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
Vvi18g0606 . . . . . . Aed3g1753 . . Aev07g1995 Ahy17g3065 Ahy17g1693 Aip07g03337 Aip07g01718 . . . Amo17g1195 Apr9g1020 . . . . . . . Bva06g02617 . . Car02g01217 Cca05g01151 . . . Dod08g1174 Dod08g1174 . . . . . . Gma14g01828 Gma02g02055 . . . . . . . . Lal18g1191 . . . . . . . . . . . . . . . . . . . . . Mal8g2204 . . . . . . . Mtr5g2258 . . . . Phco2g00383 . . . . . Pste8g00643 . . . . . . . Pvu1g0329 . . . . . . Ssu6g2525 . Sto5g0608 Sto9g3117 Tpr4g2550 . . . Tsu05g02601 . . . . . . . . . . Vivi4g05433 Vra6g1036 .
Vvi18g0607 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0608 . . . . . . . . . . . . . Aip07g01711 . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma06g00821 . Gma02g02057 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0609 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0610 Acco10g2216 . Accr4g00560 . . . . Aed10g0104 . . . . . . Alju08g0584 . . . . . . . . . Bisa09g1440 . . . . . . Cca03g01341 Dere04g0795 . . . Enph1g1551 . Glsi08g1361 . . . . . . . . . Lal4g0167 . . Lal8g0702 . . Lan14g0857 . . Lan14g0857 . . Lapu9g01676 . . . Lele01g0472 Lele02g0457 Lele03g0481 Lele04g0476 . . . . . . . . Mepo3g07694 . . . . . . . Phac9g02404 . Phco7g01018 . . . . . Pste2g00147 . . . . . Pumo10g01023 . Pvu9g1501 . Rops10g01655 . Seca4g00608 . Spst9g01044 . . Ssu1g3208 . . . . Trre5g05537 . . . Vian4g01744 . . . Vimu10g02647 . Viun9g02712 . Vivi3g00347 . . Vra5g0966
Vvi18g0611 . . . . . . . . . . . . . . . . . . . Apr5g1040 . . . . . . . . . . . . . . . . . . . . Gma04g00830 . . . Gso4g0773 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g3121 . . . . . . . . . . . . . . . . . .
Vvi18g0612 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car05g03161 . . . . . . . . . . . . . . . . . . Lal4g0314 . . . . . Lan14g0710 . . . . . . . . . . . . . . . . . Lja1g3636 . . Mal2g0603 . . . . . . . Mtr3g4154 . . . . . . . Psa5g0443 . . . . . . . . . . . . . . . . . . . . . Tpr7g0342 . . . Tsu07g00375 . . . . . . . . . . . .
Vvi18g0613 . . . . . Adu07g01493 Aed3g1756 . . Aev07g1998 . Ahy17g1683 . Aip07g01707 . . . Amo17g1181 Apr9g1023 . . Arst7g02548 . . . . Bva06g02218 Bva10g00581 . Car02g01220 Cca05g01155 . . . . Dod08g1168 . . . . . . Gma14g01832 Gma02g02060 . . . . . . . Lal6g0436 . . . . . . . . . . . Lasa2g01208 . . . . . . . . . . Mal8g2199 . . Mepo7g01654 . Mesa17g02919 . . Mtr5g2259 . . Phac8g02406 . Phco3g01184 . . . . . Pste8g01758 . . . . . Pumo9g01463 . Pvu8g1909 . Rops9g01398 . . . Spst8g00011 Ssu6g2534 . . Sto9g3456 Tpr4g2552 . . Trre9g03537 Tsu05g02602 . . Vian7g02055 . Vifa1g01116 . Vimu1g01718 . Viun8g01654 . . Vra6g1034 .
Vvi18g0614 . . . . . . Aed3g1757 . . . . Ahy17g1682 . Aip07g01706 . . . Amo17g1180 Apr9g1024 . . . . . . . Bva06g02615 . . Car02g01222 Cca05g01156 . . . . Dod08g1167 . . . . . . Gma14g01833 Gma02g02061 . . . . . . . . Lal18g1193 . . . . . . . . . . . . . . . . . . . . . Mal8g2198 . . . . . . . Mtr5g2261 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu6g2535 . . Sto9g3122 Tpr4g2554 . . . Tsu05g02606 . . . . . . . . . . . Vra6g1033 .
