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
Vvi16g0889 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco5g00826 . . . . . . . . . . . . . Pvu4g1098 Pvu7g0899 . . . . . . . . . . . . . . . . . . . . . . . . Vivi2g06967 . . .
Vvi16g0890 . . . . . . . Aed7g0581 Aev05g2923 . Ahy15g3526 . Aip05g03834 . . . . . . Apr6g0710 . . . . . . Bva03g01401 Bva04g01146 . . . Cca08g00649 . . Dod02g3044 . . . . . Gma16g01580 . . . Gso16g1522 . . . Lal1g0829 . . . . . . . . . . . . . . . . . . . . . . . Lja2g2613 . . Mal6g2821 . . . . . . . Mtr6g1420 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr2g4391 . . . Tsu06g03130 . . . . . . . . . . . Vra1g1853
Vvi16g0891 . . . . . . . . . . . . . . . . . . . . Arst5g04448 Arst9g00220 . . . . Bva03g01398 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco5g00872 Phco6g02275 . . . . . . . . . . . . Pvu4g1067 Pvu7g0898 . . . . Spst4g03320 . . . . . . . . . . . . . . . . . . Viun7g03009 . . . .
Vvi16g0892 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu7g02048 . Lasa6g04097 . . . . . . . . . . . . . Mepo4g04243 . . . . . . . . . Phco6g02482 . . . . . . . . . . . . . Pvu7g0719 . . . . . . . . . . . . . Trre1g05406 . . . . . . . Vimu3g03061 . . . Vivi1g04373 . .
Vvi16g0893 . . . . . Adu09g02370 . Aed11g1709 . Aev09g2227 Ahy15g3542 . Aip05g03856 Aip09g04016 . . . Amo19g4439 . . . Arst9g03124 . . . . Bva03g01397 Bva04g01150 . . Cca02g02258 Cca06g01790 . . . Dod06g0785 . . . . . . . . . . . . . . Lal9g0809 . . . . . . . . . . Lapu7g02047 . Lasa6g04095 . . . . . . . . . Lja5g0629 Mal1g2043 . . . . Mesa1g04651 . . Mtr1g3754 . . . . Phco6g02480 . . . . . Pste4g02970 . . Pte16g00272 Pte9g00342 . Pumo3g00945 . Pvu7g0720 . Rops6g02737 . Seca8g07390 . Spst10g00971 Ssu7g0782 Ssu2g2855 . . Tpr1g0750 . . Trre1g05402 Tsu01g04414 . . Vian3g00629 . Vifa3g02924 . Vimu3g03060 . Viun7g03261 . Vivi1g04377 Vra8g2237 Vra11g0289
Vvi16g0894 . . . . . . Aed1g2264 . . Aev09g2226 . Ahy19g3557 . Aip09g04017 . . . . . . . . . . . . Bva03g01396 Bva04g01152 . . Cca02g02256 . . . . Dod06g0788 . . . . Gma10g02231 . . . . . . . . . . Lal24g0043 . . . . . . . . . . . . . . . . . . . . . Lja5g0631 Mal1g2044 . . . . . . . Mtr1g3752 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu7g0786 . Sto10g2478 . . . . . Tsu01g04413 . . . . . . . . . . . Vra8g2235 .
Vvi16g0895 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0896 . . . . Adu05g03462 . . . . . . . . . . . . . . . Arst5g04449 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco5g00873 . . . . . . . . . . . . . Pvu4g1066 Pvu7g0896 . . . . Spst4g03322 . . . . . . . . . . . . . . . . . . . . . . .
Vvi16g0897 . . . . . Adu09g02367 . . Aev05g2914 Aev09g2225 Ahy15g3543 Ahy19g3559 Aip05g03857 Aip09g04018 . . . . . . . Arst9g03121 . . . . . Bva04g01153 . . . . . . Dod02g3033 Dod06g0789 . . . . . . . . . . . . . . Lal9g0810 . . . . . . . . . . Lapu7g02044 . Lasa6g04092 . . . . . . . . . Lja5g0632 . . . Mepo4g04238 . . . . . . . . . Phco6g02477 . . Psa6g4524 . . Pste4g02964 . . Pte18g00396 . . Pumo3g00949 . Pvu7g0723 . . . Seca8g07388 . Spst10g00968 . . . . . . . Trre1g05398 . . . Vian3g00632 . Vifa3g02921 . Vimu3g03056 . Viun7g03256 . Vivi1g04381 . .
