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
Vvi18g0096 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0097 . . . . . . . . Aev08g0136 . Ahy17g2167 . Aip07g02313 . . . . . . . . . . . . . Bva06g01834 Bva10g01008 . Car05g03326 . . . . . . . . . . Gma04g00159 Gma06g00150 . . Gso4g0150 Gso4g0150 . . Lal4g0039 . . . . . Lan14g0978 . . . . . . . . . . . . . . . . . Lja1g3432 . . Mal2g0385 . . . . . . . Mtr3g4347 . . . . . . . Psa5g0231 . . . . . . . . . . . . . . . . . . Sto5g0041 . . Tpr7g0159 . . . Tsu07g00180 . . . . . . . . . . . .
Vvi18g0098 . . . . . . . Aed9g0158 Aev08g0137 . Ahy17g2168 . Aip07g02314 . . . . . . . . . . . . . Bva06g01835 Bva10g01007 . Car05g03325 . Cca07g00197 . . . . . . . . Gma04g00160 Gma06g00151 . . Gso4g0151 Gso4g0151 . . Lal4g0040 Lal17g0035 Lal21g0078 . . . Lan14g0976 Lan14g0976 Lan14g0976 . . . . . . . . . . . . . . . Lja1g3433 . . Mal2g0388 . . . . . . . Mtr3g4346 . . Phco7g00217 . . . . Psa5g0234 . . . . . . . . Pvu9g0115 . Rops10g02541 . . . . . . . Sto5g0042 . . Tpr7g0160 . . . Tsu07g00181 Vian4g02460 . Vifa2g04587 . . . Viun9g03757 . . . . Vra5g1717
Vvi18g0099 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0100 . . . . . . . Aed9g0159 Aev08g0140 . Ahy17g2169 . Aip07g02315 . . . Amo17g2020 . . . . . . . . . . Bva10g01006 . Car05g03324 . Cca07g00198 . . . . . . . . Gma04g00161 Gma06g00152 . . Gso4g0152 Gso4g0152 . . . Lal17g0036 Lal21g0079 . . . . . . . . . . . . . . . . . . . . . Lja1g3434 . . Mal2g0390 . . . . . . . Mtr3g4345 . . . . . . . . . . . . . . . . Pvu9g0114 . Rops10g02540 . . . . . . . . Sto9g3745 . Tpr7g0163 . . . Tsu07g00184 Vian4g02459 . Vifa2g04586 . . . Viun9g03755 . . . . Vra5g1716
Vvi18g0101 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g01836 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0044 . . . . . . . . . . . . . . . . . . .
Vvi18g0102 . . . . Adu08g00220 . Aed11g0007 Aed9g0160 . . Ahy17g2171 . Aip07g02318 . . . Amo17g2022 . Apr9g0694 . . . . Bach3g02483 . Bisa05g0516 Bva06g01837 Bva10g01005 . Car05g03323 Cca05g00430 Cca07g00199 . Dere05g2905 . . . . . . Gma04g00162 Gma06g00154 Gma14g02183 Gma17g02498 Gso4g0153 Gso4g0153 Gso4g0153 Gso4g0153 Lal4g0041 Lal17g0037 . . . . Lan14g0975 Lan14g0975 . . . . . . . Lasa5g04609 . . . . . Lele26g0022 . Lele28g0027 Lja1g3436 . . Mal2g0391 . . . . . . . Mtr3g4344 . . . Phco2g00013 . . . . . Pste8g01493 . . . . . Pumo9g00011 Pvu9g0113 Pvu1g0012 Rops10g02539 Rops9g02538 . . . Spst8g02086 Ssu5g0011 . Sto5g0046 . . Tpr7g0165 . . . Tsu07g00187 Vian4g02458 Vian7g00953 Vifa2g04585 . . . Viun9g03754 Viun8g00028 . Vivi3g00740 Vra6g1988 Vra5g1715
Vvi18g0103 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0104 . Acco05g3030 . Accr3g00029 . . . . . . . . . . . Alju07g2989 . . Apr9g0691 . . . . . . Bisa05g0518 Bva06g01839 Bva10g01004 . . Cca05g00429 . . Dere05g2900 . . . Enph7g1527 . Glsi10g0053 . . . . . . . . . . . . . . . . . . . . . Lapu8g01067 . . . . . . Lele25g0016 Lele26g0024 Lele27g2068 Lele28g0029 . Lja5g3362 . . . . . . . . . . . . . Phco2g00014 . Prci2g0034 . . . Pste8g01489 . . . . . Pumo9g00012 . Pvu1g0013 . Rops9g02539 . Seca8g04157 . Spst8g02084 Ssu5g0012 . Sto5g0049 . . . . . . . . Vian7g00952 . . . . . Viun8g00030 . . Vra6g1989 .
