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
Vvi18g1316 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1317 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1318 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1319 . . . . . . . . Aev08g0872 . Ahy17g2718 . Aip07g02967 . . . . . . . . . . . . . . . . . . . . . . . . . . . Gma04g02317 . . . Gso4g2030 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mtr3g3029 . . . . . . . . . . . . . . . . . . . . . . . . . . Sto5g0334 . . Tpr2g5420 . . . . . . . . . . . . . . . .
Vvi18g1320 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1321 . Acco05g2787 . Accr3g00259 . . . . . . Ahy17g2713 . Aip07g02964 . . Alju07g2737 Amo17g2625 . Apr9g0745 . . . . . . Bisa05g0862 . . . . Cca05g00066 . . Dere05g2566 . . . Enph7g1337 . Glsi10g1247 Gma04g02316 . . . Gso4g2029 . . . . . . . . . . . . . . . . . . Lasa6g00880 . . . . . Lele26g0232 Lele27g1867 . Lja1g4947 . Mal1g5100 Mal2g1880 . . . . . Mibi08g2439 Mtr1g0880 Mtr3g3030 . Phac1g00891 . Phco2g00748 . Prci2g0350 Psa6g0916 . . Pste8g02034 . . . . . Pumo9g01099 . Pvu1g0666 . Rops9g02459 . Seca8g02552 . Spst8g01437 . . Sto5g0333 . Tpr1g3082 Tpr2g5419 . . Tsu01g01005 . . . . Vifa3g04081 . Vimu1g02402 . Viun8g00981 . Vivi4g04624 Vra6g1428 .
Vvi18g1322 . . . . . . . . . . Ahy17g2712 . Aip07g02963 . . . Amo17g2624 . . . . . . . . . . . . . . Cca03g01052 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja1g4946 . . . . . . . . . . Mtr3g3031 . . . . . . . . . . . . . . . . . . . . . . . . . Ssu1g2909 . . . . . . . . . . . . . . . . . . . .
Vvi18g1323 . . . . Adu08g00511 . . . Aev08g0871 . Ahy17g2710 . Aip07g02958 . . . Amo17g2619 . . . Arst8g00657 . . . . . . . . . . . . . . . . . . . Gma04g02315 Gma06g01082 . . Gso4g2028 Gso4g2028 . . . Lal17g0516 . . . . . . . . . . Lapu9g01418 . . . . . . . . . . . Lja1g4944 . . Mal2g1879 Mepo3g06468 . Mesa9g03979 . . . . Mtr3g3032 . . Phco7g01339 . . . . . Pste2g03291 . . . . . Pumo10g01329 . Pvu9g1381 . Rops10g02000 . Seca4g02439 . . . . . . . . Tpr2g5417 Trre5g03694 . . . Vian4g01453 . Vifa2g02816 . Vimu10g02362 . Viun9g02289 . Vivi3g02957 . . .
Vvi18g1324 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1325 Acco10g2472 Acco05g2789 Accr4g00301 Accr3g00257 Adu08g00509 . . Aed10g0383 . . . . . . Alju08g0307 Alju07g2739 . . Apr9g0744 . Arst8g00655 . Bach12g00915 . Bisa09g0995 Bisa05g0859 Bva06g02914 . . . Cca05g00065 Cca03g01051 Dere04g1143 Dere05g2568 . . Enph1g1766 Enph7g1339 Glsi08g1037 Glsi10g1250 Gma04g02314 Gma06g01083 . . Gso4g2027 Gso4g2027 . . Lal4g0446 . Lal21g0538 . . . Lan14g0577 . Lan14g0577 . . . Lapu9g01417 . . . . . . . . . . . Lja1g4943 . . Mal2g1877 Mepo3g06470 . . . Mibi05g0259 Mibi08g2441 . Mtr3g3035 Phac9g01013 . Phco7g01725 Phco2g00747 Prci15g0382 Prci2g0348 . Psa5g1914 . Pste8g02035 . . . . . . Pvu9g1382 Pvu1g0665 Rops10g00999 Rops9g02451 Seca4g01948 . . Spst8g01441 . Ssu1g2907 Sto5g1150 Sto9g2820 . Tpr2g5412 . . . . . . . . . Vimu1g02403 . . Vivi3g02956 Vivi3g02956 . .
