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
Vvi16g0999 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1000 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1001 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1002 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1003 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1004 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1005 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1006 . . . . Adu05g03439 . . . Aev05g2863 . Ahy15g3601 . Aip05g03918 . . . . . . Apr6g0638 Arst5g04414 . . . . . . Bva04g01192 . . . Cca08g00734 . . Dod02g2977 . . . . . Gma09g01234 . . . Gso9g1064 . . . . . Lal9g0831 . . . . . . . . . . . . . . . . . . . . . Lja2g2692 . . Mal8g2914 . . . . . . . Mtr6g1317 . . Phco5g00791 . . . . . . . Pte16g00325 . . . Pumo6g02517 . Pvu4g1129 . Rops5g01060 . Seca10g03824 . Spst4g03266 . . . . . . Tpr2g4293 . . . Tsu06g02990 Vian8g00997 . Vifa1g04397 . Vimu8g02239 . Viun4g02039 . Vivi2g05376 . . .
Vvi16g1007 . . . . . . Aed1g2310 . . . . . . . . . . . . . . . . . . . Bva03g01306 . . . Cca02g02210 . . . . . . . . . Gma10g02189 . . . . . . . . . . . . Lal13g0058 . . . . . . . . . Lasa6g04031 . . . . . . . . . Lja5g0672 Mal1g2106 . . Mepo4g04198 . Mesa1g04583 . . Mtr1g3698 . . Phac7g01150 . Phco6g02433 . . Psa6g4468 . . . . . Pte16g00326 . . . . Pvu7g0769 . Rops6g02677 . Seca8g07338 . Spst10g00922 Ssu7g0831 . . . Tpr1g0806 . . Trre1g05336 Tsu01g04368 . . Vian3g00671 . Vifa3g02862 . . . Viun7g03188 . Vivi1g04455 Vra8g2194 .
Vvi16g1008 Acco01g0215 . Accr1g00020 . Adu05g03440 . . Aed7g0652 Aev05g2862 . Ahy15g3602 . Aip05g03919 . Alju02g3687 . . . . Apr6g0637 Arst5g04416 . Bach1g01109 . Bisa01g0815 . Bva03g01305 Bva04g01193 . . . Cca08g00735 Dere06g1280 . Dod02g2976 . Enph12g0858 . Glsi01g1458 . Gma16g01532 . . . Gso16g1455 . . . . . Lal9g0833 Lal24g0059 . . . . . . . . . . . . Lele45g0135 Lele46g0160 . Lele48g1297 . . . . Lja2g2693 . . Mal8g2915 . . . . Mibi01g3439 . . Mtr6g1318 . . Phco5g00793 . . . . . . . . Pte9g00386 . . Pumo6g02515 . Pvu4g1128 . Rops5g01059 . Seca10g03823 . Spst4g03269 . . . Sto10g2328 . . Tpr2g4294 Trre11g01243 . . . Vian8g00996 . Vifa1g04395 . Vimu8g02240 . Viun4g02036 . Vivi2g05377 . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi16g0999 Chr16 18221979 18224792 +
Vvi Vvi16g1000 Chr16 18234631 18235601 -
Vvi Vvi16g1001 Chr16 18247257 18248671 +
Vvi Vvi16g1002 Chr16 18253419 18256261 +
Vvi Vvi16g1003 Chr16 18258722 18259303 +
Vvi Vvi16g1004 Chr16 18269683 18270249 +
Vvi Vvi16g1005 Chr16 18275489 18276902 -
Vvi Vvi16g1006 Chr16 18302977 18312966 +
Adu Adu05g03439 Chr05 106808954 106814799 +
Aev Aev05g2863 Chr05 29568461 29573599 -
Ahy Ahy15g3601 Chr15 158733059 158739976 +
Aip Aip05g03918 Chr05 147345928 147351963 +
Apr Apr6g0638 Chr6 9365822 9372377 -
Arst Arst5g04414 Chr5 105484592 105490508 +
Bva Bva04g01192 Chr04 8131114 8137661 +
Cca Cca08g00734 Chr08 13855653 13870592 +
Dod Dod02g2977 Chr02 63352072 63354863 -
Gma Gma09g01234 Chr09 33931256 33941861 -
Gso Gso9g1064 Chr9 30774899 30782922 -
Lal Lal9g0831 Chr9 6046667 6054077 +
Lja Lja2g2692 Chr2 38452694 38465266 +
Mal Mal8g2914 Chr8 77929004 77937777 +
Mtr Mtr6g1317 Chr6 19765493 19771227 +
Phco Phco5g00791 Chr5 9337214 9344743 +
Pte Pte16g00325 Chr16 4312582 4318376 +
Pumo Pumo6g02517 Chr6 58773216 58777377 -
Pvu Pvu4g1129 Chr4 34715860 34723773 -
Rops Rops5g01060 Chr5 21627002 21635599 -
