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
Vvi16g0569 . . . . Adu03g00899 . Aed5g0125 . . . Ahy13g1128 . Aip03g01236 . . . Amo13g1156 . Apr5g0583 . Arst3g01166 . Bach9g01410 . . . . Bva07g00927 . Car06g03007 Cca04g00144 . . . Dod03g2592 . . . . . Gma09g02054 . . . Gso9g1838 . . . . . Lal9g0036 . . . . . . . . . Lapu11g01034 . Lasa7g00950 . . . . . . . . . Lja3g0153 . . . . . . . . . Mtr4g1222 . . . Phco9g00191 . . . . . Pste1g00608 . . . . . Pumo11g02186 . Pvu11g0161 . Rops3g00177 . Seca6g00283 . Spst2g02881 . Ssu3g3202 . Sto7g2390 . . . . . . . Vian5g01771 . Vifa6g00092 . Vimu5g02712 . Viun11g02854 . Vivi5g01629 . Vra2g0146 .
Vvi16g0570 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0571 . . . . Adu03g00898 . . . . . Ahy13g1127 . Aip03g01235 . . . Amo13g1157 . Apr5g0582 . Arst3g01164 . Bach9g01409 . . . . Bva07g00928 . Car06g03010 . . . . Dod03g2593 . . . . . Gma09g02053 . . . Gso9g1837 . . . . . . . . . . . . . . . Lapu11g01033 . Lasa7g00951 . . . . . . . . . Lja3g0154 . . . . . . . . . Mtr4g1220 . . . Phco9g00193 . . . . . Pste1g00612 . . . . . . . Pvu11g0163 . . . . . Spst2g02880 . . . . . . . . . . . . . . . Vimu5g02711 . . . Vivi5g01631 . . .
Vvi16g0572 . . . . Adu03g00897 . Aed5g0127 . . . Ahy13g1126 . Aip03g01234 . . . Amo13g1158 . Apr5g0581 . Arst3g01163 . . . . . . . . Car06g03011 Cca04g00145 . . . Dod03g2594 . . . . . Gma09g02052 . . . Gso9g1836 . . . . . . . . . . . . . . . Lapu11g01032 . Lasa7g00952 . . . . . . . . . Lja3g0156 . . . . . . . . . Mtr4g1219 . . . Phco9g00194 . . . . . Pste1g00615 . . . . . Pumo11g02184 . Pvu11g0164 . Rops3g00178 . Seca6g00286 . Spst2g02879 . Ssu3g3200 . Sto7g2391 . . . . . . . Vian5g01769 . Vifa6g00091 . . . Viun11g02848 . Vivi5g01636 . Vra2g0148 .
Vvi16g0573 . . . . Adu03g00896 . Aed5g0128 . . . Ahy13g1125 . Aip03g01233 . . . Amo13g1159 . Apr5g0580 . Arst3g01162 . . . . . . Bva07g00931 . Car06g03012 Cca04g00147 . . . Dod03g2596 . . . . . Gma09g02051 . . . Gso9g1835 . . . . . . . . . . . . . . . Lapu11g01031 . Lasa7g00953 . . . . . . . . . Lja3g0158 . . . . . . . . . Mtr4g1218 . . . Phco9g00195 . . . . . Pste1g00619 . . . . . Pumo11g02183 . Pvu11g0165 . Rops3g00179 . Seca6g00290 . Spst2g02878 . Ssu3g3199 . Sto7g2392 . Tpr4g1289 . . . Tsu06g01056 . Vian5g01768 . Vifa6g00088 . Vimu5g02708 . Viun11g02846 . Vivi5g01639 . Vra2g0149 .
Vvi16g0574 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0575 . . . . . . Aed5g0130 . . . Ahy13g1123 . Aip03g01232 . . . Amo13g1163 . Apr5g0579 . . . . . . . . Bva07g00934 . Car06g03013 Cca04g00148 . . . Dod03g2598 . . . . . . . . . . . . . . . . . . . . . . . . . Lapu11g01030 . . . . . . . . . . . Lja3g0159 . . . . . . . . . Mtr4g1217 . . . Phco9g00197 . . . . . Pste1g00625 . . . . . Pumo11g02181 . Pvu11g0167 . Rops3g00180 . Seca6g00296 . . . Ssu3g3197 . . . Tpr4g1288 . . . Tsu06g01055 . Vian5g01767 . . . . . Viun11g02845 . . . Vra2g0150 .
