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
Vvi19g0750 . . . . . . Aed3g2584 . . . . Ahy11g0555 . Aip01g00541 . . . Amo11g0355 . Apr9g1834 . . . Bach3g00940 . . Bva12g02632 . Car02g02126 . Cca05g02016 . . . . Dod05g0687 . . . . . . Gma02g02802 Gma14g00132 . . . . . Lal22g0049 . . . . . . . . . . . . . Lasa2g02338 . . . . . . . . . . . Mal8g0244 . Mepo7g02918 . Mesa17g04513 . . . Mtr5g3406 . . . Phco3g00159 . . . Psa2g0189 . Pste8g00296 . . . . . Pumo9g01800 . Pvu8g2870 . Rops9g00225 . Seca6g02930 . Spst8g00970 Ssu6g3561 . . . . Tpr4g0208 . Trre9g05193 . Tsu05g04019 . Vian7g01115 . Vifa1g03500 . Vimu1g00308 . Viun8g02972 . Vivi7g02587 Vra6g0143 .
Vvi19g0751 . . . . . . Aed3g2585 Aed4g2380 . . . . . . . . . . . . . . . . . . Bva12g02631 . . . Cca05g02017 Cca09g01211 . . . . . . . . . Gma18g00717 . Gma14g00131 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja6g1259 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Ssu6g3562 Ssu9g1073 . . . . . . . . . . . . . . . . . . Vra6g0142 Vra6g0142
Vvi19g0752 . . . . . Adu07g00173 Aed3g2586 . . . Ahy17g0240 . Aip07g00178 . . . . . . Apr9g1835 . Arst7g00275 . Bach3g00942 . . Bva12g02629 . . . Cca05g02018 . . . Dod08g0179 . . . . . . . Gma02g02804 . . . . . Lal18g1614 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco3g00157 . . . . . Pste8g00292 . . . . . Pumo9g01798 . Pvu8g2872 . Rops9g00218 . Seca8g00205 . Spst8g00972 Ssu6g3563 . . . . . . . . . . . . . . Vimu1g00305 . Viun8g02973 . . Vra6g0141 .
Vvi19g0753 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0754 . . . . . . . . . . . . . . . . . . . . . . . . . . . . Car02g02129 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal8g0239 . . . . . . . Mtr5g3412 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr4g0213 . . . Tsu05g04025 . . . . . . . . . . . .
Vvi19g0755 . Acco05g0651 . Accr3g02193 . Adu07g00172 . . Aev07g0146 . Ahy17g0239 . Aip07g00177 . . Alju07g0694 . . . Apr9g1836 . Arst7g00273 . Bach3g00943 . Bisa05g2829 Bva12g02628 . . . Cca05g02019 . . Dere05g0171 Dod08g0177 . . Enph7g1911 . Glsi10g2755 . . Gma02g02805 Gma14g00130 . . . . . . . . . . . . . . . . . . . Lasa2g02344 . . . . . Lele26g1730 . Lele28g1738 . . . . . Mepo7g02919 . Mesa17g04516 . Mibi08g0572 . . . . . Phco3g00156 . Prci2g3074 . Psa2g0182 . Pste8g00290 . . . . . Pumo9g01797 . Pvu8g2873 . Rops9g00217 . Seca6g02928 . Spst8g00973 Ssu6g3564 . . Sto5g1843 . . . Trre9g05197 . . . Vian7g01113 . Vifa1g03508 . Vimu1g00304 . Viun8g02975 . Vivi7g02584 Vra6g0140 .