Seca Seca10g03824 Chr10 79661952 79669208 -
Spst Spst4g03266 Chr4 72344765 72346101 +
Tpr Tpr2g4293 Chr2 46322522 46332933 +
Tsu Tsu06g02990 Chr06 39262226 39274360 +
Vian Vian8g00997 Chr8 26522652 26531708 -
Vifa Vifa1g04397 Chr1 683783466 683790088 -
Vimu Vimu8g02239 Chr8 29140048 29145558 +
Viun Viun4g02039 Chr4 36159147 36166233 -
Vivi Vivi2g05376 Chr2 178640599 178650083 +
Vvi Vvi16g1007 Chr16 18315897 18316919 +
Aed Aed1g2310 Chr1 19157303 19158387 +
Bva Bva03g01306 Chr03 12718664 12719922 -
Cca Cca02g02210 Chr02 42623142 42624496 -
Gma Gma10g02189 Chr10 49478959 49479514 -
Lal Lal13g0058 Chr13 362586 363614 +
Lasa Lasa6g04031 Chr6 612925272 612926312 -
Lja Lja5g0672 Chr5 6047625 6049134 +
Mal Mal1g2106 Chr1 27580420 27581643 +
Mepo Mepo4g04198 Chr4 51864552 51865978 -
Mesa Mesa1g04583 Chr1 71767334 71768344 -
Mtr Mtr1g3698 Chr1 48642116 48643587 -
Phac Phac7g01150 Chr7 7227043 7228656 +
Phco Phco6g02433 Chr6 45766241 45767254 -
Psa Psa6g4468 Chr6 391562275 391564459 -
Pte Pte16g00326 Chr16 4319486 4320631 +
Pvu Pvu7g0769 Chr7 6887423 6888992 +
Rops Rops6g02677 Chr6 48173396 48174781 -
Seca Seca8g07338 Chr8 170093454 170094479 -
Spst Spst10g00922 Chr10 9994518 9995531 -
Ssu Ssu7g0831 Chr7 16655788 16656801 +
Tpr Tpr1g0806 Chr1 6741577 6742915 +
Trre Trre1g05336 Chr1 59213899 59214882 -
Tsu Tsu01g04368 Chr01 51546729 51548132 -
Vian Vian3g00671 Chr3 6792952 6793965 +
Vifa Vifa3g02862 Chr3 804558170 804559210 -
Viun Viun7g03188 Chr7 34425292 34427073 -
Vivi Vivi1g04455 Chr1 94922038 94923433 +
Vra Vra8g2194 Chr8 40314505 40315941 -
Vvi Vvi16g1008 Chr16 18318188 18324425 -
Acco Acco01g0215 Chr01 2460313 2465938 +
Accr Accr1g00020 Chr1 832398 847126 +
Adu Adu05g03440 Chr05 106824856 106829381 -
Aed Aed7g0652 Chr7 4810154 4816730 -
Aev Aev05g2862 Chr05 29561711 29566293 +
Ahy Ahy15g3602 Chr15 158742056 158746505 -
Aip Aip05g03919 Chr05 147353721 147358157 -
Alju Alju02g3687 Chr02 55593265 55598272 -
Apr Apr6g0637 Chr6 9355815 9362787 +
Arst Arst5g04416 Chr5 105500139 105505138 -
Bach Bach1g01109 Chr1 24142452 24148194 +
Bisa Bisa01g0815 Chr01 13101334 13118454 -
Bva Bva03g01305 Chr03 12712812 12718241 +
Bva Bva04g01193 Chr04 8139623 8146284 -
Cca Cca08g00735 Chr08 13877373 13884685 -
Dere Dere06g1280 Chr06 25162802 25171205 +
Dod Dod02g2976 Chr02 63327406 63334375 +
Enph Enph12g0858 Chr12 15289434 15296662 +
Glsi Glsi01g1458 Chr01 74603581 74610920 +
Gma Gma16g01532 Chr16 35655888 35662061 +
Gso Gso16g1455 Chr16 34788760 34795939 +
Lal Lal9g0833 Chr9 6056070 6063285 -
Lal Lal24g0059 Chr24 364826 370159 -
Lele Lele45g0135 Chr45 1226170 1231489 +
Lele Lele46g0160 Chr46 971338 980308 +
Lele Lele48g1297 Chr48 17232428 17238257 -
Lja Lja2g2693 Chr2 38467265 38474414 -
Mal Mal8g2915 Chr8 77940437 77947982 -
Mibi Mibi01g3439 Chr01 60077350 60082372 -
Mtr Mtr6g1318 Chr6 19773363 19781174 -
Phco Phco5g00793 Chr5 9347075 9353306 -
Pte Pte9g00386 Chr9 4485777 4491334 -
Pumo Pumo6g02515 Chr6 58764739 58769277 +
Pvu Pvu4g1128 Chr4 34707787 34713610 +
Rops Rops5g01059 Chr5 21612904 21620141 +
Seca Seca10g03823 Chr10 79630963 79639798 +
Spst Spst4g03269 Chr4 72372854 72375199 -
Sto Sto10g2328 Chr10 33549151 33555754 +
Tpr Tpr2g4294 Chr2 46336011 46342516 -
Trre Trre11g01243 Chr11 12066723 12075529 -
Vian Vian8g00996 Chr8 26514517 26520539 +
Vifa Vifa1g04395 Chr1 683682375 683694806 +
Vimu Vimu8g02240 Chr8 29148798 29154884 -
Viun Viun4g02036 Chr4 36146693 36153407 +
Vivi Vivi2g05377 Chr2 178664313 178672137 -