Vvi18g0105 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva06g01840 Bva10g01003 . . . . . . . . . . . . . . . . . . . . Lal4g0042 Lal17g0040 Lal21g0080 . . . Lan14g0974 Lan14g0974 Lan14g0974 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto9g3744 . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi18g0096 Chr18 838799 839295 +
Vvi Vvi18g0097 Chr18 852845 856255 +
Aev Aev08g0136 Chr08 748919 750842 +
Ahy Ahy17g2167 Chr17 103531705 103535241 +
Aip Aip07g02313 Chr07 96152181 96155514 +
Bva Bva06g01834 Chr06 12616419 12623813 +
Bva Bva10g01008 Chr10 7405764 7407540 -
Car Car05g03326 Chr05 77995021 77999040 -
Gma Gma04g00159 Chr04 1336274 1341076 +
Gma Gma06g00150 Chr06 1317737 1321168 +
Gso Gso4g0150 Chr4 1312153 1317232 +
Gso Gso4g0150 Chr4 1312153 1317232 +
Lal Lal4g0039 Chr4 224409 234426 +
Lan Lan14g0978 Chr14 16078037 16080971 -
Lja Lja1g3432 Chr1 42806155 42809467 +
Mal Mal2g0385 Chr2 4260140 4263310 +
Mtr Mtr3g4347 Chr3 57442313 57446284 -
Psa Psa5g0231 Chr5 16629896 16632855 +
Sto Sto5g0041 Chr5 256826 260523 +
Tpr Tpr7g0159 Chr7 1290650 1293429 +
Tsu Tsu07g00180 Chr07 1344010 1346417 +
Vvi Vvi18g0098 Chr18 874340 900898 +
Aed Aed9g0158 Chr9 1128332 1146371 +
Aev Aev08g0137 Chr08 761736 774831 +
Ahy Ahy17g2168 Chr17 103568457 103582721 +
Aip Aip07g02314 Chr07 96185196 96200432 +
Bva Bva06g01835 Chr06 12625453 12639394 +
Bva Bva10g01007 Chr10 7387663 7402209 -
Car Car05g03325 Chr05 77960612 77976974 -
Cca Cca07g00197 Chr07 2520013 2534128 +
Gma Gma04g00160 Chr04 1355663 1372286 +
Gma Gma06g00151 Chr06 1336522 1352857 +
Gso Gso4g0151 Chr4 1332816 1349926 +
Gso Gso4g0151 Chr4 1332816 1349926 +
Lal Lal4g0040 Chr4 235925 253931 +
Lal Lal17g0035 Chr17 204538 218606 +
Lal Lal21g0078 Chr21 543303 557757 +
Lan Lan14g0976 Chr14 16053163 16068278 -
Lan Lan14g0976 Chr14 16053163 16068278 -
Lan Lan14g0976 Chr14 16053163 16068278 -
Lja Lja1g3433 Chr1 42823261 42838380 +
Mal Mal2g0388 Chr2 4309028 4328470 +
Mtr Mtr3g4346 Chr3 57411916 57429376 -
Phco Phco7g00217 Chr7 1455230 1462155 +
Psa Psa5g0234 Chr5 16746294 16762618 +
Pvu Pvu9g0115 Chr9 1841055 1856731 -
Rops Rops10g02541 Chr10 44261442 44278559 -
Sto Sto5g0042 Chr5 273469 287185 +
Tpr Tpr7g0160 Chr7 1301958 1318343 +
Tsu Tsu07g00181 Chr07 1360856 1378160 +
Vian Vian4g02460 Chr4 41204741 41227245 -
Vifa Vifa2g04587 Chr2 1350962538 1350979272 -
Viun Viun9g03757 Chr9 42541596 42555526 -
Vra Vra5g1717 Chr5 23429157 23445058 -
Vvi Vvi18g0099 Chr18 908791 913154 -
Vvi Vvi18g0100 Chr18 914534 922232 -
