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
Vvi16g1009 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva04g01194 . . . Cca08g00736 . . . . . . . . Gma16g01531 . . . Gso16g1454 . . . . . Lal9g0834 . . . . . . . . . . . . . . . . . . . . . Lja2g2694 . . Mal8g2917 . . . . . . . Mtr6g1325 . . Phco5g00794 . . . . . . . . Pte9g00387 . . Pumo6g02514 . Pvu4g1127 . Rops5g01058 . . . Spst4g03271 . . . . . . Tpr2g4295 Trre11g01244 . . Tsu06g02992 Vian8g00995 . . . Vimu8g02241 . Viun4g02035 . . . . .
Vvi16g1010 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1011 . . . . Adu05g03441 . . Aed7g0653 Aev05g2860 . Ahy15g3603 . Aip05g03920 . . . . . . Apr6g0636 Arst5g04419 . Bach1g01107 . . . Bva03g01304 Bva04g01195 . . . Cca08g00738 . . Dod02g2974 . . . . . Gma16g01530 . . . Gso16g1453 . . . Lal1g0848 . . . . . Lan13g0824 . . . . . . . Lasa1g02478 . . . . . . . . . Lja2g2695 . . Mal8g2918 . . . . . . . Mtr6g1326 . . . . . . . . . . . . . . . . Pvu4g1126 . . . Seca10g03817 . Spst4g03273 . . . . . . Tpr2g4296 Trre11g01247 . . . . . Vifa1g04393 . Vimu8g02242 . Viun4g02033 . Vivi2g05381 . . .
Vvi16g1012 . . . . Adu05g03442 . Aed1g2311 Aed7g0654 Aev05g2856 . Ahy15g3604 . Aip05g03921 . . . . . . Apr6g0635 Arst5g04420 . Bach1g01106 . . . Bva03g01303 Bva04g01197 . . Cca02g02209 Cca08g00739 . . Dod02g2973 . . . Glsi01g1440 . Gma10g02188 . . . Gso10g2057 . . . . Lal2g0952 Lal9g0840 . . . . . . . . . . Lapu7g02005 . Lasa6g04029 . . . . . . . . . Lja5g0674 Mal1g2108 . . Mepo4g04197 . Mesa1g04582 . . Mtr1g3697 . . Phac7g01151 . Phco6g02432 . . Psa6g4466 . . Pste4g02823 . Pte9g00392 . Pte9g00392 Pumo6g02512 . Pvu4g1125 Pvu7g0770 Rops5g01056 Rops6g02676 Seca10g03807 Seca10g03807 Spst4g01880 Spst10g00920 Ssu7g0832 . . . Tpr1g0807 . . Trre1g05335 Tsu01g04366 . Vian8g00993 Vian3g00672 . Vifa3g02861 Vimu8g02244 Vimu3g02990 Viun4g02032 Viun7g03187 . Vivi1g04456 Vra8g2193 .
Vvi16g1013 . . . . Adu05g03443 . . . Aev05g2855 . Ahy15g3605 . Aip05g03922 . . . . . . Apr6g0634 Arst5g04421 . . . Bisa01g0818 . . Bva04g01198 . . . Cca08g00740 Dere06g1278 . Dod02g2972 . . . Glsi01g1439 . Gma09g01227 . . . Gso9g1059 . . . . Lal2g0953 Lal9g0841 . . . . . . . . . Lapu4g00708 . . . . Lele46g0159 . Lele48g1299 . . . . Lja2g2696 . . Mal8g2925 . . . . Mibi01g3445 . . Mtr6g1332 . . . . Prci14g2216 . . . . . . Pte9g00401 . . . . Pvu4g1124 . . . Seca10g03802 . Spst4g03277 . . . Sto10g2321 . . . . . . . Vian8g00992 . Vifa1g04387 . Vimu8g02246 . Viun4g02030 . Vivi2g05383 . . .
Vvi16g1014 . . . . . . Aed1g2312 . . . . . . . . . . . . . . . . . . . Bva03g01302 . . . Cca02g02208 . . . . . . . . . Gma10g02187 . . . Gso10g2056 . . . . . . . Lal12g0069 . . . . . . . . . . . . . . . . . . . . Lja5g0675 Mal1g2109 . . . . . . . Mtr1g3696 . . . . . . . Psa6g4464 . . . . . . . . . . . . . . . . . Ssu7g0836 . . . Tpr1g0808 . . . Tsu01g04365 . . . . . . . . . . . Vra8g2192 .
