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
Vvi16g1099 Acco09g1935 . Accr7g00232 . Adu08g00471 . . . . . Ahy15g3637 Ahy16g2731 Aip05g03950 Aip06g03077 Alju08g0276 . . . . . Arst8g00602 . Bach12g00944 . Bisa09g0965 . Bva12g01991 Bva06g02945 . . . . Dere04g1173 . . . Enph1g1794 . Glsi08g1001 . . . . . . . . . . . . . . . . . . . . . Lapu9g01384 . Lasa5g02963 . Lele01g0222 Lele02g0219 Lele03g0229 Lele44g0178 . . . . . Lja1g5742 . . Mepo3g06504 . Mesa9g04027 . Mibi05g0230 . . . Phac9g01076 . Phco7g01383 . Prci15g0337 . . Psa6g0903 . . . . . . Pumo10g01365 . Pvu9g1416 . Rops10g02051 . Seca4g02504 . Spst9g01424 . . . . Sto5g1224 . . Trre5g03785 . . . Vian4g01418 . Vifa2g02760 . Vimu10g02429 . Viun9g02244 . Vivi3g02899 . . .
Vvi16g1100 Acco10g2501 . Accr4g00272 . Adu08g00472 . . . . . . . . . Alju08g0277 . . . . . Arst8g00603 . Bach12g00943 . . . Bva12g01992 Bva06g02944 . . . . . . . . Enph1g1793 . Glsi08g1003 . . . . . . . . . . Lal4g0465 . . . . . . . . . . Lapu9g01385 . . . . . . . . . . . . Lja1g5743 . . . . . . . . . . . . Phco7g01379 . Prci15g0339 . . Psa6g0894 Pste2g03370 . . . . . . . Pvu9g1415 . . . . . Spst9g01423 . . . . . . . . . . . . . . . Vimu10g02428 . . . Vivi4g04668 . . .
Vvi16g1101 . . . . . . . . . . . Ahy16g2732 . Aip06g03078 . . . Amo16g3458 . . . . . . . . Bva12g01994 Bva06g02943 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g5744 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1102 . . . . . . . Aed11g1762 . . . . . Aip06g03080 . . . . . . . . . . . . Bva12g01995 Bva06g02941 . . . Cca06g01838 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g5746 . . . . . . . . . . . . . . . . Psa5g1887 . . . . . . . . . . . . . . . . . . Ssu2g2920 . . . . . . . . . . . . . . . . . . . Vra11g0239
Vvi16g1103 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva12g01996 Bva06g02940 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr6g1198 . . . . . . Psa5g1886 . . . . . . . . . . Pvu1g0341 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g1104 . . Accr4g00276 . Adu08g00476 . . . . . . . . . . . . . . . Arst8g00608 . Bach12g00939 . Bisa09g0968 . Bva12g01997 Bva06g02939 . . . . Dere04g1170 . . . . . Glsi08g1007 . . . . . . . . . . . . . . . . . . . . . Lapu9g01388 . Lasa5g02957 . . Lele02g0221 Lele03g0232 Lele04g0225 . . . . . . . . Mepo3g06500 . Mesa9g04019 . . . . . . . Phco7g01376 . Prci15g0345 . Psa5g1884 . Pste2g03361 . . . . . Pumo10g01361 . Pvu9g1413 . Rops10g02045 . Seca4g02498 . Spst9g01419 . . . . . . . Trre5g03772 . . . Vian4g01423 . Vifa2g02768 . Vimu10g02422 . Viun9g02255 . Vivi3g02908 . . .
Vvi16g1105 Acco10g2497 . Accr4g00278 . Adu08g00477 . . . . . . . . . Alju08g0280 . . . . . Arst8g00609 . . . Bisa09g0969 . Bva12g01998 . . . . . Dere04g1169 . . . Enph1g1789 . Glsi08g1008 . . . . . . . . . . . . . . . . . . . . . Lapu9g01389 . Lasa5g02956 . Lele01g0227 Lele02g0222 Lele03g0233 Lele04g0226 . . . . . . . . Mepo3g06498 . Mesa9g04018 . Mibi05g0233 . . . . . Phco7g01375 . Prci15g0346 . Psa5g1883 . Pste2g03360 . . . . . Pumo10g01360 . Pvu9g1412 . Rops10g02044 . Seca4g02497 . Spst9g01418 . . . . . . . Trre5g03770 . . . Vian4g01424 . Vifa2g02770 . Vimu10g02421 . Viun9g02256 . Vivi3g02909 . . .
