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
Vvi1g0471 . . Accr9g01979 . . . . . . . . . . . Alju09g0263 . . . . Apr3g1617 . . . . Bisa11g0538 . Bva01g01606 Bva11g00640 Car06g01766 . . . Dere09g2155 . . . Enph13g0608 . Glsi05g0274 . . . . . . . . . . . . . Lal16g0757 Lal15g0723 . . . . . . . . Lasa7g02981 . Lele49g1210 Lele50g1631 Lele51g1230 Lele52g1587 . . . . . . . . Mepo2g03063 . . . Mibi12g0213 . . . Phac2g01468 . Phco4g01792 . Prci10g2789 . . Psa7g2951 Pste3g04135 . Pte14g00420 . . . . . Pvu2g0958 . . . . . Spst3g02242 . . . Sto11g0588 Sto6g2657 . . Trre7g01895 . . . . . . . Vimu11g02588 . . . Vivi5g03848 . . .
Vvi1g0472 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0473 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0474 Acco11g0209 . Accr9g01983 . . . . . . . . . . . Alju09g0256 . . . . Apr3g1610 . . . . Bisa11g0533 . Bva01g01603 Bva11g00637 . . . . Dere09g2159 . . . Enph13g0611 . Glsi05g0270 . . . . . . . . . . . . . Lal16g0760 . . . . . . . . . . . Lele49g1207 Lele50g1634 Lele51g1227 Lele52g1589 . . . . . . . . . . . . Mibi12g0209 . . . . . Phco4g01799 . Prci10g2800 . . . Pste3g04129 . . . . . . . Pvu2g0963 . . . . . Spst3g02248 . . . Sto11g0586 Sto6g2651 . . . . . . . . . . Vimu11g02594 . . . . . . .
Vvi1g0475 Acco11g0206 . Accr9g01985 . . . . . . . . . . . Alju09g0253 . . . Apr7g1325 Apr3g1607 . . . . Bisa11g0528 . Bva01g01602 Bva11g00635 Car06g01771 . . . Dere09g2163 . . . Enph13g0613 . Glsi05g0266 . . . . . . . . . . . . . Lal16g0763 Lal15g0725 . . . . . . . . Lasa7g02968 . Lele49g1204 Lele50g1637 Lele51g1225 Lele52g1591 . . . . Lja2g3225 . Mal1g5030 . Mepo2g03055 . . . Mibi12g0207 . Mtr1g0948 . . . Phco4g01802 . Prci10g2804 . . . Pste3g04126 . . Pte3g00350 . . . . Pvu2g0968 . . . . . Spst3g02250 . . . Sto11g0582 Sto6g2648 Tpr1g3017 . Trre7g01911 . Tsu01g01073 . . . . . Vimu11g02596 . . . . . . .
Vvi1g0476 . . . . . . . . . . . . . . . . . . . Apr3g1606 . . . . . . Bva01g01599 Bva11g00633 Car06g01773 . . . . . . . . . . . . . . . . . . . . . . . Lal16g0764 . . . . . . . . . Lasa7g02960 . . . . . . . . . . Lja4g0128 . . Mepo2g03051 . . . . . . . . . Phco4g01804 . . . . Psa7g0245 Pste3g04125 . Pte14g00422 . . . . . Pvu2g0969 . . . . . Spst3g02251 . . . Sto11g0580 . . . Trre7g01914 . . . . . . . Vimu11g02598 . . . Vivi5g03825 . . .
Vvi1g0477 . . . . . . . . . . . . . . . . . . Apr7g1322 . . . . . . . . Bva11g00632 . . . . . . . . . . . . . . . . . . . . Lal6g1038 . . . . . . . . . . . . . . . . . . . . . . . Lja2g3231 . Mal1g5028 . . . . . . . Mtr1g0950 . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto11g0577 . Tpr1g3015 . . . Tsu01g01076 . . . . . . . . . . . . .
Vvi1g0478 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto11g0576 . . . . . . . . . . . . . . . . . . .
Vvi1g0479 . . . . . . . . . . . . . . . . . . . Apr3g1603 . . . . . . Bva01g01596 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Pvu2g0974 . . . . . Spst3g02255 . . . . . . . . . . . . . . . Vimu11g02604 . . . . . . .
