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
Vvi18g0156 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0157 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0158 . . . . . . . . Aev08g0159 . Ahy17g2211 . Aip07g02365 . . . Amo17g2076 . . . . . . . . . Bva06g01863 . . . . Cca07g00225 . . . . . . . . Gma04g00186 Gma06g00176 . . Gso4g0177 Gso4g0177 . . . . Lal21g0094 . . . . . . . . . . . . . . . . . . . . . Lja1g3460 . . Mal2g0424 . . . . . . . Mtr3g4319 . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0079 . . . . . . Tsu07g00219 . . . . . . . . . . . .
Vvi18g0159 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0080 . . . . . . . . . . . . . . . . . . .
Vvi18g0160 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0161 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car04g03039 . . . . . . . . . . . . . . . . . . . . Lal17g0510 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa5g1436 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0162 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0163 . . . . Adu08g00195 . . Aed9g0184 Aev08g0161 . Ahy17g2213 . Aip07g02366 . . . Amo17g2078 . . . Arst8g00232 . Bach12g00056 . . . Bva06g01864 Bva10g00976 . Car05g03301 . Cca07g00226 . . . . . . . . Gma04g00187 . . . Gso4g0178 . . . Lal4g0441 Lal17g0047 . . . . . . . . . . . . Lasa5g04583 . . . . . . . . . . . . Mal2g0425 Mepo3g07810 . Mesa9g05550 . . . . Mtr3g4318 . . Phco7g00240 . . . . . Pste2g02929 . . . . . . . Pvu9g0214 . Rops10g02515 . Seca4g00352 . . . . . Sto5g0081 . . Tpr7g0188 Trre5g05736 . . Tsu07g00221 Vian4g02435 . Vifa2g04547 . Vimu10g03533 . Viun9g03723 . Vivi3g00676 . . Vra5g1694
Vvi18g0164 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g0165 . Acco05g3005 . Accr3g00055 . Adu06g01318 Aed11g0017 . . Aev07g0654 . Ahy16g0028 . Aip06g00021 . Alju07g2964 . . Apr9g0681 . . Arst6g01741 . . . Bisa05g0564 . . Car04g03616 . Cca05g00419 . . Dere05g2859 . Dod08g2316 . Enph7g1508 . Glsi10g0087 . . Gma14g01478 . . . . . . . . . . . . . . . . . . Lapu8g01058 . Lasa6g00329 . . . . Lele25g0044 Lele26g0053 . Lele28g0052 . Lja5g3352 Mal1g6146 . . Mepo4g01937 . Mesa1g00019 . Mibi08g2634 Mtr1g0757 . . Phac1g00007 . Phco2g00024 . Prci2g0065 . . . . . . . . . Pumo9g00024 . Pvu1g0023 . Rops9g02563 . Seca8g04121 . Spst8g02063 Ssu5g0026 . . . Tpr1g3911 . . Trre1g00026 Tsu01g00162 . . Vian7g00942 . . . . . Viun8g00049 . Vivi4g05967 Vra6g1998 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Car Car04g03039 Chr04 58301880 58304742 +
Psa Psa5g1436 Chr5 111328671 111331890 +
Vvi Vvi18g0156 Chr18 1431364 1433475 +
Vvi Vvi18g0157 Chr18 1434124 1435914 +
Vvi Vvi18g0158 Chr18 1440188 1440625 +
Aev Aev08g0159 Chr08 913339 914496 +
Ahy Ahy17g2211 Chr17 105892916 105894549 +
Aip Aip07g02365 Chr07 98373094 98374509 +
Amo Amo17g2076 Chr17 106014025 106015554 +
Bva Bva06g01863 Chr06 12773784 12775112 +
Cca Cca07g00225 Chr07 2891348 2893220 +
Gma Gma04g00186 Chr04 1594776 1596507 +
Gma Gma06g00176 Chr06 1551737 1552226 +
Gso Gso4g0177 Chr4 1567758 1569391 +
Gso Gso4g0177 Chr4 1567758 1569391 +
Lal Lal21g0094 Chr21 643261 644454 +
Lja Lja1g3460 Chr1 43103311 43109218 +
Mal Mal2g0424 Chr2 4697037 4698304 -
Mtr Mtr3g4319 Chr3 57115821 57118213 +
Sto Sto5g0079 Chr5 501814 505192 +
Tsu Tsu07g00219 Chr07 1636941 1637255 -
Vvi Vvi18g0159 Chr18 1443190 1444174 -
Sto Sto5g0080 Chr5 506266 506887 -
Vvi Vvi18g0160 Chr18 1446646 1449144 -
Vvi Vvi18g0161 Chr18 1449246 1451159 -
Car Car04g03039 Chr04 58301880 58304742 +
Lal Lal17g0510 Chr17 3530514 3532379 -
