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
Vvi18g0076 . . . . . . . Aed9g0146 Aev08g0123 . Ahy17g2149 . Aip07g02288 . . . Amo17g1991 . . . . . . . . . . Bva10g01017 . Car05g03342 . Cca07g00185 . . . . . . . . Gma04g00146 Gma06g00138 . . Gso4g0141 Gso4g0141 . . . . Lal21g0069 . . . . . . . . . Lapu9g02370 . Lasa5g04633 . . . . . . . . . Lja1g2286 . . Mal2g0362 Mepo3g07755 . . . . . . Mtr3g4362 . . . . . . . . . . . . . . . . Pvu9g0067 . . . . . Spst9g00193 . . . . . . Tpr7g0147 Trre5g05809 . . Tsu07g00166 . . . . . . . . Vivi3g00787 . . Vra5g1733
Vvi18g0077 . . . . . . . Aed9g0147 Aev08g0124 . Ahy17g2150 . Aip07g02291 . . . Amo17g1995 . . . . . . . . . Bva06g01827 Bva10g01016 . . . Cca07g00186 . . . . . . . . Gma04g00147 Gma06g00139 . . Gso4g0142 Gso4g0142 . . . . . . . . . . . . . . . . Lasa5g04631 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa5g0224 . . . . . . . . Pvu9g0066 . . . . . Spst9g00195 . . . . Sto9g3748 . . . . . . . . . . . . . . Vivi3g00786 . . Vra5g1732
Vvi18g0078 . . . . . . . Aed9g0148 Aev08g0125 . Ahy17g2151 . Aip07g02292 . . . Amo17g1996 . . . . . . . . . . Bva10g01015 . Car05g03341 . Cca07g00187 . . . . . . . . Gma04g00148 Gma06g00140 . . Gso4g0143 Gso4g0143 . . Lal4g0027 . . . . . . . . . . . Lapu9g02368 . Lasa5g04630 . . . . . . . . . Lja1g2287 . . Mal2g0364 Mepo3g07757 . Mesa9g05597 . . . . Mtr3g4361 . . . . . . . Psa5g0225 . . . . . . . . Pvu9g0065 . . . . . . . . . . Sto9g3747 . Tpr7g0149 Trre5g05807 . . Tsu07g00168 . . . . . . . . Vivi3g00785 . . Vra5g1731
Vvi18g0079 . . . . . . . Aed9g0149 Aev08g0126 . Ahy17g2152 . Aip07g02293 . . . Amo17g1998 . . . Arst8g00281 . . . . . Bva06g01828 Bva10g01014 . Car05g03340 . Cca07g00188 . . . . . . . . Gma04g00149 Gma06g00141 . . Gso4g0144 Gso4g0144 . . Lal4g0031 . Lal21g0070 . . . Lan14g0985 . Lan14g0985 . . . . . . . . . . . . . . . Lja1g2290 . . Mal2g0366 . . . . . . . Mtr3g4360 . . . . . . . Psa5g0226 . . . . . . . . Pvu9g0127 . Rops10g02555 . Seca4g00291 . . . . . Sto5g0032 . . Tpr7g0150 . . . Tsu07g00169 Vian4g02470 . Vifa2g04609 . . . Viun9g03770 . . . . Vra5g1729
Vvi18g0080 . . . . . . . Aed9g0150 Aev08g0127 . Ahy17g2153 . Aip07g02294 . . . Amo17g1999 . . . . . . . . . Bva06g01829 Bva10g01013 . Car05g03339 . Cca07g00189 . . . . . . . . Gma04g00151 Gma06g00142 . . Gso4g0145 Gso4g0145 . . Lal4g0033 . Lal21g0071 . . . Lan14g0984 . Lan14g0984 . . . . . . . . . . . . . . . . . . Mal2g0372 . . . . . . . Mtr3g4359 . . . . . . . Psa5g0227 . . . . . . . . Pvu9g0126 . . . . . . . . . Sto5g0033 . . Tpr7g0151 . . . Tsu07g00171 . . . . . . . . . . . Vra5g1728
Vvi18g0081 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0082 . . . . . . . . Aev08g0128 . Ahy17g2155 . Aip07g02295 . . . Amo17g2000 . . . . . . . . . . . . Car05g03338 . . . . . . . . . . . . . . . . . . Lal4g0034 . . . . . Lan14g0983 . . . . . . . . . . . . . . . . . Lja1g2291 . . Mal2g0373 . . . . . . . Mtr3g4357 . . . . . . . Psa5g0228 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0083 . . . . . . . . Aev08g0129 . Ahy17g2156 . Aip07g02296 . . . . . . . . . . . . . Bva06g01830 Bva10g01012 . Car05g03337 . . . . . . . . . . Gma04g00152 Gma06g00143 . . Gso4g0146 Gso4g0146 . . Lal4g0035 . Lal21g0072 . . . Lan14g0982 . Lan14g0982 . . . . . Lasa5g04626 . . . . . . . . . Lja1g2292 . . Mal2g0374 . . . . . . . Mtr3g4356 . . . . . . . Psa5g0229 . . . . . . . . Pvu9g0125 . Rops10g02550 . Seca4g00292 . . . . . . Sto9g3746 . Tpr7g0152 . . . Tsu07g00172 Vian4g02469 . Vifa2g04600 . . . Viun9g03767 . . . . .