Vvi16g1106 . . . . . . Aed1g2333 Aed7g0687 . Aev09g2153 . Ahy19g2841 . Aip09g03301 . . . Amo19g3613 . Apr6g0605 . . . . . . . . . . Cca02g02186 Cca08g00770 . . . Dod06g0867 . . . . Gma10g02165 . . . Gso10g2031 . . . . . . . Lal12g0077 . . . . . . . . . . . . . . . . . . . Lja2g2745 . Mal1g2133 . . . . . . . Mtr1g3675 . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto10g2251 . Tpr1g0829 . . . Tsu01g04343 . . . . . . . . . . . . .
Vvi16g1107 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva12g01985 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g0893 . . . . . . . . . . . . . . . . . . Sto9g2783 . . . . . . . . . . . . . . . . . . .
Vvi16g1108 . . . . . . . . Aev08g0833 . Ahy17g2647 . Aip07g02869 . . . . . Apr1g0706 . . . . . . . Bva12g01984 . . . . . . . . . . . . . . . . . . . . . . Lal4g0468 . . . . . . . . . . . . . . . . . . . . . . Lja1g4886 . . . . . . . . . . . . . . . . . Psa5g1866 Psa6g0892 . . . . . . . . . . . . . . . . . . Sto9g2781 Sto5g1231 . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Aed Aed11g1762 Chr11 21083873 21086467 +
Cca Cca06g01838 Chr06 33788656 33792072 +
Ssu Ssu2g2920 Chr2 90532465 90535121 +
Vra Vra11g0239 Chr11 1624094 1627199 -
Aed Aed11g1762 Chr11 21083873 21086467 +
Cca Cca06g01838 Chr06 33788656 33792072 +
Ssu Ssu2g2920 Chr2 90532465 90535121 +
Vra Vra11g0239 Chr11 1624094 1627199 -
Psa Psa6g0894 Chr6 33238546 33241824 +
Vvi Vvi16g1099 Chr16 19332709 19333734 -
Acco Acco09g1935 Chr09 36311179 36312096 -
Accr Accr7g00232 Chr7 2977420 2978325 +
Adu Adu08g00471 Chr08 8566085 8568237 -
Ahy Ahy15g3637 Chr15 159142107 159143278 +
Ahy Ahy16g2731 Chr16 139891918 139893098 -
Aip Aip05g03950 Chr05 147779824 147780927 -
Aip Aip06g03077 Chr06 125805986 125806933 -
Alju Alju08g0276 Chr08 2019265 2020317 -
Arst Arst8g00602 Chr8 8537885 8540052 -
Bach Bach12g00944 Chr12 6686867 6687964 +
Bisa Bisa09g0965 Chr09 14097269 14098345 -
Bva Bva12g01991 Chr12 15759007 15760879 -
Bva Bva06g02945 Chr06 18341741 18343647 +
Dere Dere04g1173 Chr04 13106282 13107364 +
Enph Enph1g1794 Chr1 42930846 42931952 +
Glsi Glsi08g1001 Chr08 7417693 7418751 -
Lapu Lapu9g01384 Chr9 28081520 28083478 -
Lasa Lasa5g02963 Chr5 521918454 521919548 +
Lele Lele01g0222 Chr01 1269962 1271008 -
Lele Lele02g0219 Chr02 1220601 1221647 -
Lele Lele03g0229 Chr03 1245446 1247984 -
Lele Lele44g0178 Chr44 1105169 1106074 +
Lja Lja1g5742 Chr1 101912952 101914225 -
Mepo Mepo3g06504 Chr3 79020823 79022713 +
Mesa Mesa9g04027 Chr9 72729256 72730344 +
Mibi Mibi05g0230 Chr05 2363941 2364915 -
Phac Phac9g01076 Chr9 8230034 8232264 +
Phco Phco7g01383 Chr7 12553353 12554378 +
Prci Prci15g0337 Chr15 2235618 2237514 -
Psa Psa6g0903 Chr6 33933724 33937010 +
Pumo Pumo10g01365 Chr10 18125628 18127654 +
Pvu Pvu9g1416 Chr9 20103112 20105454 +
Rops Rops10g02051 Chr10 37301735 37303504 +
Seca Seca4g02504 Chr4 42785226 42786293 +
Spst Spst9g01424 Chr9 14184463 14185485 +
Sto Sto5g1224 Chr5 8244548 8246140 +
Trre Trre5g03785 Chr5 38138360 38139445 +
Vian Vian4g01418 Chr4 28643281 28644300 -
Vifa Vifa2g02760 Chr2 764142945 764144021 -
Vimu Vimu10g02429 Chr10 35240164 35243409 +