Vvi19g0756 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja6g1257 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0757 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0758 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi19g0759 . Acco05g1030 . Accr3g01876 . Adu07g00170 Aed3g2587 . Aev07g0144 . Ahy17g0238 . Aip07g00174 . . Alju07g1029 . . . Apr9g1837 . Arst7g00272 . Bach3g00945 . Bisa05g2048 Bva12g02627 . Car02g02131 . Cca05g02021 . . Dere05g1395 Dod08g0175 . . Enph7g0129 . Glsi10g1913 . . Gma02g02807 Gma14g00129 . . . . . . Lal6g0037 . . . . . . . . . . . . Lasa2g02345 . . . . Lele25g1471 Lele26g1503 Lele27g0607 Lele28g1496 . . . Mal8g0237 . Mepo7g02921 . Mesa17g04518 . Mibi08g0885 . Mtr5g3414 . . . Phco3g00154 . Prci2g2446 . Psa2g0181 . Pste8g00289 . . . Pte4g00344 . Pumo9g01795 . Pvu8g2875 . Rops9g00216 . Seca8g00200 . Spst8g00975 Ssu6g3566 . . Sto5g1840 . Tpr4g0214 . Trre9g05199 . Tsu05g04027 . Vian7g01111 . Vifa1g03514 . Vimu1g00303 . Viun8g02977 . Vivi7g02582 Vra6g0139 .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Aed Aed3g2584 Chr3 27926064 27930070 -
Cca Cca05g02016 Chr05 40014011 40018503 -
Mal Mal8g0244 Chr8 3628480 3634626 +
Mtr Mtr5g3406 Chr5 42942547 42948670 -
Ssu Ssu6g3561 Chr6 79218130 79222201 -
Tpr Tpr4g0208 Chr4 2165679 2170594 -
Tsu Tsu05g04019 Chr05 51064441 51068563 -
Vra Vra6g0143 Chr6 1011657 1016474 +
Vvi Vvi19g0750 Chr19 8241030 8246977 -
Aed Aed3g2584 Chr3 27926064 27930070 -
Ahy Ahy11g0555 Chr11 8537092 8542470 +
Aip Aip01g00541 Chr01 8011441 8017813 +
Amo Amo11g0355 Chr11 5619333 5625718 +
Apr Apr9g1834 Chr9 27123721 27128039 -
Bach Bach3g00940 Chr3 20005634 20010781 -
Bva Bva12g02632 Chr12 19408317 19412522 +
Car Car02g02126 Chr02 51591772 51595852 -
Cca Cca05g02016 Chr05 40014011 40018503 -
Dod Dod05g0687 Chr05 10307516 10313269 +
Gma Gma02g02802 Chr02 53626153 53630033 -
Gma Gma14g00132 Chr14 1076441 1080058 +
Lal Lal22g0049 Chr22 297354 302689 +
Lasa Lasa2g02338 Chr2 499515801 499519312 -
Mal Mal8g0244 Chr8 3628480 3634626 +
Mepo Mepo7g02918 Chr7 40168915 40175156 -
Mesa Mesa17g04513 Chr17 76303362 76309000 -
Mtr Mtr5g3406 Chr5 42942547 42948670 -
Phco Phco3g00159 Chr3 1023384 1029113 +
Psa Psa2g0189 Chr2 7178552 7183495 +
Pste Pste8g00296 Chr8 1618004 1623759 +
Pumo Pumo9g01800 Chr9 47139066 47143792 +
Pvu Pvu8g2870 Chr8 58565529 58570029 -
Rops Rops9g00225 Chr9 2781859 2786040 +
Seca Seca6g02930 Chr6 94985593 94992996 +
Spst Spst8g00970 Chr8 8509935 8514310 -
Ssu Ssu6g3561 Chr6 79218130 79222201 -
Tpr Tpr4g0208 Chr4 2165679 2170594 -
Trre Trre9g05193 Chr9 57084689 57087719 -
Tsu Tsu05g04019 Chr05 51064441 51068563 -
Vian Vian7g01115 Chr7 19303792 19308138 +
Vifa Vifa1g03500 Chr1 544138021 544141634 -
Vimu Vimu1g00308 Chr1 1845592 1850905 +
Viun Viun8g02972 Chr8 37190671 37195307 -
Vivi Vivi7g02587 Chr7 89699487 89703296 +
Vra Vra6g0143 Chr6 1011657 1016474 +
Vvi Vvi19g0751 Chr19 8269837 8270550 +