Vvi18g0615 . . . . . . Aed3g1758 Aed10g0102 Aev08g1132 . Ahy17g3067 . Aip07g03340 . . . Amo17g2981 . Apr9g1025 Apr5g1042 . . . . . . Bva06g02614 . . Car02g01226 Cca05g01157 Cca03g01342 . . . . . . . . Gma04g00828 Gma06g00818 . Gma02g02062 Gso4g0772 Gso4g0772 . Gso4g0772 . . . . . . . . . . . . . . . . . . . . . . . . Lja1g3637 . Mal8g2197 . . . . . . . Mtr5g2262 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu6g2536 Ssu1g3209 Sto5g0610 Sto9g3123 Tpr4g2555 . . . Tsu05g02607 . . . . . . . . . . . Vra6g1028 Vra5g0967
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Bva Bva10g00581 Chr10 5224239 5228112 -
Bva Bva06g02218 Chr06 14536232 14540141 +
Sto Sto9g3456 Chr9 33971498 33975300 -
Pste Pste2g00147 Chr2 648781 652456 +
Vvi Vvi18g0606 Chr18 6351256 6376057 +
Aed Aed3g1753 Chr3 22130802 22131458 +
Aev Aev07g1995 Chr07 21111441 21123470 +
Ahy Ahy17g3065 Chr17 131936491 131967216 +
Ahy Ahy17g1693 Chr17 38848765 38857670 -
Aip Aip07g03337 Chr07 122724252 122750455 +
Aip Aip07g01718 Chr07 35812090 35820180 -
Amo Amo17g1195 Chr17 33063082 33072277 +
Apr Apr9g1020 Chr9 19481103 19497790 +
Bva Bva06g02617 Chr06 16529371 16539569 -
Car Car02g01217 Chr02 36811812 36832111 +
Cca Cca05g01151 Chr05 28893493 28917446 +
Dod Dod08g1174 Chr08 15197229 15224278 -
Dod Dod08g1174 Chr08 15197229 15224278 -
Gma Gma14g01828 Chr14 48803336 48827541 +
Gma Gma02g02055 Chr02 46214757 46237604 +
Lal Lal18g1191 Chr18 14786903 14799429 +
Mal Mal8g2204 Chr8 47061665 47087836 -
Mtr Mtr5g2258 Chr5 29611830 29640048 +
Phco Phco2g00383 Chr2 3301540 3306144 -
Pste Pste8g00643 Chr8 3307750 3314557 +
Pvu Pvu1g0329 Chr1 3131586 3133313 -
Ssu Ssu6g2525 Chr6 59473157 59509063 +
Sto Sto5g0608 Chr5 3993695 3996947 +
Sto Sto9g3117 Chr9 31845352 31847267 +
Tpr Tpr4g2550 Chr4 27798415 27817601 +
Tsu Tsu05g02601 Chr05 35676568 35701559 +
Vivi Vivi4g05433 Chr4 188270808 188275703 +
Vra Vra6g1036 Chr6 14716161 14733814 -
Vvi Vvi18g0607 Chr18 6382777 6387945 -
Vvi Vvi18g0608 Chr18 6388506 6390338 +
Aip Aip07g01711 Chr07 35279502 35280512 -
Gma Gma06g00821 Chr06 7559208 7560219 -
Gma Gma02g02057 Chr02 46263884 46266358 +
Vvi Vvi18g0609 Chr18 6394172 6394480 +
Vvi Vvi18g0610 Chr18 6398183 6402500 -
Acco Acco10g2216 Chr10 34166698 34170125 +
Accr Accr4g00560 Chr4 5503156 5508689 -
Aed Aed10g0104 Chr10 804776 807178 +
Alju Alju08g0584 Chr08 4289492 4293105 -
Bisa Bisa09g1440 Chr09 20847304 20851674 +
Cca Cca03g01341 Chr03 31399856 31406788 -
Dere Dere04g0795 Chr04 8092049 8095354 +
Enph Enph1g1551 Chr1 40781695 40785818 +
Glsi Glsi08g1361 Chr08 9916085 9920006 -
Lal Lal4g0167 Chr4 1048844 1052156 +
