811 Chr4 22330077 22337915 +
Ahy Ahy16g3099 Chr16 146816007 146824311 +
Aip Aip06g03329 Chr06 129944395 129952702 +
Alju Alju07g2250 Chr07 48432990 48438501 -
Arst Arst6g03634 Chr6 104414771 104423072 +
Bva Bva10g00352 Chr10 4120695 4128133 +
Car Car05g02977 Chr05 74677245 74682346 -
Car Car04g03168 Chr04 59962079 59967993 +
Cca Cca03g01548 Chr03 34198833 34205050 +
Cca Cca05g00543 Chr05 12252937 12259269 -
Dod Dod08g1663 Chr08 39566234 39572594 +
Enph Enph7g0978 Chr7 15453335 15460344 -
Glsi Glsi10g0722 Chr10 4579516 4585227 -
Gma Gma14g01106 Chr14 16070216 16077561 -
Gma Gma04g00635 Chr04 5821157 5827751 -
Gma Gma06g00624 Chr06 5638925 5644197 -
Gso Gso14g1018 Chr14 15930098 15937614 -
Gso Gso14g1018 Chr14 15930098 15937614 -
Gso Gso14g1018 Chr14 15930098 15937614 -
Lal Lal21g0347 Chr21 2360673 2367391 +
Lal Lal4g0225 Chr4 1416318 1423623 -
Lal Lal17g0241 Chr17 1492042 1498558 -
Lal Lal8g1560 Chr8 19927632 19934374 +
Lan Lan3g1061 Chr3 22918413 22925088 -
Lan Lan3g1061 Chr3 22918413 22925088 -
Lan Lan3g1061 Chr3 22918413 22925088 -
Lan Lan3g1061 Chr3 22918413 22925088 -
Lja Lja1g3860 Chr1 48721397 48726888 +
Mal Mal2g0858 Chr2 9959060 9965133 +
Mal Mal1g5509 Chr1 130117986 130123517 +
Mepo Mepo4g00646 Chr4 8760458 8768202 -
Mesa Mesa1g00678 Chr1 8755816 8761469 -
Mtr Mtr3g3935 Chr3 53102625 53110427 -
Mtr Mtr1g0204 Chr1 2336451 2344323 +
Phco Phco2g00610 Chr2 6022865 6035496 -
Prci Prci2g0990 Chr2 7337525 7344289 +
Pvu Pvu1g0541 Chr1 6031467 6039713 -
Spst Spst8g01567 Chr8 17558563 17569564 -
Ssu Ssu1g3437 Chr1 88213664 88218853 +
Sto Sto5g0829 Chr5 5594292 5595169 +
Tpr Tpr7g0612 Chr7 5284169 5290175 +
Tpr Tpr1g3384 Chr1 38202704 38210258 +
Trre Trre1g00712 Chr1 5358992 5364921 -
Tsu Tsu07g00625 Chr07 4966681 4973301 +
Tsu Tsu01g00703 Chr01 6173749 6181086 -
Vimu Vimu1g02580 Chr1 37324487 37330632 +
Vivi Vivi4g05074 Chr4 181691507 181704024 +
Vra Vra3g1209 Chr3 12856148 12858883 +
Vra Vra6g1555 Chr6 30752346 30759467 +
Vvi Vvi4g0498 Chr4 4580991 4584770 +
Vvi Vvi4g0499 Chr4 4585355 4586272 +
Bva Bva10g00353 Chr10 4128503 4129438 +
Car Car05g02976 Chr05 74675160 74676391 -
Cca Cca03g01549 Chr03 34207910 34209008 -
Gma Gma06g00623 Chr06 5632310 5638207 -
Lapu Lapu9g01872 Chr9 33532041 33532975 +
Lasa Lasa5g04092 Chr5 629339395 629340354 -
Lja Lja1g3861 Chr1 48727370 48728299 +
Mal Mal2g0859 Chr2 9966078 9967031 +
Mepo Mepo3g07453 Chr3 87907177 87908127 -
Mesa Mesa9g05062 Chr9 85157060 85158019 -
Mtr Mtr3g3934 Chr3 53101059 53102009 -
Phco Phco7g00779 Chr7 6054254 6055189 -
Pumo Pumo10g00059 Chr10 1215494 1216682 +
Pvu Pvu9g0975 Chr9 14701434 14702369 -