Vvi16g0898 . . . . . . . . . . . . . . . . . . . Apr6g0704 . Arst9g00221 . . . . . . . . . . . . . . . . . . Gma16g01578 . . . Gso16g1520 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco6g02278 . . . . . . . . . . . . Pvu4g1224 Pvu7g0895 . . . . . Spst10g00765 . . . . . . . . . . . . . . Vimu8g02092 Vimu3g02844 . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi16g0889 Chr16 17009235 17012208 +
Phco Phco5g00826 Chr5 10155178 10158349 +
Pvu Pvu4g1098 Chr4 32456455 32460001 -
Pvu Pvu7g0899 Chr7 8751535 8755066 -
Vivi Vivi2g06967 Chr2 210931927 210935897 +
Vvi Vvi16g0890 Chr16 17013691 17015121 +
Aed Aed7g0581 Chr7 4249972 4256054 +
Aev Aev05g2923 Chr05 30049972 30056975 -
Ahy Ahy15g3526 Chr15 157983048 157989507 +
Aip Aip05g03834 Chr05 146510550 146516663 +
Apr Apr6g0710 Chr6 11094525 11101954 -
Bva Bva03g01401 Chr03 13419505 13423663 -
Bva Bva04g01146 Chr04 7709820 7714978 +
Cca Cca08g00649 Chr08 11810740 11821633 +
Dod Dod02g3044 Chr02 64579433 64586281 -
Gma Gma16g01580 Chr16 36460152 36464473 -
Gso Gso16g1522 Chr16 35564917 35570533 -
Lal Lal1g0829 Chr1 5723055 5732022 +
Lja Lja2g2613 Chr2 35676692 35685550 +
Mal Mal6g2821 Chr6 73856584 73865833 +
Mtr Mtr6g1420 Chr6 22613531 22622090 +
Tpr Tpr2g4391 Chr2 47835973 47843782 +
Tsu Tsu06g03130 Chr06 41531414 41538338 +
Vra Vra1g1853 Chr1 35395120 35399677 -
Vvi Vvi16g0891 Chr16 17017538 17025694 +
Arst Arst5g04448 Chr5 105778411 105789814 +
Arst Arst9g00220 Chr9 1803635 1806936 +
Bva Bva03g01398 Chr03 13397904 13402700 -
Phco Phco5g00872 Chr5 12255156 12257225 +
Phco Phco6g02275 Chr6 43996329 43998965 +
Pvu Pvu4g1067 Chr4 29411476 29414389 -
Pvu Pvu7g0898 Chr7 8744730 8747307 -
Spst Spst4g03320 Chr4 73114033 73117164 +
Viun Viun7g03009 Chr7 33079544 33082639 +
Vvi Vvi16g0892 Chr16 17028242 17029223 +
Lapu Lapu7g02048 Chr7 36701077 36715989 +
Lasa Lasa6g04097 Chr6 617475832 617478966 +
Mepo Mepo4g04243 Chr4 52263835 52266598 +
Phco Phco6g02482 Chr6 46244123 46246954 +
Pvu Pvu7g0719 Chr7 6351209 6354040 -
Trre Trre1g05406 Chr1 59713809 59717429 +
Vimu Vimu3g03061 Chr3 44437133 44440604 +
Vivi Vivi1g04373 Chr1 93299072 93302830 -
Vvi Vvi16g0893 Chr16 17034692 17035183 -
Adu Adu09g02370 Chr09 111039510 111040385 +
Aed Aed11g1709 Chr11 20728402 20730926 -
Aev Aev09g2227 Chr09 24956986 24961982 +
Ahy Ahy15g3542 Chr15 158182179 158184406 -
Aip Aip05g03856 Chr05 146773276 146775572 -
Aip Aip09g04016 Chr09 146505079 146506334 -
Amo Amo19g4439 Chr19 161429046 161430017 +
Arst Arst9g03124 Chr9 108936479 108937569 +
Bva Bva03g01397 Chr03 13393619 13395870 +
Bva Bva04g01150 Chr04 7744453 7746550 -
Cca Cca02g02258 Chr02 43138344 43139979 +
Cca Cca06g01790 Chr06 33256750 33258005 -
Dod Dod06g0785 Chr06 9614220 9615235 -
Lal Lal9g0809 Chr9 5845374 5846332 -
Lapu Lapu7g02047 Chr7 36697673 36698544 +
Lasa Lasa6g04095 Chr6 617167913 617168842 +
Lja Lja5g0629 Chr5 5623210 5626181 -
Mal Mal1g2043 Chr1 26780402 26781238 -
Mesa Mesa1g04651 Chr1 72429426 72435722 +
Mtr Mtr1g3754 Chr1 49127033 49129356 +
Phco Phco6g02480 Chr6 46239020 46240641 +
Pste Pste4g02970 Chr4 21142709 21144387 +
Pte Pte16g00272 Chr16 3642275 3642807 +
Pte Pte9g00342 Chr9 4045622 4046769 -
Pumo Pumo3g00945 Chr3 14562302 14563928 -
Pvu Pvu7g0720 Chr7 6357415 6359458 -
Rops Rops6g02737 Chr6 49193739 49195861 +
Seca Seca8g07390 Chr8 170820114 170822129 +
Spst Spst10g00971 Chr10 10422550 10424125 +
Ssu Ssu7g0782 Chr7 15721974 15722688 -
