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
Vvi1g0591 . . . . . . . Aed5g2607 . Aev03g3391 . Ahy13g3949 . Aip03g04385 . . . . Apr7g0074 Apr2g1519 . . . . . . Bva01g01427 Bva11g00522 Car06g00213 . Cca06g00193 Cca09g02769 . . . Dod04g3129 . . . . . . . . . . . . . . . Lal23g0672 Lal16g0970 . . . . . . . . . . . . . . . . . . . Lja2g3324 Lja4g0074 Mal1g4945 Mal5g0361 . . . . . . Mtr1g1033 Mtr8g3822 . . . . . . . Psa7g0076 . . . . . . . . . . . . . . . . Ssu2g1128 Ssu5g3434 Sto11g0395 . . Tpr3g0283 . . Tsu01g01154 Tsu02g00086 . . . . . . . . . . . .
Vvi1g0592 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0593 . . . . . . . . . . . . . . . . . . Apr7g0073 . . . . . . . Bva01g01424 Bva11g00519 Car04g02826 . Cca06g00192 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lja2g3326 . Mal1g4943 . . . . . . . Mtr1g1035 . . . . . . . Psa6g1185 . . . . . . . . . . . . . . . . . Ssu2g1127 . . . Tpr1g2950 . . . Tsu01g01155 . . . . . . . . . . . Vra11g1388 .
Vvi1g0594 . . . . Adu03g04011 . . Aed5g2609 . . . . . Aip03g04389 . . . Amo13g4979 . . Arst3g05282 . . . . . Bva01g01419 . . . . Cca09g02772 . . . . . . . . . . . . . . . . . . . . Lal16g0969 . . . . . . . . . Lasa7g05219 . . . . . . . . . . . . . Mepo2g05041 . Mesa13g00094 . . . . . . . Phco4g03672 . . . . . Pste3g00020 . . . . . Pumo6g00115 . Pvu2g3339 . Rops2g00116 . Seca12g06935 . Spst3g00719 . . Ssu5g3438 . . . . Trre7g05915 . . . Vian1g04168 . Vifa6g04080 . Vimu11g04868 . Viun3g00125 . Vivi5g06579 . . .
Vvi1g0595 . . . . . . . . . Aev03g3395 . Ahy13g3953 . Aip03g04390 . . . . . Apr2g1523 . . . . . . . Bva11g00518 Car06g00208 . . . . . . Dod04g3132 . . . . . . . . . . . . . . . . . Lal15g0944 . . . . . . . . . . . . . . . . . . . Lja4g0070 . Mal5g0366 . . . . . . . Mtr8g3827 . . . . . . . . . . . . . . . . . . . . . . . . . . Sto11g0368 . . Tpr3g0275 . . . Tsu02g00082 . . . . . . . . . . . .
Vvi1g0596 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0597 Acco05g1359 Acco05g1359 Accr3g01627 Accr3g01627 . . . . . Aev03g0709 . Ahy13g3537 . Aip03g03985 Alju07g1299 Alju07g1299 . Amo13g4503 . . . . . Bach3g01075 Bisa05g1447 Bisa05g1447 . . Car06g00033 . . Cca01g00471 Dere05g1097 Dere05g1097 . Dod04g0202 . . Glsi10g1754 Glsi10g1754 . . . Gma18g00397 . . . . . . . . . . . . . . . . Lapu6g01021 Lapu6g01021 Lasa3g01145 Lasa2g01482 . . . . . . . . . . . . Mepo3g05355 Mepo7g02074 . . Mibi08g1126 Mibi08g1126 . . . . Phco2g02615 Phco3g00554 Prci2g2079 Prci2g2079 . . Pste8g01518 Pste8g01518 . . . Pte8g00622 . Pumo9g02494 Pvu1g2363 Pvu8g2467 . Rops9g01027 . Seca6g02367 Spst8g00345 Spst1g02287 . . . . . . Trre5g00691 . . . . Vian7g01713 . Vifa1g01674 Vimu1g01139 Vimu1g01139 . Viun8g02108 . . . .