Viun Viun9g02244 Chr9 31904161 31906101 -
Vivi Vivi3g02899 Chr3 48351930 48353866 -
Vvi Vvi16g1100 Chr16 19347350 19354221 -
Acco Acco10g2501 Chr10 36273207 36276626 +
Accr Accr4g00272 Chr4 2731997 2734095 -
Adu Adu08g00472 Chr08 8601257 8604252 -
Alju Alju08g0277 Chr08 2033993 2039395 -
Arst Arst8g00603 Chr8 8573255 8575990 -
Bach Bach12g00943 Chr12 6672979 6675507 +
Bva Bva12g01992 Chr12 15769983 15772997 -
Bva Bva06g02944 Chr06 18332392 18334479 +
Enph Enph1g1793 Chr1 42914881 42918184 +
Glsi Glsi08g1003 Chr08 7435332 7438228 -
Lal Lal4g0465 Chr4 3276171 3279271 +
Lapu Lapu9g01385 Chr9 28106201 28109784 -
Lja Lja1g5743 Chr1 101984869 101987952 -
Phco Phco7g01379 Chr7 12521140 12525360 +
Prci Prci15g0339 Chr15 2253533 2256246 -
Psa Psa6g0894 Chr6 33238546 33241824 +
Pste Pste2g03370 Chr2 33756853 33759968 +
Pvu Pvu9g1415 Chr9 20074794 20077719 +
Spst Spst9g01423 Chr9 14154520 14156849 +
Vimu Vimu10g02428 Chr10 35208579 35213783 +
Vivi Vivi4g04668 Chr4 174959181 174963463 -
Vvi Vvi16g1101 Chr16 19358677 19364731 +
Ahy Ahy16g2732 Chr16 139924008 139927030 +
Aip Aip06g03078 Chr06 125837239 125840311 +
Amo Amo16g3458 Chr16 143530428 143534072 +
Bva Bva12g01994 Chr12 15792513 15793907 +
Bva Bva06g02943 Chr06 18329132 18331905 -
Lja Lja1g5744 Chr1 101993516 102002672 +
Vvi Vvi16g1102 Chr16 19366109 19368456 -
Aed Aed11g1762 Chr11 21083873 21086467 +
Aip Aip06g03080 Chr06 125855325 125858627 -
Bva Bva12g01995 Chr12 15794277 15797593 -
Bva Bva06g02941 Chr06 18325511 18329080 +
Cca Cca06g01838 Chr06 33788656 33792072 +
Lja Lja1g5746 Chr1 102039078 102042862 -
Psa Psa5g1887 Chr5 145367084 145369977 +
Ssu Ssu2g2920 Chr2 90532465 90535121 +
Vra Vra11g0239 Chr11 1624094 1627199 -
Vvi Vvi16g1103 Chr16 19382475 19386092 +
Bva Bva12g01996 Chr12 15800929 15803972 +
Bva Bva06g02940 Chr06 18320399 18325916 -
Mtr Mtr6g1198 Chr6 16828538 16833849 +
Psa Psa5g1886 Chr5 145263296 145266351 -
Pvu Pvu1g0341 Chr1 3243584 3245323 +
Vvi Vvi16g1104 Chr16 19388296 19394147 +
Accr Accr4g00276 Chr4 2748112 2749390 +
Adu Adu08g00476 Chr08 8618876 8620725 +
Arst Arst8g00608 Chr8 8590479 8592836 +
Bach Bach12g00939 Chr12 6655184 6657499 -
Bisa Bisa09g0968 Chr09 14164283 14167324 +
Bva Bva12g01997 Chr12 15804395 15806596 +
Bva Bva06g02939 Chr06 18313239 18315689 -
Dere Dere04g1170 Chr04 13070852 13074161 -
Glsi Glsi08g1007 Chr08 7453657 7457564 +
Lapu Lapu9g01388 Chr9 28129143 28131787 +
Lasa Lasa5g02957 Chr5 520978566 520981628 -
Lele Lele02g0221 Chr02 1239636 1249545 +
Lele Lele03g0232 Chr03 1265724 1272339 +
Lele Lele04g0225 Chr04 1341921 1344543 +
Mepo Mepo3g06500 Chr3 78974086 78977530 -
Mesa Mesa9g04019 Chr9 72615413 72628707 -
Phco Phco7g01376 Chr7 12488431 12491000 -
Prci Prci15g0345 Chr15 2272921 2277439 +
Psa Psa5g1884 Chr5 145110231 145114554 -
Pste Pste2g03361 Chr2 33683958 33688297 -
Pumo Pumo10g01361 Chr10 18066605 18069806 -
Pvu Pvu9g1413 Chr9 20048833 20051762 -
Rops Rops10g02045 Chr10 37091269 37093903 -
Seca Seca4g02498 Chr4 42634813 42638801 -
Spst Spst9g01419 Chr9 14111561 14114080 -
Trre Trre5g03772 Chr5 37806076 37809573 -
Vian Vian4g01423 Chr4 28713131 28716494 +