Vvi18g0084 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0085 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi18g0076 Chr18 697127 703782 -
Aed Aed9g0146 Chr9 1020046 1024568 -
Aev Aev08g0123 Chr08 681694 685215 -
Ahy Ahy17g2149 Chr17 103058449 103062788 -
Aip Aip07g02288 Chr07 95689124 95694193 -
Amo Amo17g1991 Chr17 102419565 102423774 -
Bva Bva10g01017 Chr10 7446629 7451460 +
Car Car05g03342 Chr05 78124991 78130003 +
Cca Cca07g00185 Chr07 2317480 2321916 -
Gma Gma04g00146 Chr04 1238460 1242645 -
Gma Gma06g00138 Chr06 1209064 1213642 -
Gso Gso4g0141 Chr4 1217726 1222316 -
Gso Gso4g0141 Chr4 1217726 1222316 -
Lal Lal21g0069 Chr21 491433 496136 -
Lapu Lapu9g02370 Chr9 38262208 38267823 +
Lasa Lasa5g04633 Chr5 681852733 681856219 +
Lja Lja1g2286 Chr1 26597527 26601881 -
Mal Mal2g0362 Chr2 3948870 3953152 -
Mepo Mepo3g07755 Chr3 90745817 90750337 -
Mtr Mtr3g4362 Chr3 57577291 57582256 +
Pvu Pvu9g0067 Chr9 1130669 1134989 +
Spst Spst9g00193 Chr9 1684188 1690426 -
Tpr Tpr7g0147 Chr7 1186975 1191516 -
Trre Trre5g05809 Chr5 57882897 57886544 +
Tsu Tsu07g00166 Chr07 1242377 1246640 -
Vivi Vivi3g00787 Chr3 12943058 12946845 +
Vra Vra5g1733 Chr5 23548252 23552671 +
Vvi Vvi18g0077 Chr18 708911 712359 +
Aed Aed9g0147 Chr9 1029760 1033729 +
Aev Aev08g0124 Chr08 690586 692696 +
Ahy Ahy17g2150 Chr17 103100576 103103975 +
Aip Aip07g02291 Chr07 95729189 95731535 +
Amo Amo17g1995 Chr17 102462538 102464988 +
Bva Bva06g01827 Chr06 12580083 12582329 +
Bva Bva10g01016 Chr10 7441430 7444699 -
Cca Cca07g00186 Chr07 2346616 2349662 +
Gma Gma04g00147 Chr04 1247945 1251325 +
Gma Gma06g00139 Chr06 1218141 1221436 +
Gso Gso4g0142 Chr4 1227316 1230666 +
Gso Gso4g0142 Chr4 1227316 1230666 +
Lasa Lasa5g04631 Chr5 681809936 681812828 -
Psa Psa5g0224 Chr5 15981433 15984263 +
Pvu Pvu9g0066 Chr9 1112275 1113235 -
Spst Spst9g00195 Chr9 1705952 1708358 +
Sto Sto9g3748 Chr9 35636016 35637500 -
Vivi Vivi3g00786 Chr3 12917537 12920127 -
Vra Vra5g1732 Chr5 23540982 23544401 -
Vvi Vvi18g0078 Chr18 713594 722552 -
Aed Aed9g0148 Chr9 1030917 1037402 -
Aev Aev08g0125 Chr08 694566 696586 -
Ahy Ahy17g2151 Chr17 103104158 103106244 -
Aip Aip07g02292 Chr07 95732038 95733710 -
Amo Amo17g1996 Chr17 102466197 102467239 -
Bva Bva10g01015 Chr10 7438082 7441322 +
Car Car05g03341 Chr05 78118349 78122402 +
Cca Cca07g00187 Chr07 2350171 2354209 -
Gma Gma04g00148 Chr04 1252301 1263125 -