Vvi16g0576 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0577 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0578 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi16g0569 Chr16 11481605 11488372 -
Adu Adu03g00899 Chr03 8926548 8929319 +
Aed Aed5g0125 Chr5 933974 936557 -
Ahy Ahy13g1128 Chr13 12697564 12700353 +
Aip Aip03g01236 Chr03 12251794 12254610 +
Amo Amo13g1156 Chr13 15054326 15057064 -
Apr Apr5g0583 Chr5 7942487 7945558 +
Arst Arst3g01166 Chr3 9009402 9011960 +
Bach Bach9g01410 Chr9 12374250 12377934 +
Bva Bva07g00927 Chr07 11377456 11384120 -
Car Car06g03007 Chr06 51502919 51506825 -
Cca Cca04g00144 Chr04 1328707 1331441 -
Dod Dod03g2592 Chr03 57551462 57555154 -
Gma Gma09g02054 Chr09 46188019 46191951 +
Gso Gso9g1838 Chr9 42806072 42809843 +
Lal Lal9g0036 Chr9 245711 248521 -
Lapu Lapu11g01034 Chr11 12637079 12641901 +
Lasa Lasa7g00950 Chr7 113241707 113243840 -
Lja Lja3g0153 Chr3 1600520 1603389 -
Mtr Mtr4g1222 Chr4 17800392 17804090 +
Phco Phco9g00191 Chr9 1238541 1242958 -
Pste Pste1g00608 Chr1 1977266 1979788 -
Pumo Pumo11g02186 Chr11 54265338 54269460 +
Pvu Pvu11g0161 Chr11 1220844 1225809 -
Rops Rops3g00177 Chr3 2400027 2405670 -
Seca Seca6g00283 Chr6 7042065 7046595 -
Spst Spst2g02881 Chr2 28626003 28628518 +
Ssu Ssu3g3202 Chr3 88158686 88161787 +
Sto Sto7g2390 Chr7 29448735 29451363 -
Vian Vian5g01771 Chr5 39986045 39988647 +
Vifa Vifa6g00092 Chr6 26568524 26570330 -
Vimu Vimu5g02712 Chr5 36902755 36905331 +
Viun Viun11g02854 Chr11 40528075 40530951 +
Vivi Vivi5g01629 Chr5 53987427 53991794 -
Vra Vra2g0146 Chr2 1143226 1146142 -
Vvi Vvi16g0570 Chr16 11491301 11491585 +
Vvi Vvi16g0571 Chr16 11494880 11495563 +
Adu Adu03g00898 Chr03 8914409 8915319 +
Ahy Ahy13g1127 Chr13 12693869 12694793 +
Aip Aip03g01235 Chr03 12249305 12250237 +
Amo Amo13g1157 Chr13 15059413 15060426 -
Apr Apr5g0582 Chr5 7940470 7941582 +
Arst Arst3g01164 Chr3 8997141 8997996 +
Bach Bach9g01409 Chr9 12367730 12372597 -
Bva Bva07g00928 Chr07 11385918 11386664 +
Car Car06g03010 Chr06 51566760 51568216 +
Dod Dod03g2593 Chr03 57556728 57557715 -
Gma Gma09g02053 Chr09 46182403 46183119 +
Gso Gso9g1837 Chr9 42800637 42801629 +
Lapu Lapu11g01033 Chr11 12635229 12636672 +
Lasa Lasa7g00951 Chr7 113376287 113376970 +
Lja Lja3g0154 Chr3 1604506 1605727 -
Mtr Mtr4g1220 Chr4 17763456 17764347 +
Phco Phco9g00193 Chr9 1260365 1261178 -
Pste Pste1g00612 Chr1 1985837 1987938 -
Pvu Pvu11g0163 Chr11 1250633 1251310 -
Spst Spst2g02880 Chr2 28624083 28624760 +
Vimu Vimu5g02711 Chr5 36900543 36902116 +
Vivi Vivi5g01631 Chr5 54148019 54148910 +
Vvi Vvi16g0572 Chr16 11534331 11542073 +
Adu Adu03g00897 Chr03 8909685 8913607 +
Aed Aed5g0127 Chr5 940375 944619 +
Ahy Ahy13g1126 Chr13 12688948 12691782 +
Aip Aip03g01234 Chr03 12244414 12248410 +
Amo Amo13g1158 Chr13 15061257 15065206 -
Apr Apr5g0581 Chr5 7934416 7939033 -
Arst Arst3g01163 Chr3 8992351 8995199 +
Car Car06g03011 Chr06 51602816 51607791 +
Cca Cca04g00145 Chr04 1336905 1339041 +
Dod Dod03g2594 Chr03 57560667 57564113 +
Gma Gma09g02052 Chr09 46178140 46180476 -
Gso Gso9g1836 Chr9 42795057 42798951 -
Lapu Lapu11g01032 Chr11 12629130 12633712 -
Lasa Lasa7g00952 Chr7 113579000 113581695 +
Lja Lja3g0156 Chr3 1614977 1618820 +