Lal Lal8g0702 Chr8 4987609 4989782 +
Lan Lan14g0857 Chr14 15251841 15254840 -
Lan Lan14g0857 Chr14 15251841 15254840 -
Lapu Lapu9g01676 Chr9 31497095 31502396 -
Lele Lele01g0472 Chr01 2777438 2780201 -
Lele Lele02g0457 Chr02 2740003 2742988 -
Lele Lele03g0481 Chr03 2780659 2783425 -
Lele Lele04g0476 Chr04 2860193 2861808 -
Mepo Mepo3g07694 Chr3 90291693 90296690 +
Phac Phac9g02404 Chr9 22872874 22878163 -
Phco Phco7g01018 Chr7 8338312 8343927 +
Pste Pste2g00147 Chr2 648781 652456 +
Pumo Pumo10g01023 Chr10 13288521 13290558 +
Pvu Pvu9g1501 Chr9 21259631 21265245 -
Rops Rops10g01655 Chr10 30451165 30451449 +
Seca Seca4g00608 Chr4 9987037 9992238 -
Spst Spst9g01044 Chr9 9333391 9338768 +
Ssu Ssu1g3208 Chr1 83639553 83640348 -
Trre Trre5g05537 Chr5 55834934 55840401 +
Vian Vian4g01744 Chr4 33586727 33593783 -
Vimu Vimu10g02647 Chr10 37835571 37837115 -
Viun Viun9g02712 Chr9 35938079 35942745 -
Vivi Vivi3g00347 Chr3 6172597 6176534 +
Vra Vra5g0966 Chr5 15979148 15984343 -
Vvi Vvi18g0611 Chr18 6406367 6409616 -
Apr Apr5g1040 Chr5 15012024 15016387 -
Gma Gma04g00830 Chr04 8109651 8111871 +
Gso Gso4g0773 Chr4 7911536 7916842 +
Sto Sto9g3121 Chr9 31864540 31867455 -
Vvi Vvi18g0612 Chr18 6411758 6415993 -
Car Car05g03161 Chr05 76531172 76536783 +
Lal Lal4g0314 Chr4 2061298 2066387 +
Lan Lan14g0710 Chr14 14081380 14088361 -
Lja Lja1g3636 Chr1 45154025 45159405 -
Mal Mal2g0603 Chr2 6960403 6966017 -
Mtr Mtr3g4154 Chr3 55438080 55442916 +
Psa Psa5g0443 Chr5 36153174 36156960 -
Tpr Tpr7g0342 Chr7 2743581 2748849 -
Tsu Tsu07g00375 Chr07 2810672 2815680 -
Vvi Vvi18g0613 Chr18 6430726 6437564 +
Adu Adu07g01493 Chr07 32231825 32236205 +
Aed Aed3g1756 Chr3 22158392 22164199 +
Aev Aev07g1998 Chr07 21150264 21160473 +
Ahy Ahy17g1683 Chr17 38200323 38206595 -
Aip Aip07g01707 Chr07 35209546 35217576 -
Amo Amo17g1181 Chr17 32680045 32686109 -
Apr Apr9g1023 Chr9 19550696 19557590 +
Arst Arst7g02548 Chr7 64008476 64014509 +
Bva Bva06g02218 Chr06 14536232 14540141 +
Bva Bva10g00581 Chr10 5224239 5228112 -
Car Car02g01220 Chr02 36934229 36940694 +
Cca Cca05g01155 Chr05 28952674 28959496 +
Dod Dod08g1168 Chr08 15110182 15111335 -
Gma Gma14g01832 Chr14 48861024 48868539 +
Gma Gma02g02060 Chr02 46275965 46282700 +
Lal Lal6g0436 Chr6 2735332 2740894 -
Lasa Lasa2g01208 Chr2 433212328 433218976 -
Mal Mal8g2199 Chr8 46893387 46901301 -
Mepo Mepo7g01654 Chr7 25930253 25939246 +
Mesa Mesa17g02919 Chr17 51970127 51978403 +
Mtr Mtr5g2259 Chr5 29665411 29674139 +
Phac Phac8g02406 Chr8 33515039 33522613 +
Phco Phco3g01184 Chr3 10334123 10341187 -
Pste Pste8g01758 Chr8 11827107 11834818 -
