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
Vvi4g1354 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal15g1537 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1355 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal5g3256 . . . . . . . Mtr8g2339 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr4g4349 . . . Tsu04g03584 . . . . . . . . . . . .
Vvi4g1356 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal5g3255 . . . . . . . Mtr8g2338 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr4g4350 . . . . . . . . . . . . . . . .
Vvi4g1357 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1358 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal5g3254 . . . . . . . Mtr8g2335 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr4g4360 . . . . . . . . . . . . . . . .
Vvi4g1359 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr8g2334 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr4g4368 . . . . . . . . . . . . . . . .
Vvi4g1360 . . . . . . . Aed7g1264 . . . . . . . . . . . . . . . . . . . . . . . Cca11g00914 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu5g0779 . Sto11g1423 . . . . . . . . . . . . . . . . . .
Vvi4g1361 . Acco06g2504 . Accr5g00628 . Adu03g04230 . . . . . . . . . Alju03g0846 . . . . . Arst3g05597 . . . Bisa07g0515 Bva05g01599 . . . . . . Dere02g2423 . . . Enph4g0482 . Glsi11g2737 Gma11g00764 . . . Gso11g0712 . . . . Lal15g1538 . . . . . . . . . . . . . Lasa7g03624 . . . . Lele13g0509 Lele14g0434 Lele15g1961 Lele16g1986 . . . Mal5g3253 . Mepo2g03550 . Mesa13g01609 . Mibi06g0630 . Mtr8g2333 . Phac2g03111 . Phco4g02350 . Prci3g0599 . . . . . . . . . Pumo6g01574 . Pvu2g2108 . Rops2g01721 . Seca12g05254 . Spst3g00320 . . Sto6g4001 . . Tpr4g4370 . Trre7g04094 . Tsu04g03587 . Vian1g02948 . Vifa6g02098 . Vimu11g01348 . Viun3g01805 . Vivi5g04922 . .
Vvi4g1362 . . . . . . . . . . . . . . . . . . Apr3g2044 . . . . . . . . . . . . . . . . . . . . . . . Gma02g00386 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g1363 Acco12g0284 . Accr10g01719 . Adu01g00837 . . Aed7g1265 . . . . . . Alju12g1801 . . . Apr3g0405 . Arst1g01131 . Bach10g00702 . . . Bva08g00934 . . . . Cca11g00916 Dere13g0800 . . . . . Glsi09g0703 . . . . . . . . . . . . . . . . . . . . . . . Lasa4g02007 . Lele53g1254 . Lele55g0232 . . . . . . . . . Mepo1g02209 . . . Mibi10g1747 . . . . . Phco8g00341 . Prci5g2180 . . . Pste7g01882 . . . . . . . Pvu3g2765 . . . . . Spst3g03737 . . Ssu5g0781 . Sto11g1422 . . . . . . . . . . Vimu11g00831 . . . Vivi1g03209 . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi4g1354 Chr4 20426687 20444957 +
Lal Lal15g1537 Chr15 17455564 17461298 -
Vvi Vvi4g1355 Chr4 20452250 20454129 +
Mal Mal5g3256 Chr5 95621943 95626933 -
Mtr Mtr8g2339 Chr8 33877597 33889238 -
Tpr Tpr4g4349 Chr4 50735921 50745378 +
Tsu Tsu04g03584 Chr04 44922313 44938838 +
Vvi Vvi4g1356 Chr4 20460180 20462036 +
Mal Mal5g3255 Chr5 95593514 95597877 -
Mtr Mtr8g2338 Chr8 33869594 33873396 -
Tpr Tpr4g4350 Chr4 50764208 50771556 +
Vvi Vvi4g1357 Chr4 20463107 20463646 +
Vvi Vvi4g1358 Chr4 20471195 20473374 +
Mal Mal5g3254 Chr5 95572721 95577664 -
Mtr Mtr8g2335 Chr8 33847425 33848309 -
Tpr Tpr4g4360 Chr4 50845243 50856720 +
Vvi Vvi4g1359 Chr4 20474492 20475588 +
Mtr Mtr8g2334 Chr8 33834996 33852487 -
Tpr Tpr4g4368 Chr4 50930979 50937874 +
Vvi Vvi4g1360 Chr4 20475612 20476579 +
Aed Aed7g1264 Chr7 10286242 10288718 +
Cca Cca11g00914 Chr11 18849586 18858249 +
Ssu Ssu5g0779 Chr5 19845164 19845514 +
Sto Sto11g1423 Chr11 13586304 13593447 -
Vvi Vvi4g1361 Chr4 20478861 20481237 -
Acco Acco06g2504 Chr06 22320606 22321253 -
Accr Accr5g00628 Chr5 28895616 28896266 +
Adu Adu03g04230 Chr03 131303191 131303932 -
Alju Alju03g0846 Chr03 33913596 33914243 +
Arst Arst3g05597 Chr3 130067334 130068097 -
Bisa Bisa07g0515 Chr07 12906171 12906845 +
Bva Bva05g01599 Chr05 13017772 13024513 +
Dere Dere02g2423 Chr02 25763895 25764557 -