Mtr Mtr4g1219 Chr4 17751464 17754883 -
Phco Phco9g00194 Chr9 1262290 1264598 +
Pste Pste1g00615 Chr1 1991149 1994924 +
Pumo Pumo11g02184 Chr11 54256086 54259958 -
Pvu Pvu11g0164 Chr11 1252479 1255151 +
Rops Rops3g00178 Chr3 2409841 2413438 +
Seca Seca6g00286 Chr6 7104636 7108763 +
Spst Spst2g02879 Chr2 28619800 28622072 -
Ssu Ssu3g3200 Chr3 88147871 88150237 -
Sto Sto7g2391 Chr7 29457227 29459993 +
Vian Vian5g01769 Chr5 39980015 39982302 -
Vifa Vifa6g00091 Chr6 25958668 25960271 +
Viun Viun11g02848 Chr11 40519445 40523330 -
Vivi Vivi5g01636 Chr5 54376510 54378766 +
Vra Vra2g0148 Chr2 1149422 1153216 +
Vvi Vvi16g0573 Chr16 11544324 11556663 -
Adu Adu03g00896 Chr03 8901391 8906991 +
Aed Aed5g0128 Chr5 945514 951800 -
Ahy Ahy13g1125 Chr13 12680416 12686102 +
Aip Aip03g01233 Chr03 12236189 12241664 +
Amo Amo13g1159 Chr13 15075660 15081023 -
Apr Apr5g0580 Chr5 7926824 7933449 +
Arst Arst3g01162 Chr3 8984059 8989648 +
Bva Bva07g00931 Chr07 11399436 11404898 -
Car Car06g03012 Chr06 51616260 51625168 -
Cca Cca04g00147 Chr04 1341671 1348341 -
Dod Dod03g2596 Chr03 57567654 57569933 -
Gma Gma09g02051 Chr09 46166758 46173484 +
Gso Gso9g1835 Chr9 42785028 42791614 +
Lapu Lapu11g01031 Chr11 12622236 12627951 +
Lasa Lasa7g00953 Chr7 113909784 113915336 -
Lja Lja3g0158 Chr3 1625094 1631075 -
Mtr Mtr4g1218 Chr4 17741876 17748228 +
Phco Phco9g00195 Chr9 1268687 1273924 -
Pste Pste1g00619 Chr1 1996937 2003704 -
Pumo Pumo11g02183 Chr11 54247135 54254055 +
Pvu Pvu11g0165 Chr11 1259066 1264677 -
Rops Rops3g00179 Chr3 2415972 2422074 -
Seca Seca6g00290 Chr6 7139474 7145903 -
Spst Spst2g02878 Chr2 28608097 28613655 +
Ssu Ssu3g3199 Chr3 88129132 88130245 +
Sto Sto7g2392 Chr7 29464865 29473531 -
Tpr Tpr4g1289 Chr4 12455030 12461242 +
Tsu Tsu06g01056 Chr06 9626753 9633039 +
Vian Vian5g01768 Chr5 39970079 39975257 +
Vifa Vifa6g00088 Chr6 24715235 24720589 +
Vimu Vimu5g02708 Chr5 36887403 36892534 +
Viun Viun11g02846 Chr11 40511233 40516884 +
Vivi Vivi5g01639 Chr5 54492166 54497237 -
Vra Vra2g0149 Chr2 1155456 1161235 -
Vvi Vvi16g0574 Chr16 11582540 11582827 -
Vvi Vvi16g0575 Chr16 11604893 11606067 +
Aed Aed5g0130 Chr5 954328 955423 +
Ahy Ahy13g1123 Chr13 12668234 12669448 -
Aip Aip03g01232 Chr03 12224754 12225309 -
Amo Amo13g1163 Chr13 15108971 15110378 +
Apr Apr5g0579 Chr5 7906117 7907245 -
Bva Bva07g00934 Chr07 11410062 11411467 +
Car Car06g03013 Chr06 51634117 51635482 -
Cca Cca04g00148 Chr04 1352909 1354295 +
Dod Dod03g2598 Chr03 57572932 57574216 +
Lapu Lapu11g01030 Chr11 12619986 12621747 -
Lja Lja3g0159 Chr3 1632273 1633654 +
Mtr Mtr4g1217 Chr4 17734600 17735721 -
Phco Phco9g00197 Chr9 1281988 1282758 +
Pste Pste1g00625 Chr1 2015243 2016204 +
Pumo Pumo11g02181 Chr11 54240958 54242194 -
Pvu Pvu11g0167 Chr11 1270147 1271173 +
Rops Rops3g00180 Chr3 2423116 2424125 +
Seca Seca6g00296 Chr6 7661035 7661799 +
Ssu Ssu3g3197 Chr3 88121112 88121877 -
Tpr Tpr4g1288 Chr4 12449429 12450496 -
Tsu Tsu06g01055 Chr06 9621870 9622816 -
Vian Vian5g01767 Chr5 39965844 39966604 -
Viun Viun11g02845 Chr11 40502163 40503235 -
Vra Vra2g0150 Chr2 1164330 1165393 +
Vvi Vvi16g0576 Chr16 11631077 11631298 +
Vvi Vvi16g0577 Chr16 11652221 11652655 -
Vvi Vvi16g0578 Chr16 11668130 11668483 +