Vvi1g0598 . . . . . . . . . . . Ahy13g3538 . Aip03g03986 . . . Amo13g4504 Apr7g0071 Apr2g1524 . . . . . . . . Car06g00207 . Cca06g00191 Cca01g00470 . . . Dod04g0201 . . . . . . . Gma18g00398 . . . . . Lal22g0970 Lal18g0523 Lal23g0674 . Lal15g0943 . . . . . . . . . . . . . . . . . . Lja2g3327 Lja4g0069 Mal1g4932 Mal5g0367 . . . . . . Mtr1g1039 Mtr8g3828 . . . . . . Psa6g1179 . . . . . . . . . . . . . . . . . Ssu2g1126 . Sto11g0350 . Tpr1g2946 Tpr3g0274 . . Tsu01g01162 Tsu02g00081 . . . . . . . . . . Vra11g1387 .
Vvi1g0599 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva01g01417 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g2350 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi1g0600 . . . . . . . . . . . . . . . . . . . . . . . . . . . Bva11g00517 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi1g0591 Chr1 5829740 5831755 -
Aed Aed5g2607 Chr5 26769246 26771510 +
Aev Aev03g3391 Chr03 31502391 31504572 +
Ahy Ahy13g3949 Chr13 138860190 138862394 +
Aip Aip03g04385 Chr03 128207107 128210129 +
Apr Apr7g0074 Chr7 3038746 3040724 -
Apr Apr2g1519 Chr2 21097854 21099826 +
Bva Bva01g01427 Chr01 15774047 15776223 -
Bva Bva11g00522 Chr11 8820356 8822699 -
Car Car06g00213 Chr06 2298246 2300438 -
Cca Cca06g00193 Chr06 4675458 4677358 -
Cca Cca09g02769 Chr09 53314553 53316773 +
Dod Dod04g3129 Chr04 54925218 54927038 +
Lal Lal23g0672 Chr23 9391036 9393242 +
Lal Lal16g0970 Chr16 6455093 6458067 -
Lja Lja2g3324 Chr2 75373385 75375477 +
Lja Lja4g0074 Chr4 597924 600106 -
Mal Mal1g4945 Chr1 119603802 119606563 -
Mal Mal5g0361 Chr5 5608186 5610001 +
Mtr Mtr1g1033 Chr1 11750424 11752639 +
Mtr Mtr8g3822 Chr8 48848922 48851109 +
Psa Psa7g0076 Chr7 5543594 5546009 -
Ssu Ssu2g1128 Chr2 51420399 51422168 -
Ssu Ssu5g3434 Chr5 84822921 84824756 +
Sto Sto11g0395 Chr11 5036257 5038439 -
Tpr Tpr3g0283 Chr3 3206398 3208765 -
Tsu Tsu01g01154 Chr01 10694761 10696091 +
Tsu Tsu02g00086 Chr02 586070 588104 -
Vvi Vvi1g0592 Chr1 5836688 5846071 -
Vvi Vvi1g0593 Chr1 5848050 5850416 -
Apr Apr7g0073 Chr7 3027929 3030449 +
Bva Bva01g01424 Chr01 15754299 15756737 +
Bva Bva11g00519 Chr11 8803504 8806233 +
Car Car04g02826 Chr04 54916288 54918678 +
Cca Cca06g00192 Chr06 4659592 4662216 +
Lja Lja2g3326 Chr2 75430791 75433569 -
Mal Mal1g4943 Chr1 119567121 119569502 +
Mtr Mtr1g1035 Chr1 11766852 11769714 -
Psa Psa6g1185 Chr6 47049306 47052671 +
Ssu Ssu2g1127 Chr2 51409834 51412224 +
Tpr Tpr1g2950 Chr1 33873114 33875899 +