Vvi16g1015 . . . . . . Aed1g2313 Aed11g1743 Aev05g2851 Aev09g2185 Ahy15g3607 Ahy19g3587 Aip05g03925 Aip09g04045 . . . . . . . . . . . . Bva03g01301 Bva04g01199 . . Cca02g02207 Cca06g01820 . . Dod02g2970 Dod06g0844 . . . . Gma10g02186 . . . Gso10g2055 . . . . . . Lal24g0060 . . . . . . . . . . . . . . . . . . . . Lja2g2698 . . Mal8g2926 . . . . . . . Mtr6g1333 . . . . . . . . . . . . . . . . . . . . . . . . Ssu7g0838 Ssu2g2895 Sto10g2319 . . Tpr2g4298 . . . . . . . . . . . . . . . Vra11g0257
Vvi16g1016 . . . . . . . . . . . . . . . . . . . Apr6g0627 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mepo5g03468 . . . . . . . . . . . . . . . . . . . . . . . Pvu4g0488 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1017 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1018 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Aed Aed11g1743 Chr11 20974015 20979449 +
Cca Cca06g01820 Chr06 33617173 33621249 +
Ssu Ssu2g2895 Chr2 90223441 90227441 +
Vra Vra11g0257 Chr11 1776657 1780870 -
Spst Spst4g01880 Chr4 59381163 59382644 +
Vvi Vvi16g1009 Chr16 18325525 18328635 +
Bva Bva04g01194 Chr04 8146294 8153097 +
Cca Cca08g00736 Chr08 13884966 13888344 +
Gma Gma16g01531 Chr16 35651850 35655027 -
Gso Gso16g1454 Chr16 34784854 34787947 -
Lal Lal9g0834 Chr9 6063562 6066753 +
Lja Lja2g2694 Chr2 38475114 38479277 +
Mal Mal8g2917 Chr8 77955735 77960525 +
Mtr Mtr6g1325 Chr6 20054690 20059109 +
Phco Phco5g00794 Chr5 9353388 9358209 +
Pte Pte9g00387 Chr9 4491413 4497246 +
Pumo Pumo6g02514 Chr6 58756052 58759865 -
Pvu Pvu4g1127 Chr4 34702500 34706945 -
Rops Rops5g01058 Chr5 21607704 21612893 -
Spst Spst4g03271 Chr4 72380085 72386547 +
Tpr Tpr2g4295 Chr2 46343967 46348984 +
Trre Trre11g01244 Chr11 12077472 12080652 +
Tsu Tsu06g02992 Chr06 39291572 39298314 +
Vian Vian8g00995 Chr8 26508336 26512563 -
Vimu Vimu8g02241 Chr8 29155523 29161376 +
Viun Viun4g02035 Chr4 36142073 36146040 -
Vvi Vvi16g1010 Chr16 18329026 18336276 -
Vvi Vvi16g1011 Chr16 18339081 18344098 +
Adu Adu05g03441 Chr05 106829967 106833342 +
Aed Aed7g0653 Chr7 4816121 4824776 +
Aev Aev05g2860 Chr05 29553504 29557500 -
Ahy Ahy15g3603 Chr15 158747502 158751775 +
Aip Aip05g03920 Chr05 147359216 147363482 +
Apr Apr6g0636 Chr6 9337628 9345531 -
Arst Arst5g04419 Chr5 105505681 105509955 +
Bach Bach1g01107 Chr1 24131758 24137035 -
Bva Bva03g01304 Chr03 12704721 12711516 -
Bva Bva04g01195 Chr04 8154137 8163841 +
Cca Cca08g00738 Chr08 13962970 13971458 +
Dod Dod02g2974 Chr02 63317309 63322792 -
Gma Gma16g01530 Chr16 35643426 35649881 -
Gso Gso16g1453 Chr16 34776458 34782936 -
Lal Lal1g0848 Chr1 5900897 5907413 -
Lan Lan13g0824 Chr13 9011862 9018545 -
Lasa Lasa1g02478 Chr1 304636170 304654677 -
Lja Lja2g2695 Chr2 38487750 38504639 +
Mal Mal8g2918 Chr8 77963349 77977706 +
Mtr Mtr6g1326 Chr6 20063671 20077461 +
Pvu Pvu4g1126 Chr4 34688607 34697898 -
Seca Seca10g03817 Chr10 79326745 79326981 -
Spst Spst4g03273 Chr4 72396262 72404613 +