Rops Rops10g01422 Chr10 27334417 27335340 -
Seca Seca4g00949 Chr4 15359766 15361006 +
Ssu Ssu1g3438 Chr1 88220979 88221902 +
Sto Sto5g0831 Chr5 5600586 5601512 +
Tpr Tpr7g0613 Chr7 5290720 5291676 +
Trre Trre5g05247 Chr5 53581928 53587162 -
Tsu Tsu07g00626 Chr07 4973791 4974738 +
Vian Vian4g01949 Chr4 36094061 36094996 +
Vivi Vivi3g01309 Chr3 21422262 21423224 +
Vvi Vvi4g0500 Chr4 4590126 4594658 +
Adu Adu08g02505 Chr08 41007728 41012103 +
Aev Aev08g2627 Chr08 24713972 24717287 -
Ahy Ahy18g2651 Chr18 129389739 129394468 +
Aip Aip08g03045 Chr08 119895063 119899731 +
Arst Arst8g03455 Chr8 45380402 45384797 +
Bach Bach12g00514 Chr12 3489972 3493090 -
Bva Bva10g00354 Chr10 4131407 4135363 +
Bva Bva06g02414 Chr06 15484770 15487897 -
Car Car05g02975 Chr05 74667119 74671945 -
Cca Cca03g01550 Chr03 34214795 34220101 +
Dod Dod09g0930 Chr09 29190486 29195450 -
Gma Gma04g00634 Chr04 5810300 5815773 -
Gma Gma06g00622 Chr06 5628180 5632275 -
Lal Lal4g0224 Chr4 1410179 1415233 -
Lal Lal17g0240 Chr17 1484165 1489294 -
Lapu Lapu9g01873 Chr9 33538644 33544211 +
Lasa Lasa5g04091 Chr5 629246321 629249687 -
Lja Lja1g3862 Chr1 48732388 48737216 +
Mal Mal2g0860 Chr2 9972623 9976822 +
Mepo Mepo3g07452 Chr3 87891622 87896214 -
Mesa Mesa9g05061 Chr9 85149019 85153137 -
Mtr Mtr3g3933 Chr3 53087295 53092335 -
Phco Phco7g00778 Chr7 6042453 6046903 -
Pste Pste2g01801 Chr2 18420011 18425332 -
Pte Pte3g01112 Chr3 9509232 9514521 +
Pte Pte1g02362 Chr1 44404125 44408725 +
Pumo Pumo10g00060 Chr10 1229219 1234705 +
Pvu Pvu9g0974 Chr9 14686368 14691768 -
Rops Rops10g01421 Chr10 27319378 27324966 -
Seca Seca4g00951 Chr4 15396812 15402311 +
Ssu Ssu1g3439 Chr1 88241048 88245269 +
Sto Sto5g0832 Chr5 5606832 5610980 +
Tpr Tpr7g0614 Chr7 5295736 5300628 +
Trre Trre5g05246 Chr5 53578126 53581902 -
Tsu Tsu07g00627 Chr07 4977854 4982307 +
Vian Vian4g01951 Chr4 36121814 36126071 +
Vimu Vimu10g02927 Chr10 40329019 40332183 +
Vivi Vivi3g01311 Chr3 21433928 21438029 +
Vra Vra3g1192 Chr3 12682349 12690408 -
Vvi Vvi4g0501 Chr4 4596157 4599280 -
Acco Acco05g2281 Chr05 38773066 38777806 +
Accr Accr3g00727 Chr3 8134357 8139172 -
Adu Adu06g02801 Chr06 105230681 105236540 -
Alju Alju07g2246 Chr07 48410721 48415514 +
Apr Apr5g1122 Chr5 15827965 15832461 +
Apr Apr7g0415 Chr7 10257205 10262905 -
Arst Arst6g03636 Chr6 104425057 104431165 -
Bach Bach3g01939 Chr3 27351123 27355702 -
Dere Dere05g2146 Chr05 31628024 31635005 -
Enph Enph7g0975 Chr7 15436123 15441867 +
Glsi Glsi10g0719 Chr10 4563660 4568838 +
Gma Gma14g01105 Chr14 15544992 15551060 +
Gma Gma17g01980 Chr17 35406071 35412670 -
Lal Lal25g1069 Chr25 13958953 13964716 +
