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
Vvi16g1279 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1280 . . . . Adu10g01497 . . . . . . . . . Alju08g0200 . . . Apr1g0617 . Arst10g01930 . Bach12g01022 . Bisa09g0869 . Bva12g01894 Bva06g03025 . . . . Dere04g1275 . . . Enph1g1850 . . . . . . . . . . . . Lal4g0529 Lal21g0589 . . . . . . . . . Lapu9g01296 . Lasa5g03107 . Lele01g0158 . . Lele04g0162 . . . . Lja1g4746 . . . Mepo3g06613 . Mesa9g04158 . Mibi05g0167 . . . Phac9g01325 . Phco7g01486 . Prci15g0244 . Psa5g1718 . Pste2g03505 . . . . . . . Pvu9g0488 . . . . . Spst9g01528 . . . Sto9g2696 Sto5g1341 . . Trre5g03981 . . . . . . . . . . . Vivi3g02734 . . .
Vvi16g1281 . . . . . . . . . . . . . . . . . . Apr1g0618 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g1340 . . . . . . . . . . . . . . . . . .
Vvi16g1282 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1283 . . . . . . . . . . . . . . . . . . Apr1g0619 . . . . . . . Bva12g01897 Bva06g03024 . . . . . . . . . . . . . . . . . . . . Lal17g0602 Lal4g0527 Lal21g0588 . . . Lan15g0615 Lan15g0615 Lan15g0615 . . . . . . . . . . . . . . . Lja1g4748 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g2697 Sto5g1339 . . . . . . . . . . . . . . . . . .
Vvi16g1284 . . . . . . . . . . . . . . . . . . Apr1g0620 . . . . . . . Bva12g01898 Bva06g03023 . . . . . . . . . . . . . . . . . . . . Lal17g0601 Lal4g0526 . . . . Lan15g0644 Lan15g0644 . . . . . . . . . . . . . . . . Lja1g4749 . . . . . . . . . . . . . . . . . Psa5g1721 . . . . . . . . . . . . . . . . . . . Sto9g2698 Sto5g1338 . . . . . . . . . . . . . . . . . .
Vvi16g1285 . . . . . . . . . . . . . . . . . . Apr1g0621 . . . . . . . Bva12g01899 Bva06g03022 . . . . . . . . . . . . . . . . . . . . Lal17g0600 Lal4g0525 Lal21g0587 . . . Lan15g0645 Lan15g0645 Lan15g0645 . . . . . . . . . . . . . . . Lja1g4750 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g2699 . . . . . . . . . . . . . . . . . . .
Vvi16g1286 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1287 . . . . . . . . . . . . . . . . . . Apr1g0623 . . . . . . . Bva12g01901 Bva06g03020 . . . . . . . . . . . . . . . . . . . . . Lal4g0524 Lal21g0585 . . . . . . . . . . . . . . . . . . . . . Lja1g4754 . . . . . . . . . . . . . . . . . Psa5g1726 . . . . . . . . . . . . . . . . . . . Sto9g2704 Sto5g1335 . . . . . . . . . . . . . . . . . .
Vvi16g1288 . . . . . . . . . . . . . . . . . . Apr1g0624 . . . . . . . Bva12g01902 . . . . . . . . . . . . . . . . . . . . . Lal17g0598 . . . . . Lan15g0647 . . . . . . . . . . . . . . . . . Lja1g4755 . . . . . . . . . . . . . . . . . Psa5g1727 . . . . . . . . . . . . . . . . . . . . Sto5g1334 . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi16g1279 Chr16 21357596 21361368 +
Vvi Vvi16g1280 Chr16 21361857 21365048 -
Adu Adu10g01497 Chr10 64411174 64413002 +
Alju Alju08g0200 Chr08 1493716 1498965 -
Apr Apr1g0617 Chr1 7447183 7450124 -
Arst Arst10g01930 Chr10 63595280 63597044 +
Bach Bach12g01022 Chr12 7214967 7216992 +
Bisa Bisa09g0869 Chr09 12548904 12550932 -
Bva Bva12g01894 Chr12 15210283 15212612 -
Bva Bva06g03025 Chr06 18788220 18790220 +
Dere Dere04g1275 Chr04 14483818 14486612 +
Enph Enph1g1850 Chr1 43428892 43431854 +