Aed Aed3g2585 Chr3 27930464 27931216 +
Aed Aed4g2380 Chr4 26169396 26170073 -
Bva Bva12g02631 Chr12 19404580 19405453 -
Cca Cca05g02017 Chr05 40020208 40021268 +
Cca Cca09g01211 Chr09 34125546 34126654 +
Gma Gma18g00717 Chr18 7536213 7537294 -
Gma Gma14g00131 Chr14 1074169 1075164 -
Lja Lja6g1259 Chr6 36711941 36712956 -
Ssu Ssu6g3562 Chr6 79238689 79239462 +
Ssu Ssu9g1073 Chr9 42101774 42102532 +
Vra Vra6g0142 Chr6 1009257 1010292 -
Vra Vra6g0142 Chr6 1009257 1010292 -
Vvi Vvi19g0752 Chr19 8279965 8282858 -
Adu Adu07g00173 Chr07 1567197 1572782 +
Aed Aed3g2586 Chr3 27935131 27938244 -
Ahy Ahy17g0240 Chr17 2280298 2283852 +
Aip Aip07g00178 Chr07 1383447 1386793 +
Apr Apr9g1835 Chr9 27139540 27143263 -
Arst Arst7g00275 Chr7 1718823 1722474 +
Bach Bach3g00942 Chr3 20024886 20026573 -
Bva Bva12g02629 Chr12 19390030 19394311 +
Cca Cca05g02018 Chr05 40026130 40029931 -
Dod Dod08g0179 Chr08 1867553 1872114 +
Gma Gma02g02804 Chr02 53638303 53641779 -
Lal Lal18g1614 Chr18 17575208 17578794 -
Phco Phco3g00157 Chr3 1013829 1017339 +
Pste Pste8g00292 Chr8 1599845 1603412 +
Pumo Pumo9g01798 Chr9 47115479 47119321 +
Pvu Pvu8g2872 Chr8 58577466 58580947 -
Rops Rops9g00218 Chr9 2747282 2752807 +
Seca Seca8g00205 Chr8 2528350 2531945 +
Spst Spst8g00972 Chr8 8518762 8525752 -
Ssu Ssu6g3563 Chr6 79244818 79248167 -
Vimu Vimu1g00305 Chr1 1835918 1839463 +
Viun Viun8g02973 Chr8 37201425 37205356 -
Vra Vra6g0141 Chr6 1001970 1005513 +
Vvi Vvi19g0753 Chr19 8297271 8297894 +
Vvi Vvi19g0754 Chr19 8298292 8299513 +
Car Car02g02129 Chr02 51614001 51616906 +
Mal Mal8g0239 Chr8 3589406 3591273 -
Mtr Mtr5g3412 Chr5 43000014 43003570 +
Tpr Tpr4g0213 Chr4 2260051 2263185 +
Tsu Tsu05g04025 Chr05 51115419 51118546 +
Vvi Vvi19g0755 Chr19 8304202 8305387 +
Acco Acco05g0651 Chr05 9444767 9465108 -
Accr Accr3g02193 Chr3 40096322 40116698 +
Adu Adu07g00172 Chr07 1563590 1564989 -
Aev Aev07g0146 Chr07 825572 826762 -
Ahy Ahy17g0239 Chr17 2274276 2277162 -
Aip Aip07g00177 Chr07 1376029 1377431 -
Alju Alju07g0694 Chr07 10956896 10987539 -
Apr Apr9g1836 Chr9 27143755 27146618 +
Arst Arst7g00273 Chr7 1715160 1717810 -
Bach Bach3g00943 Chr3 20027907 20030177 +
Bisa Bisa05g2829 Chr05 68211490 68224287 -
Bva Bva12g02628 Chr12 19387320 19389737 -
Cca Cca05g02019 Chr05 40030869 40034081 +
Dere Dere05g0171 Chr05 2187141 2227547 +
Dod Dod08g0177 Chr08 1863410 1864357 -
Enph Enph7g1911 Chr7 25524765 25543656 -
Glsi Glsi10g2755 Chr10 49436725 49536065 -
Gma Gma02g02805 Chr02 53643325 53646406 +
Gma Gma14g00130 Chr14 1064461 1067482 -
Lasa Lasa2g02344 Chr2 499626853 499628053 -
Lele Lele26g1730 Chr26 20838792 20856134 +
Lele Lele28g1738 Chr28 20250619 20267963 +
Mepo Mepo7g02919 Chr7 40223656 40227419 +
Mesa Mesa17g04516 Chr17 76388184 76389894 +
Mibi Mibi08g0572 Chr08 10094616 10114831 -
Phco Phco3g00156 Chr3 1010519 1013141 -
Prci Prci2g3074 Chr2 38636258 38650339 +
Psa Psa2g0182 Chr2 6918099 6920566 +
Pste Pste8g00290 Chr8 1588014 1590708 -