Tpr Tpr2g4296 Chr2 46350528 46368058 +
Trre Trre11g01247 Chr11 12100176 12106748 +
Vifa Vifa1g04393 Chr1 683241354 683244761 -
Vimu Vimu8g02242 Chr8 29164065 29180385 +
Viun Viun4g02033 Chr4 36125150 36133096 -
Vivi Vivi2g05381 Chr2 178690874 178703654 +
Vvi Vvi16g1012 Chr16 18360079 18360711 +
Adu Adu05g03442 Chr05 106848085 106851214 +
Aed Aed1g2311 Chr1 19165258 19167148 +
Aed Aed7g0654 Chr7 4838345 4839723 +
Aev Aev05g2856 Chr05 29534107 29535605 -
Ahy Ahy15g3604 Chr15 158766019 158767949 +
Aip Aip05g03921 Chr05 147376646 147380070 +
Apr Apr6g0635 Chr6 9316442 9317982 -
Arst Arst5g04420 Chr5 105523639 105526956 +
Bach Bach1g01106 Chr1 24107775 24109074 -
Bva Bva03g01303 Chr03 12690280 12692011 -
Bva Bva04g01197 Chr04 8169888 8171305 +
Cca Cca02g02209 Chr02 42597522 42598771 -
Cca Cca08g00739 Chr08 13995048 13996432 +
Dod Dod02g2973 Chr02 63303953 63305740 -
Glsi Glsi01g1440 Chr01 73456778 73458076 -
Gma Gma10g02188 Chr10 49465910 49467025 -
Gso Gso10g2057 Chr10 47580193 47582123 -
Lal Lal2g0952 Chr2 6378966 6380798 +
Lal Lal9g0840 Chr9 6133025 6134809 +
Lapu Lapu7g02005 Chr7 36287633 36288800 -
Lasa Lasa6g04029 Chr6 612791376 612792715 -
Lja Lja5g0674 Chr5 6073274 6074802 +
Mal Mal1g2108 Chr1 27590498 27591738 +
Mepo Mepo4g04197 Chr4 51856304 51857855 -
Mesa Mesa1g04582 Chr1 71756054 71757346 -
Mtr Mtr1g3697 Chr1 48635377 48637356 -
Phac Phac7g01151 Chr7 7241470 7243256 +
Phco Phco6g02432 Chr6 45737197 45738394 -
Psa Psa6g4466 Chr6 391533094 391535039 -
Pste Pste4g02823 Chr4 19849757 19851548 -
Pte Pte9g00392 Chr9 4546779 4547791 +
Pte Pte9g00392 Chr9 4546779 4547791 +
Pumo Pumo6g02512 Chr6 58735134 58736247 -
Pvu Pvu4g1125 Chr4 34620507 34622280 -
Pvu Pvu7g0770 Chr7 6907213 6908842 +
Rops Rops5g01056 Chr5 21546642 21548379 -
Rops Rops6g02676 Chr6 48144927 48146228 -
Seca Seca10g03807 Chr10 78716422 78718038 -
Seca Seca10g03807 Chr10 78716422 78718038 -
Spst Spst4g01880 Chr4 59381163 59382644 +
Spst Spst10g00920 Chr10 9976422 9977669 -
Ssu Ssu7g0832 Chr7 16675560 16676908 +
Tpr Tpr1g0807 Chr1 6746526 6748204 +
Trre Trre1g05335 Chr1 59206788 59208069 -
Tsu Tsu01g04366 Chr01 51539058 51540246 -
Vian Vian8g00993 Chr8 26471242 26472716 -
Vian Vian3g00672 Chr3 6802957 6804139 +
Vifa Vifa3g02861 Chr3 804182321 804183685 -
Vimu Vimu8g02244 Chr8 29196482 29197057 +
Vimu Vimu3g02990 Chr3 43943056 43944804 -
Viun Viun4g02032 Chr4 36094580 36096592 -
Viun Viun7g03187 Chr7 34412245 34414573 -
Vivi Vivi1g04456 Chr1 94940943 94942678 +
Vra Vra8g2193 Chr8 40305918 40308043 -
Vvi Vvi16g1013 Chr16 18389574 18392689 +
Adu Adu05g03443 Chr05 106852588 106854443 +
Aev Aev05g2855 Chr05 29523163 29530346 -
Ahy Ahy15g3605 Chr15 158778593 158780826 +
Aip Aip05g03922 Chr05 147385049 147388362 +
Apr Apr6g0634 Chr6 9298107 9300408 -
Arst Arst5g04421 Chr5 105528239 105530426 +
Bisa Bisa01g0818 Chr01 13206139 13209762 +
Bva Bva04g01198 Chr04 8177157 8181277 +
Cca Cca08g00740 Chr08 14007857 14013755 +