Tsu Tsu01g01155 Chr01 10698577 10700848 -
Vra Vra11g1388 Chr11 16859911 16862791 +
Vvi Vvi1g0594 Chr1 5855245 5880879 -
Adu Adu03g04011 Chr03 129186215 129201985 -
Aed Aed5g2609 Chr5 26781395 26802961 -
Aip Aip03g04389 Chr03 128226555 128231095 -
Amo Amo13g4979 Chr13 148796283 148812902 -
Arst Arst3g05282 Chr3 127950243 127966648 -
Bva Bva01g01419 Chr01 15681351 15687919 +
Cca Cca09g02772 Chr09 53335060 53358387 -
Lal Lal16g0969 Chr16 6434926 6454786 +
Lasa Lasa7g05219 Chr7 715861092 715873019 -
Mepo Mepo2g05041 Chr2 58329599 58349049 -
Mesa Mesa13g00094 Chr13 1263524 1283694 +
Phco Phco4g03672 Chr4 56404535 56427429 -
Pste Pste3g00020 Chr3 103328 133030 +
Pumo Pumo6g00115 Chr6 1309447 1329173 +
Pvu Pvu2g3339 Chr2 48297997 48322293 -
Rops Rops2g00116 Chr2 1797070 1826826 +
Seca Seca12g06935 Chr12 161322881 161347655 -
Spst Spst3g00719 Chr3 10820927 10843929 +
Ssu Ssu5g3438 Chr5 84851967 84877439 -
Trre Trre7g05915 Chr7 63661330 63679150 -
Vian Vian1g04168 Chr1 64707584 64727381 -
Vifa Vifa6g04080 Chr6 1343579518 1343604232 -
Vimu Vimu11g04868 Chr11 68424404 68444574 -
Viun Viun3g00125 Chr3 598111 624963 +
Vivi Vivi5g06579 Chr5 172740404 172761266 +
Vvi Vvi1g0595 Chr1 5903915 5917506 -
Aev Aev03g3395 Chr03 31521829 31538312 -
Ahy Ahy13g3953 Chr13 138880485 138897117 -
Aip Aip03g04390 Chr03 128231189 128242454 -
Apr Apr2g1523 Chr2 21116927 21147679 -
Bva Bva11g00518 Chr11 8777556 8802819 +
Car Car06g00208 Chr06 2255195 2275258 +
Dod Dod04g3132 Chr04 54946922 54969847 -
Lal Lal15g0944 Chr15 7314174 7341569 +
Lja Lja4g0070 Chr4 557660 574619 +
Mal Mal5g0366 Chr5 5654869 5675444 -
Mtr Mtr8g3827 Chr8 48908686 48928689 -
Sto Sto11g0368 Chr11 4744769 4772932 +
Tpr Tpr3g0275 Chr3 3135320 3154076 +
Tsu Tsu02g00082 Chr02 542129 560175 +
Vvi Vvi1g0596 Chr1 5922426 5931085 +
Vvi Vvi1g0597 Chr1 5940758 5942086 -
Acco Acco05g1359 Chr05 28772671 28773981 +
Acco Acco05g1359 Chr05 28772671 28773981 +
Accr Accr3g01627 Chr3 19889829 19891136 -
Accr Accr3g01627 Chr3 19889829 19891136 -
Aev Aev03g0709 Chr03 5374483 5375802 +
Ahy Ahy13g3537 Chr13 133552906 133554613 -
Aip Aip03g03985 Chr03 123140900 123142700 -
Alju Alju07g1299 Chr07 37774595 37775905 +
Alju Alju07g1299 Chr07 37774595 37775905 +
Amo Amo13g4503 Chr13 141649741 141652272 -
Bach Bach3g01075 Chr3 21138417 21139718 +
Bisa Bisa05g1447 Chr05 25965629 25966939 +
Bisa Bisa05g1447 Chr05 25965629 25966939 +
Car Car06g00033 Chr06 424124 425832 +