Gma Gma06g00140 Chr06 1221902 1225975 -
Gso Gso4g0143 Chr4 1231267 1234698 -
Gso Gso4g0143 Chr4 1231267 1234698 -
Lal Lal4g0027 Chr4 168084 176648 -
Lapu Lapu9g02368 Chr9 38245744 38251784 +
Lasa Lasa5g04630 Chr5 681806557 681809183 +
Lja Lja1g2287 Chr1 26610480 26618862 -
Mal Mal2g0364 Chr2 3962776 3965147 -
Mepo Mepo3g07757 Chr3 90755308 90758095 -
Mesa Mesa9g05597 Chr9 91547318 91550277 +
Mtr Mtr3g4361 Chr3 57563823 57567007 +
Psa Psa5g0225 Chr5 15981433 15987601 -
Pvu Pvu9g0065 Chr9 1099878 1103868 +
Sto Sto9g3747 Chr9 35627238 35629886 +
Tpr Tpr7g0149 Chr7 1197231 1200970 -
Trre Trre5g05807 Chr5 57858806 57862571 +
Tsu Tsu07g00168 Chr07 1251857 1255957 -
Vivi Vivi3g00785 Chr3 12913718 12917286 +
Vra Vra5g1731 Chr5 23536520 23540447 +
Vvi Vvi18g0079 Chr18 728952 730694 +
Aed Aed9g0149 Chr9 1052488 1054230 +
Aev Aev08g0126 Chr08 698771 700510 +
Ahy Ahy17g2152 Chr17 103125665 103128712 +
Aip Aip07g02293 Chr07 95765247 95768356 +
Amo Amo17g1998 Chr17 102486801 102489817 +
Arst Arst8g00281 Chr8 4142312 4145216 -
Bva Bva06g01828 Chr06 12582593 12585521 +
Bva Bva10g01014 Chr10 7434771 7437595 -
Car Car05g03340 Chr05 78110522 78113448 -
Cca Cca07g00188 Chr07 2365158 2368257 +
Gma Gma04g00149 Chr04 1265567 1267819 +
Gma Gma06g00141 Chr06 1233770 1236583 +
Gso Gso4g0144 Chr4 1244151 1247032 +
Gso Gso4g0144 Chr4 1244151 1247032 +
Lal Lal4g0031 Chr4 182280 185072 +
Lal Lal21g0070 Chr21 498658 500406 +
Lan Lan14g0985 Chr14 16117474 16120000 -
Lan Lan14g0985 Chr14 16117474 16120000 -
Lja Lja1g2290 Chr1 26627922 26630710 -
Mal Mal2g0366 Chr2 3979196 3980953 +
Mtr Mtr3g4360 Chr3 57556912 57559945 -
Psa Psa5g0226 Chr5 16037865 16040717 +
Pvu Pvu9g0127 Chr9 1964558 1967427 -
Rops Rops10g02555 Chr10 44465775 44468710 -
Seca Seca4g00291 Chr4 4647759 4649531 +
Sto Sto5g0032 Chr5 206837 208585 +
Tpr Tpr7g0150 Chr7 1203101 1205893 +
Tsu Tsu07g00169 Chr07 1263105 1265625 +
Vian Vian4g02470 Chr4 41330754 41332493 -
Vifa Vifa2g04609 Chr2 1358051905 1358053671 -
Viun Viun9g03770 Chr9 42660310 42663339 -
Vra Vra5g1729 Chr5 23529488 23532653 -
Vvi Vvi18g0080 Chr18 731976 734573 -
Aed Aed9g0150 Chr9 1056297 1070635 -
Aev Aev08g0127 Chr08 702247 705064 -
Ahy Ahy17g2153 Chr17 103129733 103133688 -
Aip Aip07g02294 Chr07 95769215 95773101 -
Amo Amo17g1999 Chr17 102490692 102494643 -
Bva Bva06g01829 Chr06 12585922 12590022 -
Bva Bva10g01013 Chr10 7430498 7434547 +
Car Car05g03339 Chr05 78102971 78108060 +