Psa Psa5g1436 Chr5 111328671 111331890 +
Vvi Vvi18g0162 Chr18 1451426 1451971 -
Vvi Vvi18g0163 Chr18 1453418 1455706 +
Adu Adu08g00195 Chr08 3162313 3164472 -
Aed Aed9g0184 Chr9 1328819 1330641 +
Aev Aev08g0161 Chr08 918072 919982 +
Ahy Ahy17g2213 Chr17 106192065 106195203 +
Aip Aip07g02366 Chr07 98668250 98671286 +
Amo Amo17g2078 Chr17 106301653 106304218 +
Arst Arst8g00232 Chr8 3173970 3177076 -
Bach Bach12g00056 Chr12 410967 412590 +
Bva Bva06g01864 Chr06 12777567 12779554 +
Bva Bva10g00976 Chr10 7200971 7203463 -
Car Car05g03301 Chr05 77713723 77715948 -
Cca Cca07g00226 Chr07 2900371 2902860 +
Gma Gma04g00187 Chr04 1599400 1601946 +
Gso Gso4g0178 Chr4 1572403 1574868 +
Lal Lal4g0441 Chr4 3072338 3076704 +
Lal Lal17g0047 Chr17 281122 283895 +
Lasa Lasa5g04583 Chr5 676060623 676062302 +
Mal Mal2g0425 Chr2 4702427 4704348 +
Mepo Mepo3g07810 Chr3 91212500 91214889 +
Mesa Mesa9g05550 Chr9 90976709 90978594 -
Mtr Mtr3g4318 Chr3 57096499 57099100 -
Phco Phco7g00240 Chr7 1634888 1636762 +
Pste Pste2g02929 Chr2 29270314 29278363 +
Pvu Pvu9g0214 Chr9 4119072 4121600 -
Rops Rops10g02515 Chr10 43888351 43901956 -
Seca Seca4g00352 Chr4 5696718 5699668 +
Sto Sto5g0081 Chr5 510680 514298 +
Tpr Tpr7g0188 Chr7 1569184 1571861 +
Trre Trre5g05736 Chr5 57301891 57303794 -
Tsu Tsu07g00221 Chr07 1647346 1649430 +
Vian Vian4g02435 Chr4 40980534 40982463 -
Vifa Vifa2g04547 Chr2 1337580543 1337582338 -
Vimu Vimu10g03533 Chr10 44922107 44924043 -
Viun Viun9g03723 Chr9 42343217 42345643 -
Vivi Vivi3g00676 Chr3 11318064 11320212 -
Vra Vra5g1694 Chr5 23242050 23244371 -
Vvi Vvi18g0164 Chr18 1457918 1459889 -
Vvi Vvi18g0165 Chr18 1461375 1462209 -
Acco Acco05g3005 Chr05 44573955 44574783 -
Accr Accr3g00055 Chr3 737535 738367 +
Adu Adu06g01318 Chr06 18024809 18026106 -
Aed Aed11g0017 Chr11 138858 140040 +
Aev Aev07g0654 Chr07 4118688 4120475 +
Ahy Ahy16g0028 Chr16 282961 283992 +
Aip Aip06g00021 Chr06 191752 192982 +
Alju Alju07g2964 Chr07 54656023 54657824 -
Apr Apr9g0681 Chr9 11142719 11143807 -
Arst Arst6g01741 Chr6 18058300 18059377 -
Bisa Bisa05g0564 Chr05 9268578 9271299 +
Car Car04g03616 Chr04 65596144 65597475 -
Cca Cca05g00419 Chr05 9083799 9084834 -
Dere Dere05g2859 Chr05 39192179 39193001 -
Dod Dod08g2316 Chr08 51204807 51205022 -
Enph Enph7g1508 Chr7 20206216 20208226 -
Glsi Glsi10g0087 Chr10 689401 690208 +
Gma Gma14g01478 Chr14 31802777 31806652 +
Lapu Lapu8g01058 Chr8 28563359 28564891 -
Lasa Lasa6g00329 Chr6 9663433 9664236 -
Lele Lele25g0044 Chr25 272224 273004 +
Lele Lele26g0053 Chr26 296749 303357 +
Lele Lele28g0052 Chr28 294450 301787 +
Lja Lja5g3352 Chr5 65182895 65183709 -
Mal Mal1g6146 Chr1 140416034 140416772 -
Mepo Mepo4g01937 Chr4 24606763 24608444 -
Mesa Mesa1g00019 Chr1 246578 247421 +
Mibi Mibi08g2634 Chr08 44085047 44085855 -
Mtr Mtr1g0757 Chr1 8513189 8514445 -
Phac Phac1g00007 Chr1 183871 185112 +
Phco Phco2g00024 Chr2 427388 428338 +
Prci Prci2g0065 Chr2 566925 568155 +
Pumo Pumo9g00024 Chr9 421265 422488 +
Pvu Pvu1g0023 Chr1 269005 270145 +
Rops Rops9g02563 Chr9 48062027 48063017 +
Seca Seca8g04121 Chr8 117792222 117793396 -
Spst Spst8g02063 Chr8 28587328 28588056 -
Ssu Ssu5g0026 Chr5 438770 439601 +
Tpr Tpr1g3911 Chr1 43212140 43213319 -
Trre Trre1g00026 Chr1 226349 227240 +
Tsu Tsu01g00162 Chr01 1273911 1275206 +
Vian Vian7g00942 Chr7 17621464 17622195 -
Viun Viun8g00049 Chr8 262824 264186 +
Vivi Vivi4g05967 Chr4 196991977 196993386 -
Vra Vra6g1998 Chr6 36669033 36670174 +
Pste Pste2g02929 Chr2 29270314 29278363 +
Lal Lal17g0510 Chr17 3530514 3532379 -