Vvi1g0480 . . . . . . . . . . . . . . . . . . . Apr3g1599 . . . . . . Bva01g01590 . Car06g01774 . . . . . . . . . . . . . . . . . . . . . . . Lal16g0766 . . . . . . . . . Lasa7g02958 . . . . . . . . . . . . . . . . . . . . . . . Phco4g01812 . . . . Psa7g2962 . . . . . . . . Pvu2g0977 . . . . . Spst3g02258 . . . . . . . . . . . . . . . Vimu11g02608 . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Lasa Lasa7g02958 Chr7 562868002 562869360 +
Phco Phco4g01812 Chr4 34789228 34791944 -
Pvu Pvu2g0977 Chr2 17134773 17136639 -
Spst Spst3g02258 Chr3 65402593 65418241 -
Vimu Vimu11g02608 Chr11 46323305 46325683 -
Vvi Vvi1g0471 Chr1 4436815 4437918 +
Accr Accr9g01979 Chr9 43220190 43221299 +
Alju Alju09g0263 Chr09 3513621 3514734 -
Apr Apr3g1617 Chr3 31580110 31588079 -
Bisa Bisa11g0538 Chr11 14583240 14585224 -
Bva Bva01g01606 Chr01 17355325 17357373 -
Bva Bva11g00640 Chr11 9717763 9719395 -
Car Car06g01766 Chr06 17499543 17502539 +
Dere Dere09g2155 Chr09 30724379 30726558 +
Enph Enph13g0608 Chr13 12391864 12395068 +
Glsi Glsi05g0274 Chr05 49246380 49249812 -
Lal Lal16g0757 Chr16 4880764 4882229 +
Lal Lal15g0723 Chr15 5069095 5071386 +
Lasa Lasa7g02981 Chr7 564263235 564264099 -
Lele Lele49g1210 Chr49 8062458 8063580 -
Lele Lele50g1631 Chr50 21393706 21394788 +
Lele Lele51g1230 Chr51 8114606 8115721 -
Lele Lele52g1587 Chr52 19782112 19783225 +
Mepo Mepo2g03063 Chr2 40283474 40285852 -
Mibi Mibi12g0213 Chr12 4245390 4247001 -
Phac Phac2g01468 Chr2 13171875 13173267 +
Phco Phco4g01792 Chr4 33772126 33773013 +
Prci Prci10g2789 Chr10 36380788 36382643 +
Psa Psa7g2951 Chr7 211451196 211452805 +
Pste Pste3g04135 Chr3 36801194 36802755 -
Pte Pte14g00420 Chr14 22106019 22108050 +
Pvu Pvu2g0958 Chr2 16761443 16762906 +
Spst Spst3g02242 Chr3 64858005 64858765 +
Sto Sto11g0588 Chr11 7008051 7009561 -
Sto Sto6g2657 Chr6 33675125 33677717 -
Trre Trre7g01895 Chr7 14860427 14862147 +
Vimu Vimu11g02588 Chr11 46028805 46029726 +
Vivi Vivi5g03848 Chr5 133171888 133173181 -
Vvi Vvi1g0472 Chr1 4440986 4441396 +
Vvi Vvi1g0473 Chr1 4445206 4445589 +
Vvi Vvi1g0474 Chr1 4447965 4454333 -
Acco Acco11g0209 Chr11 2649567 2654257 +
Accr Accr9g01983 Chr9 43250931 43255635 -
Alju Alju09g0256 Chr09 3415419 3420145 +
Apr Apr3g1610 Chr3 31488620 31493336 +
Bisa Bisa11g0533 Chr11 14485441 14491594 +
Bva Bva01g01603 Chr01 17338252 17343090 +
Bva Bva11g00637 Chr11 9702414 9707071 +
Dere Dere09g2159 Chr09 30783809 30790238 -
Enph Enph13g0611 Chr13 12408825 12419557 -
Glsi Glsi05g0270 Chr05 49154462 49160525 +
Lal Lal16g0760 Chr16 4899166 4904793 -
Lele Lele49g1207 Chr49 8039194 8042474 +
Lele Lele50g1634 Chr50 21408126 21412440 -
Lele Lele51g1227 Chr51 8092232 8096623 +
Lele Lele52g1589 Chr52 19794948 19799315 -
Mibi Mibi12g0209 Chr12 4093511 4099103 +
Phco Phco4g01799 Chr4 34364292 34369512 -
Prci Prci10g2800 Chr10 36441582 36448614 -
Pste Pste3g04129 Chr3 36700801 36703460 +
Pvu Pvu2g0963 Chr2 16836568 16842564 -
Spst Spst3g02248 Chr3 65126732 65128794 -
Sto Sto11g0586 Chr11 6983140 6987577 +
Sto Sto6g2651 Chr6 33609586 33614984 +
Vimu Vimu11g02594 Chr11 46123416 46129965 -
Vvi Vvi1g0475 Chr1 4475564 4478310 -
Acco Acco11g0206 Chr11 2595751 2599246 +
Accr Accr9g01985 Chr9 43303717 43307138 -
Alju Alju09g0253 Chr09 3376852 3379052 +