Cca Cca07g00189 Chr07 2370173 2387649 -
Gma Gma04g00151 Chr04 1270942 1275841 -
Gma Gma06g00142 Chr06 1238977 1242210 -
Gso Gso4g0145 Chr4 1249595 1254483 -
Gso Gso4g0145 Chr4 1249595 1254483 -
Lal Lal4g0033 Chr4 185771 190084 -
Lal Lal21g0071 Chr21 502016 507152 -
Lan Lan14g0984 Chr14 16112472 16116920 +
Lan Lan14g0984 Chr14 16112472 16116920 +
Mal Mal2g0372 Chr2 4125105 4128812 -
Mtr Mtr3g4359 Chr3 57546539 57551132 +
Psa Psa5g0227 Chr5 16056435 16063108 -
Pvu Pvu9g0126 Chr9 1957569 1963159 +
Sto Sto5g0033 Chr5 209852 213122 -
Tpr Tpr7g0151 Chr7 1209506 1214451 -
Tsu Tsu07g00171 Chr07 1268271 1273450 -
Vra Vra5g1728 Chr5 23521847 23527389 +
Vvi Vvi18g0081 Chr18 740621 743630 -
Vvi Vvi18g0082 Chr18 746021 748732 +
Aev Aev08g0128 Chr08 706545 708360 +
Ahy Ahy17g2155 Chr17 103138148 103140006 +
Aip Aip07g02295 Chr07 95776789 95778765 +
Amo Amo17g2000 Chr17 102499284 102501229 +
Car Car05g03338 Chr05 78098571 78101901 -
Lal Lal4g0034 Chr4 190337 192728 +
Lan Lan14g0983 Chr14 16107586 16111484 -
Lja Lja1g2291 Chr1 26631705 26634658 +
Mal Mal2g0373 Chr2 4131525 4132741 +
Mtr Mtr3g4357 Chr3 57537479 57540414 -
Psa Psa5g0228 Chr5 16090707 16094610 +
Vvi Vvi18g0083 Chr18 750236 760004 -
Aev Aev08g0129 Chr08 709211 716183 -
Ahy Ahy17g2156 Chr17 103140455 103148448 -
Aip Aip07g02296 Chr07 95779654 95786719 -
Bva Bva06g01830 Chr06 12590649 12599683 -
Bva Bva10g01012 Chr10 7422415 7429977 +
Car Car05g03337 Chr05 78087112 78098301 +
Gma Gma04g00152 Chr04 1276914 1287411 -
Gma Gma06g00143 Chr06 1242218 1257503 -
Gso Gso4g0146 Chr4 1255576 1266079 -
Gso Gso4g0146 Chr4 1255576 1266079 -
Lal Lal4g0035 Chr4 193859 203141 -
Lal Lal21g0072 Chr21 508050 517311 -
Lan Lan14g0982 Chr14 16097234 16106819 +
Lan Lan14g0982 Chr14 16097234 16106819 +
Lasa Lasa5g04626 Chr5 681485219 681496217 +
Lja Lja1g2292 Chr1 26634837 26648438 -
Mal Mal2g0374 Chr2 4135085 4147156 -
Mtr Mtr3g4356 Chr3 57525545 57536936 +
Psa Psa5g0229 Chr5 16094886 16106218 -
Pvu Pvu9g0125 Chr9 1944820 1955924 +
Rops Rops10g02550 Chr10 44428655 44439773 +
Seca Seca4g00292 Chr4 4664465 4669288 -
Sto Sto9g3746 Chr9 35614611 35623678 +
Tpr Tpr7g0152 Chr7 1218576 1229275 -
Tsu Tsu07g00172 Chr07 1285200 1296689 -
Vian Vian4g02469 Chr4 41324201 41328535 +
Vifa Vifa2g04600 Chr2 1356718245 1356729467 +
Viun Viun9g03767 Chr9 42640229 42651052 +
Vvi Vvi18g0084 Chr18 761925 764099 -
Vvi Vvi18g0085 Chr18 764518 766080 -