Cca Cca01g00471 Chr01 5871363 5873104 +
Dere Dere05g1097 Chr05 17608745 17610049 -
Dere Dere05g1097 Chr05 17608745 17610049 -
Dod Dod04g0202 Chr04 2506303 2508130 +
Glsi Glsi10g1754 Chr10 12089766 12091067 -
Glsi Glsi10g1754 Chr10 12089766 12091067 -
Gma Gma18g00397 Chr18 3584669 3585964 -
Lapu Lapu6g01021 Chr6 10291629 10293192 +
Lapu Lapu6g01021 Chr6 10291629 10293192 +
Lasa Lasa3g01145 Chr3 289728494 289746610 -
Lasa Lasa2g01482 Chr2 461017680 461018999 -
Mepo Mepo3g05355 Chr3 67028466 67030078 +
Mepo Mepo7g02074 Chr7 31071210 31073007 +
Mibi Mibi08g1126 Chr08 26189269 26191069 +
Mibi Mibi08g1126 Chr08 26189269 26191069 +
Phco Phco2g02615 Chr2 55889150 55890490 +
Phco Phco3g00554 Chr3 4343353 4344666 +
Prci Prci2g2079 Chr2 15892378 15894007 -
Prci Prci2g2079 Chr2 15892378 15894007 -
Pste Pste8g01518 Chr8 8407977 8409287 -
Pste Pste8g01518 Chr8 8407977 8409287 -
Pte Pte8g00622 Chr8 28816424 28817989 +
Pumo Pumo9g02494 Chr9 59608543 59610425 -
Pvu Pvu1g2363 Chr1 48969145 48970805 +
Pvu Pvu8g2467 Chr8 55277984 55280310 -
Rops Rops9g01027 Chr9 16880622 16882151 -
Seca Seca6g02367 Chr6 85760595 85761902 -
Spst Spst8g00345 Chr8 3127909 3129216 -
Spst Spst1g02287 Chr1 31601353 31602690 -
Trre Trre5g00691 Chr5 4714265 4715578 -
Vian Vian7g01713 Chr7 26858226 26859533 -
Vifa Vifa1g01674 Chr1 274778632 274779951 -
Vimu Vimu1g01139 Chr1 8706316 8707617 -
Vimu Vimu1g01139 Chr1 8706316 8707617 -
Viun Viun8g02108 Chr8 31493695 31495372 +
Vvi Vvi1g0598 Chr1 5948703 5952982 -
Ahy Ahy13g3538 Chr13 133572321 133576222 -
Aip Aip03g03986 Chr03 123160505 123164472 -
Amo Amo13g4504 Chr13 141669944 141673985 -
Apr Apr7g0071 Chr7 2980324 2984623 +
Apr Apr2g1524 Chr2 21150723 21154438 -
Car Car06g00207 Chr06 2247100 2250874 +
Cca Cca06g00191 Chr06 4630619 4634828 +
Cca Cca01g00470 Chr01 5865414 5869162 +
Dod Dod04g0201 Chr04 2497276 2501253 +
Gma Gma18g00398 Chr18 3588651 3592278 -
Lal Lal22g0970 Chr22 8107177 8111172 -
Lal Lal18g0523 Chr18 4320145 4324084 +
Lal Lal23g0674 Chr23 9409469 9413171 -
Lal Lal15g0943 Chr15 7307008 7310386 +
Lja Lja2g3327 Chr2 75448631 75452482 -
Lja Lja4g0069 Chr4 551372 555811 +
Mal Mal1g4932 Chr1 119212691 119216283 +
Mal Mal5g0367 Chr5 5678355 5681430 +
Mtr Mtr1g1039 Chr1 11831933 11835893 -
Mtr Mtr8g3828 Chr8 48930580 48933785 -
Psa Psa6g1179 Chr6 46687433 46691929 +
Ssu Ssu2g1126 Chr2 51380591 51384332 +
Sto Sto11g0350 Chr11 4557548 4560384 -
Tpr Tpr1g2946 Chr1 33836123 33840059 +