Apr Apr7g1325 Chr7 20357505 20362283 +
Apr Apr3g1607 Chr3 31433451 31437608 +
Bisa Bisa11g0528 Chr11 14266869 14270197 +
Bva Bva01g01602 Chr01 17318330 17322524 +
Bva Bva11g00635 Chr11 9680858 9684902 +
Car Car06g01771 Chr06 17552973 17557469 -
Dere Dere09g2163 Chr09 30862367 30865838 -
Enph Enph13g0613 Chr13 12440143 12444747 -
Glsi Glsi05g0266 Chr05 49032280 49036626 +
Lal Lal16g0763 Chr16 4917484 4922070 -
Lal Lal15g0725 Chr15 5083668 5089946 -
Lasa Lasa7g02968 Chr7 563330738 563333749 +
Lele Lele49g1204 Chr49 8007610 8010858 +
Lele Lele50g1637 Chr50 21433624 21436804 -
Lele Lele51g1225 Chr51 8069344 8073517 +
Lele Lele52g1591 Chr52 19820857 19824221 -
Lja Lja2g3225 Chr2 70892805 70898071 +
Mal Mal1g5030 Chr1 121016239 121021155 +
Mepo Mepo2g03055 Chr2 40207802 40212327 +
Mibi Mibi12g0207 Chr12 4039793 4043449 +
Mtr Mtr1g0948 Chr1 10936234 10941488 -
Phco Phco4g01802 Chr4 34485431 34488980 -
Prci Prci10g2804 Chr10 36478573 36483190 -
Pste Pste3g04126 Chr3 36641632 36646508 +
Pte Pte3g00350 Chr3 2881700 2884115 -
Pvu Pvu2g0968 Chr2 16930983 16935514 -
Spst Spst3g02250 Chr3 65240436 65244376 -
Sto Sto11g0582 Chr11 6949834 6952995 +
Sto Sto6g2648 Chr6 33567509 33571563 +
Tpr Tpr1g3017 Chr1 34579537 34584639 +
Trre Trre7g01911 Chr7 15012916 15016713 -
Tsu Tsu01g01073 Chr01 9878928 9883077 -
Vimu Vimu11g02596 Chr11 46163283 46166756 -
Vvi Vvi1g0476 Chr1 4488301 4491203 -
Apr Apr3g1606 Chr3 31387025 31390698 +
Bva Bva01g01599 Chr01 17291176 17294752 +
Bva Bva11g00633 Chr11 9662286 9665171 +
Car Car06g01773 Chr06 17594473 17598044 -
Lal Lal16g0764 Chr16 4934778 4937325 -
Lasa Lasa7g02960 Chr7 563102424 563106941 +
Lja Lja4g0128 Chr4 986982 991243 -
Mepo Mepo2g03051 Chr2 40145566 40149957 +
Phco Phco4g01804 Chr4 34554902 34557981 -
Psa Psa7g0245 Chr7 16421173 16425038 -
Pste Pste3g04125 Chr3 36597829 36601445 +
Pte Pte14g00422 Chr14 22195541 22198243 -
Pvu Pvu2g0969 Chr2 17014117 17017506 -
Spst Spst3g02251 Chr3 65272748 65276236 -
Sto Sto11g0580 Chr11 6927695 6930775 +
Trre Trre7g01914 Chr7 15065179 15069569 -
Vimu Vimu11g02598 Chr11 46204266 46207594 -
Vivi Vivi5g03825 Chr5 132678519 132682365 -
Vvi Vvi1g0477 Chr1 4494130 4544155 -
Apr Apr7g1322 Chr7 20304816 20321141 +
Bva Bva11g00632 Chr11 9647123 9659225 +
Lal Lal6g1038 Chr6 7490041 7511133 -
Lja Lja2g3231 Chr2 70968797 71014737 -
Mal Mal1g5028 Chr1 120966533 120983480 +
Mtr Mtr1g0950 Chr1 10960754 10978845 -
Sto Sto11g0577 Chr11 6896446 6915221 +
Tpr Tpr1g3015 Chr1 34551809 34567587 +
Tsu Tsu01g01076 Chr01 9945954 9958930 -
Vvi Vvi1g0478 Chr1 4551079 4555749 +
Sto Sto11g0576 Chr11 6890613 6892075 -
Vvi Vvi1g0479 Chr1 4557702 4559021 +
Apr Apr3g1603 Chr3 31344021 31345479 +
Bva Bva01g01596 Chr01 17272886 17274250 +
Pvu Pvu2g0974 Chr2 17103478 17104338 -
Spst Spst3g02255 Chr3 65367895 65368266 -
Vimu Vimu11g02604 Chr11 46289606 46290130 -
Vvi Vvi1g0480 Chr1 4560997 4562355 +
Apr Apr3g1599 Chr3 31281540 31289455 +
Bva Bva01g01590 Chr01 17254832 17255932 +
Car Car06g01774 Chr06 17601397 17603984 -
Lal Lal16g0766 Chr16 4951665 4953269 -
Lasa Lasa7g02958 Chr7 562868002 562869360 +
Phco Phco4g01812 Chr4 34789228 34791944 -
Psa Psa7g2962 Chr7 214673381 214675345 -
Pvu Pvu2g0977 Chr2 17134773 17136639 -
Spst Spst3g02258 Chr3 65402593 65418241 -
Vimu Vimu11g02608 Chr11 46323305 46325683 -