Lal Lal4g0529 Chr4 3838444 3840948 +
Lal Lal21g0589 Chr21 4413312 4416321 +
Lapu Lapu9g01296 Chr9 27039913 27042306 -
Lasa Lasa5g03107 Chr5 535083172 535086282 +
Lele Lele01g0158 Chr01 909964 913230 -
Lele Lele04g0162 Chr04 905589 909597 -
Lja Lja1g4746 Chr1 64032717 64038802 -
Mepo Mepo3g06613 Chr3 80062547 80068541 +
Mesa Mesa9g04158 Chr9 74259266 74264876 +
Mibi Mibi05g0167 Chr05 1727510 1730628 -
Phac Phac9g01325 Chr9 10450391 10453448 -
Phco Phco7g01486 Chr7 13956392 13958853 +
Prci Prci15g0244 Chr15 1615840 1619319 -
Psa Psa5g1718 Chr5 133391654 133397250 -
Pste Pste2g03505 Chr2 36314770 36317889 +
Pvu Pvu9g0488 Chr9 8970681 8973861 -
Spst Spst9g01528 Chr9 15462881 15465571 +
Sto Sto9g2696 Chr9 28977756 28979248 -
Sto Sto5g1341 Chr5 9171557 9174380 +
Trre Trre5g03981 Chr5 41010389 41015626 +
Vivi Vivi3g02734 Chr3 45886613 45892509 -
Vvi Vvi16g1281 Chr16 21365418 21367855 +
Apr Apr1g0618 Chr1 7460949 7463412 +
Sto Sto5g1340 Chr5 9168799 9171125 -
Vvi Vvi16g1282 Chr16 21369586 21369672 -
Vvi Vvi16g1283 Chr16 21369890 21376087 -
Apr Apr1g0619 Chr1 7466211 7473875 -
Bva Bva12g01897 Chr12 15216231 15223509 -
Bva Bva06g03024 Chr06 18780522 18787628 +
Lal Lal17g0602 Chr17 4310760 4317582 +
Lal Lal4g0527 Chr4 3827394 3834604 +
Lal Lal21g0588 Chr21 4403515 4412353 +
Lan Lan15g0615 Chr15 13813058 13819725 -
Lan Lan15g0615 Chr15 13813058 13819725 -
Lan Lan15g0615 Chr15 13813058 13819725 -
Lja Lja1g4748 Chr1 64048060 64056297 -
Sto Sto9g2697 Chr9 28979983 28986478 -
Sto Sto5g1339 Chr5 9160682 9166815 +
Vvi Vvi16g1284 Chr16 21385096 21390551 +
Apr Apr1g0620 Chr1 7481199 7489479 +
Bva Bva12g01898 Chr12 15226682 15232380 +
Bva Bva06g03023 Chr06 18771766 18777699 -
Lal Lal17g0601 Chr17 4298309 4305286 -
Lal Lal4g0526 Chr4 3811992 3819109 -
Lan Lan15g0644 Chr15 14890642 14897675 +
Lan Lan15g0644 Chr15 14890642 14897675 +
Lja Lja1g4749 Chr1 64073760 64081976 +
Psa Psa5g1721 Chr5 133724884 133731935 +
Sto Sto9g2698 Chr9 28992402 28996518 +
Sto Sto5g1338 Chr5 9145316 9152818 -
Vvi Vvi16g1285 Chr16 21395267 21395632 -
Apr Apr1g0621 Chr1 7503689 7504301 -
Bva Bva12g01899 Chr12 15234238 15235152 -
Bva Bva06g03022 Chr06 18769810 18770569 +
Lal Lal17g0600 Chr17 4296361 4296732 +
Lal Lal4g0525 Chr4 3807066 3807455 +
Lal Lal21g0587 Chr21 4396324 4396704 +
Lan Lan15g0645 Chr15 14914758 14915159 -
Lan Lan15g0645 Chr15 14914758 14915159 -
Lan Lan15g0645 Chr15 14914758 14915159 -
Lja Lja1g4750 Chr1 64085032 64086078 -
Sto Sto9g2699 Chr9 28997891 28998637 -
Vvi Vvi16g1286 Chr16 21420087 21423229 +
Vvi Vvi16g1287 Chr16 21439666 21440769 +
Apr Apr1g0623 Chr1 7536901 7538488 +
Bva Bva12g01901 Chr12 15245896 15247294 +
Bva Bva06g03020 Chr06 18758474 18759707 -
Lal Lal4g0524 Chr4 3794807 3796279 -
Lal Lal21g0585 Chr21 4362503 4364931 -
Lja Lja1g4754 Chr1 64216215 64218057 +
Psa Psa5g1726 Chr5 134248132 134250091 +
Sto Sto9g2704 Chr9 29017053 29017801 +
Sto Sto5g1335 Chr5 9116284 9117247 -
Vvi Vvi16g1288 Chr16 21441875 21446927 +
Apr Apr1g0624 Chr1 7539836 7544723 +
Bva Bva12g01902 Chr12 15247860 15250716 +
Lal Lal17g0598 Chr17 4274635 4278699 -
Lan Lan15g0647 Chr15 15004219 15008285 +
Lja Lja1g4755 Chr1 64233571 64237402 +
Psa Psa5g1727 Chr5 134266583 134270431 +
Sto Sto5g1334 Chr5 9109435 9114527 -