Ssu Ssu2g2855 Chr2 89662060 89662672 -
Tpr Tpr1g0750 Chr1 6334864 6349427 -
Trre Trre1g05402 Chr1 59677342 59678513 +
Tsu Tsu01g04414 Chr01 51936071 51943357 +
Vian Vian3g00629 Chr3 6341135 6342597 -
Vifa Vifa3g02924 Chr3 821409156 821410055 +
Vimu Vimu3g03060 Chr3 44434999 44435670 +
Viun Viun7g03261 Chr7 34837724 34839187 +
Vivi Vivi1g04377 Chr1 93423902 93425299 -
Vra Vra8g2237 Chr8 40687636 40688680 +
Vra Vra11g0289 Chr11 2047705 2049475 +
Vvi Vvi16g0894 Chr16 17036988 17041311 -
Aed Aed1g2264 Chr1 18795045 18797524 -
Aev Aev09g2226 Chr09 24953666 24955912 +
Ahy Ahy19g3557 Chr19 158226401 158234265 -
Aip Aip09g04017 Chr09 146510463 146513058 -
Bva Bva03g01396 Chr03 13389800 13392977 +
Bva Bva04g01152 Chr04 7756268 7760835 -
Cca Cca02g02256 Chr02 43120925 43124469 +
Dod Dod06g0788 Chr06 9645156 9648189 -
Gma Gma10g02231 Chr10 49900586 49904689 +
Lal Lal24g0043 Chr24 287033 289660 -
Lja Lja5g0631 Chr5 5631723 5635144 -
Mal Mal1g2044 Chr1 26783862 26795887 -
Mtr Mtr1g3752 Chr1 49107268 49111255 +
Ssu Ssu7g0786 Chr7 15733340 15737298 -
Sto Sto10g2478 Chr10 35078809 35088077 +
Tsu Tsu01g04413 Chr01 51925003 51928404 +
Vra Vra8g2235 Chr8 40670934 40675674 +
Vvi Vvi16g0895 Chr16 17046250 17047656 +
Vvi Vvi16g0896 Chr16 17053735 17055618 -
Adu Adu05g03462 Chr05 107102722 107123891 +
Arst Arst5g04449 Chr5 105778411 105784005 +
Phco Phco5g00873 Chr5 12271885 12273075 +
Pvu Pvu4g1066 Chr4 29365951 29369464 -
Pvu Pvu7g0896 Chr7 8735363 8737831 -
Spst Spst4g03322 Chr4 73147221 73150226 +
Vvi Vvi16g0897 Chr16 17083228 17084154 +
Adu Adu09g02367 Chr09 111028475 111030626 -
Aev Aev05g2914 Chr05 29964496 29966847 -
Aev Aev09g2225 Chr09 24948151 24950219 -
Ahy Ahy15g3543 Chr15 158186109 158188641 +
Ahy Ahy19g3559 Chr19 158238342 158240560 +
Aip Aip05g03857 Chr05 146777269 146779885 +
Aip Aip09g04018 Chr09 146517199 146519396 +
Arst Arst9g03121 Chr9 108925659 108927820 -
Bva Bva04g01153 Chr04 7766201 7769361 +
Dod Dod02g3033 Chr02 64012897 64015397 -
Dod Dod06g0789 Chr06 9653001 9655413 +
Lal Lal9g0810 Chr9 5849375 5852439 +
Lapu Lapu7g02044 Chr7 36675182 36677209 -
Lasa Lasa6g04092 Chr6 617081118 617083276 -
Lja Lja5g0632 Chr5 5639908 5642328 +
Mepo Mepo4g04238 Chr4 52215420 52218386 -
Phco Phco6g02477 Chr6 46211345 46213789 -
Psa Psa6g4524 Chr6 394734456 394737261 -
Pste Pste4g02964 Chr4 21095332 21111879 -
Pte Pte18g00396 Chr18 9038025 9040241 +
Pumo Pumo3g00949 Chr3 14584460 14587110 +
Pvu Pvu7g0723 Chr7 6381663 6383889 +
Seca Seca8g07388 Chr8 170789812 170792732 -
Spst Spst10g00968 Chr10 10384732 10386726 -
Trre Trre1g05398 Chr1 59652180 59655790 -
Vian Vian3g00632 Chr3 6376896 6378866 +
Vifa Vifa3g02921 Chr3 820610587 820612769 -
Vimu Vimu3g03056 Chr3 44408366 44411605 -
Viun Viun7g03256 Chr7 34808963 34811245 -
Vivi Vivi1g04381 Chr1 93474628 93477159 +
Vvi Vvi16g0898 Chr16 17105351 17108071 -
Apr Apr6g0704 Chr6 10903231 10906221 -
Arst Arst9g00221 Chr9 1803635 1806936 +
Gma Gma16g01578 Chr16 36453194 36454940 -
Gso Gso16g1520 Chr16 35557257 35560422 -
Phco Phco6g02278 Chr6 44025071 44031837 +
Pvu Pvu4g1224 Chr4 37835572 37839980 -
Pvu Pvu7g0895 Chr7 8726416 8729228 -
Spst Spst10g00765 Chr10 8043836 8046469 +
Vimu Vimu8g02092 Chr8 27046674 27047236 +
Vimu Vimu3g02844 Chr3 42650652 42652337 +
Phco Phco5g00826 Chr5 10155178 10158349 +
Pvu Pvu4g1098 Chr4 32456455 32460001 -
Vivi Vivi2g06967 Chr2 210931927 210935897 +