   
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Select Species Gene Chromosome Start End Strand
Phco Phco7g01725 Chr7 17331408 17332464 +
Rops Rops10g00999 Chr10 21460005 21461312 -
Seca Seca4g01948 Chr4 32723914 32725624 -
Rops Rops10g00999 Chr10 21460005 21461312 -
Sto Sto5g1150 Chr5 7678687 7679631 -
Vvi Vvi18g1316 Chr18 13279241 13280607 +
Vvi Vvi18g1317 Chr18 13293650 13293913 +
Vvi Vvi18g1318 Chr18 13300388 13300859 +
Vvi Vvi18g1319 Chr18 13303082 13304738 +
Aev Aev08g0872 Chr08 5149684 5151435 -
Ahy Ahy17g2718 Chr17 124989685 124993415 -
Aip Aip07g02967 Chr07 116124100 116127091 -
Gma Gma04g02317 Chr04 53610493 53612810 -
Gso Gso4g2030 Chr4 50671770 50674434 -
Mtr Mtr3g3029 Chr3 44177046 44179181 +
Sto Sto5g0334 Chr5 2004152 2005677 -
Tpr Tpr2g5420 Chr2 61084094 61086910 -
Vvi Vvi18g1320 Chr18 13306263 13306870 -
Vvi Vvi18g1321 Chr18 13312243 13313247 +
Acco Acco05g2787 Chr05 43022734 43026674 -
Accr Accr3g00259 Chr3 2732998 2734002 +
Ahy Ahy17g2713 Chr17 124952372 124953589 +
Aip Aip07g02964 Chr07 116089584 116090818 +
Alju Alju07g2737 Chr07 52831846 52846876 -
Amo Amo17g2625 Chr17 125669029 125670353 +
Apr Apr9g0745 Chr9 13248404 13249989 +
Bisa Bisa05g0862 Chr05 14429972 14430970 +
Cca Cca05g00066 Chr05 1445024 1446615 +
Dere Dere05g2566 Chr05 36203564 36204565 -
Enph Enph7g1337 Chr7 18826070 18827068 -
Glsi Glsi10g1247 Chr10 8435343 8436084 -
Gma Gma04g02316 Chr04 53604365 53605647 +
Gso Gso4g2029 Chr4 50665892 50667240 +
Lasa Lasa6g00880 Chr6 34832704 34833705 +
Lele Lele26g0232 Chr26 1339398 1349001 +
Lele Lele27g1867 Chr27 23436106 23437104 -
Lja Lja1g4947 Chr1 68614415 68615903 +
Mal Mal1g5100 Chr1 122630097 122631098 -
Mal Mal2g1880 Chr2 22717002 22718000 +
Mibi Mibi08g2439 Chr08 42174273 42175271 -
Mtr Mtr1g0880 Chr1 10174367 10175715 +
Mtr Mtr3g3030 Chr3 44181077 44182177 -
Phac Phac1g00891 Chr1 7752646 7754346 +
Phco Phco2g00748 Chr2 8009395 8010393 +
Prci Prci2g0350 Chr2 2508707 2510006 +
Psa Psa6g0916 Chr6 34515609 34518443 +
Pste Pste8g02034 Chr8 16517253 16518251 -
Pumo Pumo9g01099 Chr9 31281424 31282767 +
Pvu Pvu1g0666 Chr1 8148616 8150031 +
Rops Rops9g02459 Chr9 45677099 45678296 +
Seca Seca8g02552 Chr8 57534533 57535531 -
Spst Spst8g01437 Chr8 13563289 13564287 -
Sto Sto5g0333 Chr5 2001574 2002572 +
Tpr Tpr1g3082 Chr1 35325485 35326807 -
Tpr Tpr2g5419 Chr2 61069983 61071171 +
Tsu Tsu01g01005 Chr01 9189192 9193626 +
Vifa Vifa3g04081 Chr3 1201258151 1201259152 -
Vimu Vimu1g02402 Chr1 34779392 34781471 -
Viun Viun8g00981 Chr8 10923556 10924952 +
Vivi Vivi4g04624 Chr4 174196019 174197287 -
Vra Vra6g1428 Chr6 28118044 28119679 -
Vvi Vvi18g1322 Chr18 13322194 13323198 -
Ahy Ahy17g2712 Chr17 124920051 124921418 +
Aip Aip07g02963 Chr07 116057279 116058593 +
Amo Amo17g2624 Chr17 125636761 125638134 +
Cca Cca03g01052 Chr03 25550249 25551667 -
Lja Lja1g4946 Chr1 68592531 68593517 -
Mtr Mtr3g3031 Chr3 44184568 44185797 -
Ssu Ssu1g2909 Chr1 76414726 76415463 +
Vvi Vvi18g1323 Chr18 13365867 13366663 -
Adu Adu08g00511 Chr08 9213680 9214867 +
Aev Aev08g0871 Chr08 5141920 5142448 +
Ahy Ahy17g2710 Chr17 124858219 124859080 +
Aip Aip07g02958 Chr07 115974063 115974548 +
Amo Amo17g2619 Chr17 125584731 125585502 +
Arst Arst8g00657 Chr8 9185498 9186622 +
Gma Gma04g02315 Chr04 53593800 53595158 +
Gma Gma06g01082 Chr06 10147107 10148444 -