Aed Aed9g0159 Chr9 1147623 1152356 -
Aev Aev08g0140 Chr08 782035 785319 -
Ahy Ahy17g2169 Chr17 103607837 103612203 -
Aip Aip07g02315 Chr07 96225661 96229262 -
Amo Amo17g2020 Chr17 103303247 103307262 +
Bva Bva10g01006 Chr10 7382549 7386436 +
Car Car05g03324 Chr05 77952376 77957262 +
Cca Cca07g00198 Chr07 2545944 2549127 -
Gma Gma04g00161 Chr04 1377965 1381864 -
Gma Gma06g00152 Chr06 1358079 1361897 -
Gso Gso4g0152 Chr4 1355039 1359799 -
Gso Gso4g0152 Chr4 1355039 1359799 -
Lal Lal17g0036 Chr17 218903 223412 -
Lal Lal21g0079 Chr21 558009 566013 -
Lja Lja1g3434 Chr1 42839295 42844829 -
Mal Mal2g0390 Chr2 4335535 4342029 -
Mtr Mtr3g4345 Chr3 57386550 57391906 +
Pvu Pvu9g0114 Chr9 1825157 1829690 +
Rops Rops10g02540 Chr10 44243547 44248071 +
Sto Sto9g3745 Chr9 35609846 35613216 +
Tpr Tpr7g0163 Chr7 1331547 1336982 -
Tsu Tsu07g00184 Chr07 1387891 1388364 -
Vian Vian4g02459 Chr4 41198517 41202342 +
Vifa Vifa2g04586 Chr2 1350084238 1350087503 +
Viun Viun9g03755 Chr9 42534649 42539424 +
Vra Vra5g1716 Chr5 23422183 23427061 +
Vvi Vvi18g0101 Chr18 922254 925402 -
Bva Bva06g01836 Chr06 12639115 12643338 -
Sto Sto5g0044 Chr5 290182 293270 -
Vvi Vvi18g0102 Chr18 927547 931993 -
Adu Adu08g00220 Chr08 3697817 3701715 +
Aed Aed11g0007 Chr11 45467 48095 -
Aed Aed9g0160 Chr9 1157260 1161552 -
Ahy Ahy17g2171 Chr17 104005408 104009327 -
Aip Aip07g02318 Chr07 96602552 96607122 -
Amo Amo17g2022 Chr17 103344330 103348591 -
Apr Apr9g0694 Chr9 11545433 11548789 +
Bach Bach3g02483 Chr3 30853740 30857533 +
Bisa Bisa05g0516 Chr05 8467601 8472620 -
Bva Bva06g01837 Chr06 12644364 12648609 -
Bva Bva10g01005 Chr10 7375136 7379660 +
Car Car05g03323 Chr05 77934999 77940257 +
Cca Cca05g00430 Chr05 9443100 9447317 +
Cca Cca07g00199 Chr07 2558175 2561021 -
Dere Dere05g2905 Chr05 39537342 39542200 +
Gma Gma04g00162 Chr04 1391515 1395367 -
Gma Gma06g00154 Chr06 1370534 1375733 -
Gma Gma14g02183 Chr14 52976765 52979584 +
Gma Gma17g02498 Chr17 42995059 42998371 +
Gso Gso4g0153 Chr4 1368094 1372240 -
Gso Gso4g0153 Chr4 1368094 1372240 -
Gso Gso4g0153 Chr4 1368094 1372240 -
Gso Gso4g0153 Chr4 1368094 1372240 -
Lal Lal4g0041 Chr4 251430 255006 -
Lal Lal17g0037 Chr17 224063 236038 -
Lan Lan14g0975 Chr14 16047442 16051781 +
Lan Lan14g0975 Chr14 16047442 16051781 +
Lasa Lasa5g04609 Chr5 678910165 678913345 +
Lele Lele26g0022 Chr26 134914 138415 -
Lele Lele28g0027 Chr28 135007 138555 -
Lja Lja1g3436 Chr1 42855554 42861436 -
Mal Mal2g0391 Chr2 4355284 4359107 -