Dere Dere06g1278 Chr06 25032177 25039107 -
Dod Dod02g2972 Chr02 63296857 63299463 -
Glsi Glsi01g1439 Chr01 73448924 73452389 -
Gma Gma09g01227 Chr09 33835401 33839216 -
Gso Gso9g1059 Chr9 30677008 30680252 -
Lal Lal2g0953 Chr2 6381974 6384580 +
Lal Lal9g0841 Chr9 6138798 6145225 +
Lapu Lapu4g00708 Chr4 15325079 15328507 -
Lele Lele46g0159 Chr46 965807 967295 -
Lele Lele48g1299 Chr48 17241190 17249109 +
Lja Lja2g2696 Chr2 38534817 38538018 +
Mal Mal8g2925 Chr8 78507569 78512282 +
Mibi Mibi01g3445 Chr01 60275967 60277937 +
Mtr Mtr6g1332 Chr6 20161187 20166004 +
Prci Prci14g2216 Chr14 29159901 29162862 +
Pte Pte9g00401 Chr9 4796975 4799707 +
Pvu Pvu4g1124 Chr4 34313181 34316257 -
Seca Seca10g03802 Chr10 78646322 78652139 -
Spst Spst4g03277 Chr4 72424361 72426528 +
Sto Sto10g2321 Chr10 33435512 33442687 -
Vian Vian8g00992 Chr8 26427309 26433000 -
Vifa Vifa1g04387 Chr1 681923761 681927871 -
Vimu Vimu8g02246 Chr8 29237209 29237559 +
Viun Viun4g02030 Chr4 36064266 36067926 -
Vivi Vivi2g05383 Chr2 178714211 178718135 +
Vvi Vvi16g1014 Chr16 18393312 18395954 -
Aed Aed1g2312 Chr1 19168148 19170793 -
Bva Bva03g01302 Chr03 12681784 12684455 +
Cca Cca02g02208 Chr02 42592353 42595284 +
Gma Gma10g02187 Chr10 49459987 49462632 +
Gso Gso10g2056 Chr10 47574686 47577516 +
Lal Lal12g0069 Chr12 443869 446379 -
Lja Lja5g0675 Chr5 6077342 6079978 -
Mal Mal1g2109 Chr1 27596508 27599159 -
Mtr Mtr1g3696 Chr1 48630515 48633674 +
Psa Psa6g4464 Chr6 391452220 391455388 +
Ssu Ssu7g0836 Chr7 16776644 16777342 -
Tpr Tpr1g0808 Chr1 6747508 6752657 -
Tsu Tsu01g04365 Chr01 51534883 51537534 +
Vra Vra8g2192 Chr8 40301395 40304417 +
Vvi Vvi16g1015 Chr16 18399053 18408081 +
Aed Aed1g2313 Chr1 19171642 19175659 +
Aed Aed11g1743 Chr11 20974015 20979449 +
Aev Aev05g2851 Chr05 29489633 29492890 -
Aev Aev09g2185 Chr09 24704391 24707511 -
Ahy Ahy15g3607 Chr15 158809367 158813767 +
Ahy Ahy19g3587 Chr19 158488275 158490855 +
Aip Aip05g03925 Chr05 147417472 147421838 +
Aip Aip09g04045 Chr09 146736322 146738794 +
Bva Bva03g01301 Chr03 12673636 12678294 -
Bva Bva04g01199 Chr04 8183312 8189408 +
Cca Cca02g02207 Chr02 42582005 42583476 -
Cca Cca06g01820 Chr06 33617173 33621249 +
Dod Dod02g2970 Chr02 63270007 63275479 -
Dod Dod06g0844 Chr06 10495923 10499473 +
Gma Gma10g02186 Chr10 49454067 49457748 -
Gso Gso10g2055 Chr10 47569511 47573351 -
Lal Lal24g0060 Chr24 371305 375334 +
Lja Lja2g2698 Chr2 38683642 38690216 +
Mal Mal8g2926 Chr8 78516620 78522092 +
Mtr Mtr6g1333 Chr6 20170847 20176532 +
Ssu Ssu7g0838 Chr7 16853032 16855256 +
Ssu Ssu2g2895 Chr2 90223441 90227441 +
Sto Sto10g2319 Chr10 33421200 33426031 -
Tpr Tpr2g4298 Chr2 46398765 46403849 +
Vra Vra11g0257 Chr11 1776657 1780870 -
Vvi Vvi16g1016 Chr16 18445146 18448567 -
Apr Apr6g0627 Chr6 9190374 9193129 +
Mepo Mepo5g03468 Chr5 42835566 42839103 -
Pvu Pvu4g0488 Chr4 5060926 5064468 +
Vvi Vvi16g1017 Chr16 18461596 18462593 +
Vvi Vvi16g1018 Chr16 18463813 18465390 -