Pumo Pumo9g01797 Chr9 47109612 47112424 -
Pvu Pvu8g2873 Chr8 58581933 58584868 +
Rops Rops9g00217 Chr9 2743773 2746258 -
Seca Seca6g02928 Chr6 94949987 94952956 -
Spst Spst8g00973 Chr8 8526223 8528717 +
Ssu Ssu6g3564 Chr6 79252272 79253413 +
Sto Sto5g1843 Chr5 13504023 13505669 -
Trre Trre9g05197 Chr9 57125354 57126745 +
Vian Vian7g01113 Chr7 19291277 19292518 -
Vifa Vifa1g03508 Chr1 544937169 544939409 +
Vimu Vimu1g00304 Chr1 1833484 1834713 -
Viun Viun8g02975 Chr8 37205753 37208065 +
Vivi Vivi7g02584 Chr7 89668172 89670884 -
Vra Vra6g0140 Chr6 999274 1001512 -
Vvi Vvi19g0756 Chr19 8316673 8317843 +
Lja Lja6g1257 Chr6 36629873 36633024 -
Vvi Vvi19g0757 Chr19 8329805 8330017 +
Vvi Vvi19g0758 Chr19 8341509 8341868 -
Vvi Vvi19g0759 Chr19 8363789 8368130 +
Acco Acco05g1030 Chr05 21396598 21400449 +
Accr Accr3g01876 Chr3 26180838 26184867 -
Adu Adu07g00170 Chr07 1556773 1558753 -
Aed Aed3g2587 Chr3 27939019 27944870 +
Aev Aev07g0144 Chr07 819632 821542 -
Ahy Ahy17g0238 Chr17 2264527 2267016 -
Aip Aip07g00174 Chr07 1362382 1364716 -
Alju Alju07g1029 Chr07 31864873 31870994 -
Apr Apr9g1837 Chr9 27150363 27153039 +
Arst Arst7g00272 Chr7 1708079 1710524 -
Bach Bach3g00945 Chr3 20034590 20037631 +
Bisa Bisa05g2048 Chr05 44988448 44992791 +
Bva Bva12g02627 Chr12 19382830 19385851 -
Car Car02g02131 Chr02 51621665 51624378 +
Cca Cca05g02021 Chr05 40048457 40050883 +
Dere Dere05g1395 Chr05 22852630 22862188 +
Dod Dod08g0175 Chr08 1844300 1847095 -
Enph Enph7g0129 Chr7 6507647 6512665 +
Glsi Glsi10g1913 Chr10 13365851 13369852 -
Gma Gma02g02807 Chr02 53651130 53653780 +
Gma Gma14g00129 Chr14 1060505 1062860 -
Lal Lal6g0037 Chr6 256728 258865 -
Lasa Lasa2g02345 Chr2 499666487 499669529 +
Lele Lele25g1471 Chr25 10998939 11004546 -
Lele Lele26g1503 Chr26 10938845 10942741 -
Lele Lele27g0607 Chr27 14049900 14054581 +
Lele Lele28g1496 Chr28 11348416 11352382 -
Mal Mal8g0237 Chr8 3579245 3582458 -
Mepo Mepo7g02921 Chr7 40232944 40236475 +
Mesa Mesa17g04518 Chr17 76422790 76426337 +
Mibi Mibi08g0885 Chr08 20575837 20579663 +
Mtr Mtr5g3414 Chr5 43011388 43014949 +
Phco Phco3g00154 Chr3 1003931 1006179 -
Prci Prci2g2446 Chr2 19855468 19859781 -
Psa Psa2g0181 Chr2 6818359 6821994 -
Pste Pste8g00289 Chr8 1584532 1586518 -
Pte Pte4g00344 Chr4 19653749 19654654 +
Pumo Pumo9g01795 Chr9 47100150 47102700 -
Pvu Pvu8g2875 Chr8 58589154 58591704 +
Rops Rops9g00216 Chr9 2729083 2731545 -
Seca Seca8g00200 Chr8 2495679 2498436 -
Spst Spst8g00975 Chr8 8532070 8534424 +
Ssu Ssu6g3566 Chr6 79289099 79291125 +
Sto Sto5g1840 Chr5 13481570 13485834 -
Tpr Tpr4g0214 Chr4 2267815 2271786 +
Trre Trre9g05199 Chr9 57132037 57137134 +
Tsu Tsu05g04027 Chr05 51124745 51128360 +
Vian Vian7g01111 Chr7 19285372 19287602 -
Vifa Vifa1g03514 Chr1 545716520 545722660 +
Vimu Vimu1g00303 Chr1 1828778 1831047 -
Viun Viun8g02977 Chr8 37211039 37213543 +
Vivi Vivi7g02582 Chr7 89653669 89657092 -
Vra Vra6g0139 Chr6 995464 998148 -