Mtr Mtr3g4344 Chr3 57373603 57377964 +
Phco Phco2g00013 Chr2 156032 158324 -
Pste Pste8g01493 Chr8 8176582 8179649 +
Pumo Pumo9g00011 Chr9 235838 238521 -
Pvu Pvu9g0113 Chr9 1799040 1803479 +
Pvu Pvu1g0012 Chr1 181478 184265 -
Rops Rops10g02539 Chr10 44212908 44221814 +
Rops Rops9g02538 Chr9 47612048 47615919 -
Spst Spst8g02086 Chr8 28972755 28975047 +
Ssu Ssu5g0011 Chr5 169597 170995 -
Sto Sto5g0046 Chr5 294933 297904 -
Tpr Tpr7g0165 Chr7 1354895 1359464 -
Tsu Tsu07g00187 Chr07 1408888 1413841 -
Vian Vian4g02458 Chr4 41186674 41190529 +
Vian Vian7g00953 Chr7 17712424 17714684 +
Vifa Vifa2g04585 Chr2 1349428879 1349433045 +
Viun Viun9g03754 Chr9 42522771 42527098 +
Viun Viun8g00028 Chr8 169039 171542 -
Vivi Vivi3g00740 Chr3 12304132 12308440 +
Vra Vra6g1988 Chr6 36580493 36583201 -
Vra Vra5g1715 Chr5 23411711 23415959 +
Vvi Vvi18g0103 Chr18 933926 934111 -
Vvi Vvi18g0104 Chr18 938209 944601 +
Acco Acco05g3030 Chr05 44742364 44749510 -
Accr Accr3g00029 Chr3 391378 397044 +
Alju Alju07g2989 Chr07 54909337 54917205 -
Apr Apr9g0691 Chr9 11422636 11429306 -
Bisa Bisa05g0518 Chr05 8486634 8492987 +
Bva Bva06g01839 Chr06 12654611 12660546 +
Bva Bva10g01004 Chr10 7364675 7372681 -
Cca Cca05g00429 Chr05 9422701 9430349 -
Dere Dere05g2900 Chr05 39502352 39506380 -
Enph Enph7g1527 Chr7 20397808 20405850 -
Glsi Glsi10g0053 Chr10 456556 467324 +
Lapu Lapu8g01067 Chr8 28646670 28653838 -
Lele Lele25g0016 Chr25 111911 117330 +
Lele Lele26g0024 Chr26 147892 153306 +
Lele Lele27g2068 Chr27 24582563 24596588 -
Lele Lele28g0029 Chr28 151255 157164 +
Lja Lja5g3362 Chr5 65729165 65736874 -
Phco Phco2g00014 Chr2 160782 166933 +
Prci Prci2g0034 Chr2 306228 312647 +
Pste Pste8g01489 Chr8 8157371 8158129 -
Pumo Pumo9g00012 Chr9 245057 252763 +
Pvu Pvu1g0013 Chr1 186295 192859 +
Rops Rops9g02539 Chr9 47618240 47629822 +
Seca Seca8g04157 Chr8 118550286 118556856 -
Spst Spst8g02084 Chr8 28868356 28872098 -
Ssu Ssu5g0012 Chr5 180288 187210 +
Sto Sto5g0049 Chr5 306947 311990 +
Vian Vian7g00952 Chr7 17703078 17708726 -
Viun Viun8g00030 Chr8 174831 181583 +
Vra Vra6g1989 Chr6 36587396 36593976 +
Vvi Vvi18g0105 Chr18 945540 948286 -
Bva Bva06g01840 Chr06 12661223 12663392 -
Bva Bva10g01003 Chr10 7362233 7364564 +
Lal Lal4g0042 Chr4 256130 258044 -
Lal Lal17g0040 Chr17 248246 250820 -
Lal Lal21g0080 Chr21 566678 569707 -
Lan Lan14g0974 Chr14 16043195 16046005 +
Lan Lan14g0974 Chr14 16043195 16046005 +
Lan Lan14g0974 Chr14 16043195 16046005 +
Sto Sto9g3744 Chr9 35604178 35606156 +