Gso Gso4g2028 Chr4 50655336 50656713 +
Gso Gso4g2028 Chr4 50655336 50656713 +
Lal Lal17g0516 Chr17 3588752 3590080 -
Lapu Lapu9g01418 Chr9 28462368 28463480 +
Lja Lja1g4944 Chr1 68582829 68585014 +
Mal Mal2g1879 Chr2 22709584 22712275 +
Mepo Mepo3g06468 Chr3 78629493 78630494 -
Mesa Mesa9g03979 Chr9 72178155 72178335 -
Mtr Mtr3g3032 Chr3 44195060 44196205 -
Phco Phco7g01339 Chr7 12104866 12105470 -
Pste Pste2g03291 Chr2 32809007 32809773 -
Pumo Pumo10g01329 Chr10 17630601 17631922 -
Pvu Pvu9g1381 Chr9 19659379 19660410 -
Rops Rops10g02000 Chr10 36475213 36476087 -
Seca Seca4g02439 Chr4 41749135 41750344 -
Tpr Tpr2g5417 Chr2 61023244 61025349 +
Trre Trre5g03694 Chr5 36455096 36456504 -
Vian Vian4g01453 Chr4 29205384 29205933 +
Vifa Vifa2g02816 Chr2 786265608 786266068 +
Vimu Vimu10g02362 Chr10 34425577 34426120 -
Viun Viun9g02289 Chr9 32302040 32303005 +
Vivi Vivi3g02957 Chr3 49363213 49364003 +
Vvi Vvi18g1324 Chr18 13389404 13389698 +
Vvi Vvi18g1325 Chr18 13397962 13399162 -
Acco Acco10g2472 Chr10 36089025 36090382 -
Acco Acco05g2789 Chr05 43031380 43034919 -
Accr Accr4g00301 Chr4 2922575 2923930 +
Accr Accr3g00257 Chr3 2712473 2713799 +
Adu Adu08g00509 Chr08 9139999 9140875 +
Aed Aed10g0383 Chr10 3109905 3111877 -
Alju Alju08g0307 Chr08 2250498 2251865 +
Alju Alju07g2739 Chr07 52852053 52855427 -
Apr Apr9g0744 Chr9 13239462 13241351 +
Arst Arst8g00655 Chr8 9111795 9112671 +
Bach Bach12g00915 Chr12 6495261 6496837 -
Bisa Bisa09g0995 Chr09 14545838 14547153 +
Bisa Bisa05g0859 Chr05 14333509 14334773 +
Bva Bva06g02914 Chr06 18175581 18178400 -
Cca Cca05g00065 Chr05 1403606 1406121 +
Cca Cca03g01051 Chr03 25535849 25537892 +
Dere Dere04g1143 Chr04 12761283 12762665 -
Dere Dere05g2568 Chr05 36228368 36233700 -
Enph Enph1g1766 Chr1 42734173 42736037 -
Enph Enph7g1339 Chr7 18837857 18839545 -
Glsi Glsi08g1037 Chr08 7623237 7629241 +
Glsi Glsi10g1250 Chr10 8443826 8449713 -
Gma Gma04g02314 Chr04 53583481 53584832 +
Gma Gma06g01083 Chr06 10157916 10159768 -
Gso Gso4g2027 Chr4 50644897 50646717 +
Gso Gso4g2027 Chr4 50644897 50646717 +
Lal Lal4g0446 Chr4 3116200 3118221 -
Lal Lal21g0538 Chr21 3915158 3917262 -
Lan Lan14g0577 Chr14 12123363 12124826 +
Lan Lan14g0577 Chr14 12123363 12124826 +
Lapu Lapu9g01417 Chr9 28447365 28449456 +
Lja Lja1g4943 Chr1 68492310 68493876 +
Mal Mal2g1877 Chr2 22686685 22687822 +
Mepo Mepo3g06470 Chr3 78639646 78640789 -
Mibi Mibi05g0259 Chr05 2593703 2595166 +
Mibi Mibi08g2441 Chr08 42189252 42190615 -
Mtr Mtr3g3035 Chr3 44207700 44209513 -
Phac Phac9g01013 Chr9 7757195 7759373 -
Phco Phco7g01725 Chr7 17331408 17332464 +
Phco Phco2g00747 Chr2 7989489 7991331 -
Prci Prci15g0382 Chr15 2500869 2502613 +
Prci Prci2g0348 Chr2 2483331 2484862 +
Psa Psa5g1914 Chr5 147443296 147445484 +
Pste Pste8g02035 Chr8 16546999 16560585 +
Pvu Pvu9g1382 Chr9 19679666 19680527 -
Pvu Pvu1g0665 Chr1 8116183 8118029 -
Rops Rops10g00999 Chr10 21460005 21461312 -
Rops Rops9g02451 Chr9 45448628 45458897 +
Seca Seca4g01948 Chr4 32723914 32725624 -
Spst Spst8g01441 Chr8 13602933 13604434 +
Ssu Ssu1g2907 Chr1 76372302 76373630 +
Sto Sto5g1150 Chr5 7678687 7679631 -
Sto Sto9g2820 Chr9 29770735 29774403 +
Tpr Tpr2g5412 Chr2 60990236 60992005 +
Vimu Vimu1g02403 Chr1 34798797 34800544 -
Vivi Vivi3g02956 Chr3 49331447 49333178 +
Vivi Vivi3g02956 Chr3 49331447 49333178 +