Vifa Vifa2g02768 Chr2 768171802 768174293 +
Vimu Vimu10g02422 Chr10 35172570 35175202 -
Viun Viun9g02255 Chr9 31952447 31955422 +
Vivi Vivi3g02908 Chr3 48486309 48490092 +
Vvi Vvi16g1105 Chr16 19396056 19401522 -
Acco Acco10g2497 Chr10 36250027 36256928 +
Accr Accr4g00278 Chr4 2753584 2757978 -
Adu Adu08g00477 Chr08 8621780 8624955 -
Alju Alju08g0280 Chr08 2057633 2063806 -
Arst Arst8g00609 Chr8 8593577 8596756 -
Bisa Bisa09g0969 Chr09 14169011 14174243 -
Bva Bva12g01998 Chr12 15806912 15812411 -
Dere Dere04g1169 Chr04 13062550 13068358 +
Enph Enph1g1789 Chr1 42883739 42888888 +
Glsi Glsi08g1008 Chr08 7458532 7463014 -
Lapu Lapu9g01389 Chr9 28132019 28138450 -
Lasa Lasa5g02956 Chr5 520831302 520836274 +
Lele Lele01g0227 Chr01 1301138 1305225 -
Lele Lele02g0222 Chr02 1251279 1255482 -
Lele Lele03g0233 Chr03 1273029 1277398 -
Lele Lele04g0226 Chr04 1347091 1353503 -
Mepo Mepo3g06498 Chr3 78966414 78972573 +
Mesa Mesa9g04018 Chr9 72606435 72612500 +
Mibi Mibi05g0233 Chr05 2398447 2403331 -
Phco Phco7g01375 Chr7 12481219 12487658 +
Prci Prci15g0346 Chr15 2278333 2283788 -
Psa Psa5g1883 Chr5 145051996 145062407 +
Pste Pste2g03360 Chr2 33676427 33682267 +
Pumo Pumo10g01360 Chr10 18060056 18065629 +
Pvu Pvu9g1412 Chr9 20041941 20048705 +
Rops Rops10g02044 Chr10 37083332 37089034 +
Seca Seca4g02497 Chr4 42628006 42633716 +
Spst Spst9g01418 Chr9 14104484 14111314 +
Trre Trre5g03770 Chr5 37780583 37784827 +
Vian Vian4g01424 Chr4 28717287 28723799 -
Vifa Vifa2g02770 Chr2 768641685 768647476 -
Vimu Vimu10g02421 Chr10 35162620 35168899 +
Viun Viun9g02256 Chr9 31955514 31962514 -
Vivi Vivi3g02909 Chr3 48492233 48502276 -
Vvi Vvi16g1106 Chr16 19448471 19454630 +
Aed Aed1g2333 Chr1 19357236 19365243 -
Aed Aed7g0687 Chr7 5085837 5092814 +
Aev Aev09g2153 Chr09 24522535 24529543 +
Ahy Ahy19g2841 Chr19 150663971 150670978 +
Aip Aip09g03301 Chr09 139399122 139406574 +
Amo Amo19g3613 Chr19 151077732 151084541 +
Apr Apr6g0605 Chr6 8694827 8704556 +
Cca Cca02g02186 Chr02 42369751 42378280 +
Cca Cca08g00770 Chr08 15100864 15111159 +
Dod Dod06g0867 Chr06 10794990 10800863 -
Gma Gma10g02165 Chr10 49206867 49213858 +
Gso Gso10g2031 Chr10 47325283 47333176 +
Lal Lal12g0077 Chr12 497529 504390 -
Lja Lja2g2745 Chr2 41384745 41400799 +
Mal Mal1g2133 Chr1 27914086 27919995 -
Mtr Mtr1g3675 Chr1 48453841 48461146 +
Sto Sto10g2251 Chr10 32583747 32594368 +
Tpr Tpr1g0829 Chr1 6901733 6909134 -
Tsu Tsu01g04343 Chr01 51383987 51390997 +
Vvi Vvi16g1107 Chr16 19457067 19462545 +
Bva Bva12g01985 Chr12 15725589 15730492 -
Psa Psa6g0893 Chr6 33192732 33202582 -
Sto Sto9g2783 Chr9 29541386 29546215 -
Vvi Vvi16g1108 Chr16 19472593 19474275 +
Aev Aev08g0833 Chr08 4872983 4875065 -
Ahy Ahy17g2647 Chr17 123373954 123377228 -
Aip Aip07g02869 Chr07 114604499 114607748 -
Apr Apr1g0706 Chr1 8423092 8425155 -
Bva Bva12g01984 Chr12 15717320 15719054 -
Lal Lal4g0468 Chr4 3298576 3301585 +
Lja Lja1g4886 Chr1 66899493 66901760 -
Psa Psa5g1866 Chr5 143221696 143225516 +
Psa Psa6g0892 Chr6 33102149 33103869 -
Sto Sto9g2781 Chr9 29534508 29536115 -
Sto Sto5g1231 Chr5 8296218 8300105 +