Tpr Tpr3g0274 Chr3 3130957 3133986 +
Tsu Tsu01g01162 Chr01 10765082 10768724 -
Tsu Tsu02g00081 Chr02 526328 529261 +
Vra Vra11g1387 Chr11 16851969 16856768 +
Vvi Vvi1g0599 Chr1 5972668 5975687 -
Bva Bva01g01417 Chr01 15673220 15677394 +
Psa Psa6g2350 Chr6 169499395 169501323 -
Vvi Vvi1g0600 Chr1 5978471 5979374 -
Bva Bva11g00517 Chr11 8774645 8776196 +
Acco Acco05g1359 Chr05 28772671 28773981 +
Accr Accr3g01627 Chr3 19889829 19891136 -
Alju Alju07g1299 Chr07 37774595 37775905 +
Bach Bach3g01075 Chr3 21138417 21139718 +
Bisa Bisa05g1447 Chr05 25965629 25966939 +
Dere Dere05g1097 Chr05 17608745 17610049 -
Glsi Glsi10g1754 Chr10 12089766 12091067 -
Lapu Lapu6g01021 Chr6 10291629 10293192 +
Lasa Lasa2g01482 Chr2 461017680 461018999 -
Mepo Mepo7g02074 Chr7 31071210 31073007 +
Mibi Mibi08g1126 Chr08 26189269 26191069 +
Phco Phco3g00554 Chr3 4343353 4344666 +
Prci Prci2g2079 Chr2 15892378 15894007 -
Pste Pste8g01518 Chr8 8407977 8409287 -
Pte Pte8g00622 Chr8 28816424 28817989 +
Pumo Pumo9g02494 Chr9 59608543 59610425 -
Pvu Pvu8g2467 Chr8 55277984 55280310 -
Rops Rops9g01027 Chr9 16880622 16882151 -
Seca Seca6g02367 Chr6 85760595 85761902 -
Spst Spst1g02287 Chr1 31601353 31602690 -
Vian Vian7g01713 Chr7 26858226 26859533 -
Vifa Vifa1g01674 Chr1 274778632 274779951 -
Vimu Vimu1g01139 Chr1 8706316 8707617 -
Viun Viun8g02108 Chr8 31493695 31495372 +
Acco Acco05g1359 Chr05 28772671 28773981 +
Accr Accr3g01627 Chr3 19889829 19891136 -
Alju Alju07g1299 Chr07 37774595 37775905 +
Bach Bach3g01075 Chr3 21138417 21139718 +
Bisa Bisa05g1447 Chr05 25965629 25966939 +
Dere Dere05g1097 Chr05 17608745 17610049 -
Glsi Glsi10g1754 Chr10 12089766 12091067 -
Lapu Lapu6g01021 Chr6 10291629 10293192 +
Lasa Lasa2g01482 Chr2 461017680 461018999 -
Mepo Mepo7g02074 Chr7 31071210 31073007 +
Mibi Mibi08g1126 Chr08 26189269 26191069 +
Phco Phco3g00554 Chr3 4343353 4344666 +
Prci Prci2g2079 Chr2 15892378 15894007 -
Pste Pste8g01518 Chr8 8407977 8409287 -
Pte Pte8g00622 Chr8 28816424 28817989 +
Pumo Pumo9g02494 Chr9 59608543 59610425 -
Pvu Pvu8g2467 Chr8 55277984 55280310 -
Rops Rops9g01027 Chr9 16880622 16882151 -
Seca Seca6g02367 Chr6 85760595 85761902 -
Spst Spst1g02287 Chr1 31601353 31602690 -
Vian Vian7g01713 Chr7 26858226 26859533 -
Vifa Vifa1g01674 Chr1 274778632 274779951 -
Vimu Vimu1g01139 Chr1 8706316 8707617 -
Viun Viun8g02108 Chr8 31493695 31495372 +
Lapu Lapu6g01021 Chr6 10291629 10293192 +