Pumo Pumo9g01463 Chr9 42154676 42162353 +
Pvu Pvu8g1909 Chr8 48587138 48594222 +
Rops Rops9g01398 Chr9 22868857 22878471 -
Spst Spst8g00011 Chr8 86606 93020 +
Ssu Ssu6g2534 Chr6 59632336 59645060 +
Sto Sto9g3456 Chr9 33971498 33975300 -
Tpr Tpr4g2552 Chr4 27846242 27853826 +
Trre Trre9g03537 Chr9 44130024 44136864 +
Tsu Tsu05g02602 Chr05 35716120 35723601 +
Vian Vian7g02055 Chr7 34605951 34614294 -
Vifa Vifa1g01116 Chr1 182491360 182497197 -
Vimu Vimu1g01718 Chr1 17765930 17774550 +
Viun Viun8g01654 Chr8 27529444 27537669 +
Vra Vra6g1034 Chr6 14580012 14590138 -
Vvi Vvi18g0614 Chr18 6439226 6441781 -
Aed Aed3g1757 Chr3 22170884 22174130 +
Ahy Ahy17g1682 Chr17 38194471 38197737 -
Aip Aip07g01706 Chr07 35197571 35208799 -
Amo Amo17g1180 Chr17 32673853 32677319 -
Apr Apr9g1024 Chr9 19559018 19562249 +
Bva Bva06g02615 Chr06 16512663 16515320 -
Car Car02g01222 Chr02 36967121 36970001 +
Cca Cca05g01156 Chr05 28961822 28965819 +
Dod Dod08g1167 Chr08 15104670 15107537 -
Gma Gma14g01833 Chr14 48872003 48875248 +
Gma Gma02g02061 Chr02 46286251 46289291 +
Lal Lal18g1193 Chr18 14808630 14811608 +
Mal Mal8g2198 Chr8 46871754 46874900 -
Mtr Mtr5g2261 Chr5 29696359 29699799 +
Ssu Ssu6g2535 Chr6 59648526 59651233 +
Sto Sto9g3122 Chr9 31869671 31872223 +
Tpr Tpr4g2554 Chr4 27867190 27871213 +
Tsu Tsu05g02606 Chr05 35795872 35799456 +
Vra Vra6g1033 Chr6 14562245 14565301 -
Vvi Vvi18g0615 Chr18 6443344 6452311 -
Aed Aed3g1758 Chr3 22175210 22181099 +
Aed Aed10g0102 Chr10 795660 801081 +
Aev Aev08g1132 Chr08 6969632 6979919 -
Ahy Ahy17g3067 Chr17 131990917 131996357 -
Aip Aip07g03340 Chr07 122778633 122782545 -
Amo Amo17g2981 Chr17 132332230 132338420 +
Apr Apr9g1025 Chr9 19562727 19568839 -
Apr Apr5g1042 Chr5 15023146 15029550 +
Bva Bva06g02614 Chr06 16506663 16512434 +
Car Car02g01226 Chr02 37089741 37096981 -
Cca Cca05g01157 Chr05 28966474 28973208 -
Cca Cca03g01342 Chr03 31413759 31419983 -
Gma Gma04g00828 Chr04 8081755 8087528 +
Gma Gma06g00818 Chr06 7537234 7542366 +
Gma Gma02g02062 Chr02 46291277 46297780 -
Gso Gso4g0772 Chr4 7899512 7905461 +
Gso Gso4g0772 Chr4 7899512 7905461 +
Gso Gso4g0772 Chr4 7899512 7905461 +
Lja Lja1g3637 Chr1 45175358 45180252 -
Mal Mal8g2197 Chr8 46862502 46870967 +
Mtr Mtr5g2262 Chr5 29699873 29710087 -
Ssu Ssu6g2536 Chr6 59652408 59664525 -
Ssu Ssu1g3209 Chr1 83664167 83669620 -
Sto Sto5g0610 Chr5 4011547 4020604 -
Sto Sto9g3123 Chr9 31873064 31878048 -
Tpr Tpr4g2555 Chr4 27878711 27887532 -
Tsu Tsu05g02607 Chr05 35800093 35806864 -
Vra Vra6g1028 Chr6 14508851 14518308 +
Vra Vra5g0967 Chr5 15985394 15991379 -
Adu Adu07g01493 Chr07 32231825 32236205 +