Enph Enph4g0482 Chr4 18154859 18155848 +
Glsi Glsi11g2737 Chr11 20458418 20459098 -
Gma Gma11g00764 Chr11 6383539 6393564 +
Gso Gso11g0712 Chr11 6325643 6335816 +
Lal Lal15g1538 Chr15 17455564 17459055 +
Lasa Lasa7g03624 Chr7 605859794 605860486 +
Lele Lele13g0509 Chr13 17280521 17281180 -
Lele Lele14g0434 Chr14 16025456 16026136 +
Lele Lele15g1961 Chr15 12332745 12333395 +
Lele Lele16g1986 Chr16 12144570 12145250 -
Mal Mal5g3253 Chr5 95561566 95571254 +
Mepo Mepo2g03550 Chr2 44984491 44985746 -
Mesa Mesa13g01609 Chr13 19266492 19267199 +
Mibi Mibi06g0630 Chr06 21812823 21813485 +
Mtr Mtr8g2333 Chr8 33801682 33813657 +
Phac Phac2g03111 Chr2 32766827 32767516 -
Phco Phco4g02350 Chr4 44645175 44645867 -
Prci Prci3g0599 Chr3 7420177 7421142 +
Pumo Pumo6g01574 Chr6 22922598 22923263 -
Pvu Pvu2g2108 Chr2 36507753 36508880 -
Rops Rops2g01721 Chr2 26443924 26444619 +
Seca Seca12g05254 Chr12 141350104 141350763 -
Spst Spst3g00320 Chr3 5907640 5908335 -
Sto Sto6g4001 Chr6 43870603 43873758 +
Tpr Tpr4g4370 Chr4 50959086 50963805 -
Trre Trre7g04094 Chr7 49164513 49165217 -
Tsu Tsu04g03587 Chr04 44951403 44957294 -
Vian Vian1g02948 Chr1 48308243 48308935 -
Vifa Vifa6g02098 Chr6 759808056 759808751 +
Vimu Vimu11g01348 Chr11 14939530 14940093 +
Viun Viun3g01805 Chr3 13307822 13308505 +
Vivi Vivi5g04922 Chr5 149430578 149431661 +
Vvi Vvi4g1362 Chr4 20496420 20500460 +
Apr Apr3g2044 Chr3 36437042 36438860 +
Gma Gma02g00386 Chr02 4024526 4032974 -
Vvi Vvi4g1363 Chr4 20501808 20503627 +
Acco Acco12g0284 Chr12 2481216 2481920 +
Accr Accr10g01719 Chr10 41304796 41308025 -
Adu Adu01g00837 Chr01 11196704 11212793 +
Aed Aed7g1265 Chr7 10290018 10294003 +
Alju Alju12g1801 Chr12 39097174 39101191 -
Apr Apr3g0405 Chr3 7888017 7892002 +
Arst Arst1g01131 Chr1 11203302 11205515 +
Bach Bach10g00702 Chr10 4948632 4950745 -
Bva Bva08g00934 Chr08 4747710 4749716 +
Cca Cca11g00916 Chr11 18982561 18992415 +
Dere Dere13g0800 Chr13 9913771 9917079 +
Glsi Glsi09g0703 Chr09 4846265 4847854 +
Lasa Lasa4g02007 Chr4 409461402 409465466 +
Lele Lele53g1254 Chr53 21124649 21126191 -
Lele Lele55g0232 Chr55 1434136 1435449 +
Mepo Mepo1g02209 Chr1 22733965 22739255 +
Mibi Mibi10g1747 Chr10 38743549 38743878 -
Phco Phco8g00341 Chr8 3154576 3157395 -
Prci Prci5g2180 Chr5 39093073 39094637 -
Pste Pste7g01882 Chr7 17230089 17234570 +
Pvu Pvu3g2765 Chr3 49506395 49509747 +
Spst Spst3g03737 Chr3 87391021 87393664 -
Ssu Ssu5g0781 Chr5 19916757 19918542 +
Sto Sto11g1422 Chr11 13581777 13584454 -
Vimu Vimu11g00831 Chr11 8615729 8618370 +
Vivi Vivi1g03209 Chr1 69910434 69912610 +
Bva Bva05g01599 Chr05 13017772 13024513 +
Acco Acco06g2504 Chr06 22320606 22321253 -
Accr Accr5g00628 Chr5 28895616 28896266 +
Adu Adu03g04230 Chr03 131303191 131303932 -
Alju Alju03g0846 Chr03 33913596 33914243 +
Arst Arst3g05597 Chr3 130067334 130068097 -
Bisa Bisa07g0515 Chr07 12906171 12906845 +
Dere Dere02g2423 Chr02 25763895 25764557 -
Enph Enph4g0482 Chr4 18154859 18155848 +
Glsi Glsi11g2737 Chr11 20458418 20459098 -
Lasa Lasa7g03624 Chr7 605859794 605860486 +
Lele Lele13g0509 Chr13 17280521 17281180 -
Lele Lele14g0434 Chr14 16025456 16026136 +
Lele Lele15g1961 Chr15 12332745 12333395 +
Lele Lele16g1986 Chr16 12144570 12145250 -
Mepo Mepo2g03550 Chr2 44984491 44985746 -
Mesa Mesa13g01609 Chr13 19266492 19267199 +
Mibi Mibi06g0630 Chr06 21812823 21813485 +
Phac Phac2g03111 Chr2 32766827 32767516 -
Phco Phco4g02350 Chr4 44645175 44645867 -
Prci Prci3g0599 Chr3 7420177 7421142 +
Pumo Pumo6g01574 Chr6 22922598 22923263 -
Pvu Pvu2g2108 Chr2 36507753 36508880 -
Rops Rops2g01721 Chr2 26443924 26444619 +
Seca Seca12g05254 Chr12 141350104 141350763 -
Spst Spst3g00320 Chr3 5907640 5908335 -
Trre Trre7g04094 Chr7 49164513 49165217 -
Vian Vian1g02948 Chr1 48308243 48308935 -
Vifa Vifa6g02098 Chr6 759808056 759808751 +
Vimu Vimu11g01348 Chr11 14939530 14940093 +
Viun Viun3g01805 Chr3 13307822 13308505 +
Vivi Vivi5g04922 Chr5 149430578 149431661 +