Lal Lal8g1562 Chr8 19954918 19956956 -
Lapu Lapu8g00600 Chr8 23630624 23636364 -
Lele Lele25g0611 Chr25 3873186 3877965 -
Lele Lele26g0623 Chr26 3981098 3986057 -
Lele Lele27g1476 Chr27 20817053 20824763 +
Lele Lele28g0607 Chr28 3897165 3902112 -
Mepo Mepo4g00645 Chr4 8750694 8756396 +
Mesa Mesa1g00677 Chr1 8744096 8749963 +
Mibi Mibi08g1972 Chr08 36690208 36695197 -
Phco Phco2g00607 Chr2 5956067 5960558 +
Prci Prci2g0995 Chr2 7368246 7373660 -
Pste Pste8g01041 Chr8 5471502 5476916 -
Pte Pte3g01113 Chr3 9514741 9520833 -
Pvu Pvu1g0537 Chr1 5978242 5983033 +
Rops Rops9g01892 Chr9 34497410 34503706 -
Seca Seca8g03118 Chr8 88478871 88480417 -
Trre Trre1g00711 Chr1 5351174 5356302 +
Vimu Vimu1g02588 Chr1 37408585 37410792 -
Vivi Vivi4g05076 Chr4 181714443 181721751 -
Vvi Vvi4g0502 Chr4 4599533 4611029 -
Aed Aed6g1135 Chr6 16008402 16015096 -
Aev Aev07g1180 Chr07 10151544 10164521 -
Ahy Ahy16g3100 Chr16 146827929 146833955 -
Aip Aip06g03330 Chr06 129955278 129961153 -
Bva Bva10g00355 Chr10 4136842 4141546 -
Bva Bva06g02413 Chr06 15478748 15483810 +
Car Car04g03171 Chr04 59999297 60006336 -
Cca Cca05g00539 Chr05 12158684 12165006 +
Dod Dod08g1665 Chr08 39593318 39600473 -
Lja Lja5g2833 Chr5 55829086 55834685 -
Mal Mal1g5510 Chr1 130126454 130132354 -
Mtr Mtr1g0206 Chr1 2355122 2361475 -
Ssu Ssu5g0587 Chr5 13236071 13241766 +
Sto Sto5g0833 Chr5 5612578 5617362 -
Tpr Tpr1g3385 Chr1 38217357 38223459 -
Tsu Tsu01g00702 Chr01 6162977 6168838 +
Vvi Vvi4g0503 Chr4 4633584 4634209 +
Adu Adu08g02507 Chr08 41027551 41029287 -
Aev Aev08g2625 Chr08 24689498 24697959 -
Ahy Ahy18g2653 Chr18 129407210 129408903 -
Aip Aip08g03047 Chr08 119912302 119918416 -
Arst Arst8g03457 Chr8 45400105 45401774 -
Bva Bva10g00356 Chr10 4144592 4145248 +
Dod Dod09g0929 Chr09 29133731 29135573 -
Gma Gma04g00633 Chr04 5801733 5803055 -
Lal Lal4g0223 Chr4 1403488 1405609 -
Lal Lal17g0239 Chr17 1479046 1480638 -
Lapu Lapu9g01874 Chr9 33550214 33552444 +
Lasa Lasa5g04087 Chr5 628536161 628536773 +
Lja Lja1g3864 Chr1 48745944 48747611 +
Mal Mal2g0861 Chr2 9980172 9980924 +
Mepo Mepo3g07451 Chr3 87882683 87884082 -
Mesa Mesa9g05060 Chr9 85134073 85134885 -
Mtr Mtr3g3932 Chr3 53078645 53080001 -
Phco Phco7g00777 Chr7 6035637 6036784 -
Pste Pste2g01792 Chr2 18329888 18332439 -
Pvu Pvu9g0973 Chr9 14680273 14681984 -
Spst Spst9g00807 Chr9 6989920 6992104 -
Sto Sto5g0834 Chr5 5621635 5622280 +
Tpr Tpr7g0615 Chr7 5318153 5319429 +
Trre Trre5g05244 Chr5 53555659 53556328 -
Vimu Vimu10g02929 Chr10 40339018 40341668 +
Vivi Vivi3g01315 Chr3 21483556 21484834 +
Pte Pte1g02362 Chr1 44404125 44408725 +