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
Vvi2g1102 . . . . . . . . . . . . . . . . . . . . . Arst1g01237 . . . . . Bva11g01370 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco8g00251 . . . . . Pste7g00527 . . . . . . . Pvu3g2850 . . . . . Spst3g03633 . . . Sto11g1343 . . . . . . . . . . . Vimu11g00975 . . . . . .
Vvi2g1103 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva08g01038 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Phco8g00248 . . . . . Pste7g00529 . . . . . . . Pvu3g2851 . . . . . Spst3g03632 . . . . . . . . . . . . . . . Vimu11g00976 . . . . . .
Vvi2g1104 . . . . . . . . Aev05g0249 . . . Aip05g00212 . . . . . . . Arst5g00303 . . . . . . . . . . . . . Dod02g0274 . . . . . . . . . . . . . Lal15g0341 . . . . . Lan18g0832 . . . . . Lapu2g00949 . . . . . . . . . . . Lja2g0717 . Mal6g0767 . Mepo5g01221 . Mesa17g01299 . . . Mtr5g1090 . Phac2g02001 . Phco4g00677 . . . Psa2g3255 . . . . Pte12g00602 . . Pumo8g01554 . Pvu2g1288 . Rops1g01367 . Seca10g01192 . Spst2g01111 . . . . . Tpr2g1346 . Trre9g01600 . Tsu05g01085 . Vian10g00970 . . . Vimu7g03295 . Viun2g01617 . . . . .
Vvi2g1105 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1106 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1107 . . . . . . Aed11g1050 . Aev05g0251 . . . Aip05g00214 . . . . . Apr7g1863 Apr3g0474 . . . . . . Bva08g01035 . . . Cca06g01102 . . . . . . . . . Gma01g01554 Gma09g02009 . . Gso1g1288 Gso1g1288 . . Lal15g0340 . . . . . Lan18g0833 . . . . . . . . . . . . . . . . . Lja2g0715 . Mal6g0769 . . . . . . . Mtr5g1088 . . . . . . . Psa2g3263 . . . . . . . . . . . . . . . . . Ssu2g2080 . . . Tpr2g1336 . . . Tsu05g01081 . . . . . . . . . . . . .
Vvi2g1108 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mal5g3167 . . . . . . . Mtr8g2258 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Tpr4g4439 . . . Tsu04g03053 . . . . . . . . . . . .
Vvi2g1109 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1110 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi2g1111 . . . . . . . . Aev05g0252 . . . Aip05g00215 . . . . . Apr7g1864 Apr3g0473 . . Bach4g00888 . . . Bva08g01034 . . . . . . . . . . . . . Gma01g01555 Gma09g02010 . . Gso1g1289 Gso1g1289 . . . . . . . . . . . . . . Lapu3g02114 Lapu3g02114 Lasa2g03644 Lasa4g01965 . . . . . . . . Lja2g0714 . Mal6g0770 . Mepo5g01217 Mepo1g02312 Mesa17g01296 Mesa29g02449 . . Mtr5g1087 . Phac2g01997 . Phco4g00679 Phco8g00247 . . Psa2g3264 . . Pste7g00532 . . . . . . Pvu2g1285 Pvu3g2852 . . . . Spst2g01107 Spst3g03630 . . Sto6g4097 . Tpr2g1335 . Trre9g01594 Trre15g02431 Tsu05g01080 . . . . . Vimu7g03292 Vimu11g00977 . . Vivi2g02595 . . .
   
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DecoBrowse

Select Species Gene Chromosome Start End Strand
Vvi Vvi2g1102 Chr2 17436530 17437873 +
Arst Arst1g01237 Chr1 12279615 12280883 -
Bva Bva11g01370 Chr11 13722876 13724198 -
Phco Phco8g00251 Chr8 2342149 2343459 +
Pste Pste7g00527 Chr7 4886876 4892253 -
Pvu Pvu3g2850 Chr3 50243419 50244959 -
Spst Spst3g03633 Chr3 86373108 86374442 +
Sto Sto11g1343 Chr11 12989157 12992495 -
Vimu Vimu11g00975 Chr11 10114582 10115892 -
Vvi Vvi2g1103 Chr2 17439361 17448268 -
Bva Bva08g01038 Chr08 5305938 5307175 +
Phco Phco8g00248 Chr8 2319208 2320503 -
Pste Pste7g00529 Chr7 4898712 4905583 -
Pvu Pvu3g2851 Chr3 50255976 50257265 +
Spst Spst3g03632 Chr3 86369447 86370745 +
Vimu Vimu11g00976 Chr11 10125709 10136280 +
Vvi Vvi2g1104 Chr2 17471136 17472056 +
Aev Aev05g0249 Chr05 1831048 1831875 -
Aip Aip05g00212 Chr05 2274268 2275319 -
Arst Arst5g00303 Chr5 2531028 2532150 +
Dod Dod02g0274 Chr02 3604317 3605820 +
Lal Lal15g0341 Chr15 2304410 2305156 +
Lan Lan18g0832 Chr18 13681091 13682233 -
Lapu Lapu2g00949 Chr2 8803334 8804913 -
Lja Lja2g0717 Chr2 6534910 6535930 +
Mal Mal6g0767 Chr6 11327153 11328028 -
Mepo Mepo5g01221 Chr5 12388040 12389308 +
Mesa Mesa17g01299 Chr17 16916772 16917683 +
Mtr Mtr5g1090 Chr5 10874685 10875992 +
Phac Phac2g02001 Chr2 21994714 21996063 +
Phco Phco4g00677 Chr4 5115615 5116319 -
Psa Psa2g3255 Chr2 369602381 369603187 -
Pte Pte12g00602 Chr12 5440443 5441574 +
Pumo Pumo8g01554 Chr8 50465443 50466669 -
Pvu Pvu2g1288 Chr2 25117567 25118766 +
Rops Rops1g01367 Chr1 30411252 30412410 -
Seca Seca10g01192 Chr10 11693710 11695010 +
Spst Spst2g01111 Chr2 9757621 9758325 +
Tpr Tpr2g1346 Chr2 15730328 15731468 +
Trre Trre9g01600 Chr9 13985996 13986811 +
Tsu Tsu05g01085 Chr05 9498136 9499100 +
Vian Vian10g00970 Chr10 10502540 10503244 +
Vimu Vimu7g03295 Chr7 27958230 27960232 +
Viun Viun2g01617 Chr2 25984703 25985674 -
Vvi Vvi2g1105 Chr2 17473391 17473669 +
Vvi Vvi2g1106 Chr2 17478430 17479578 -
Vvi Vvi2g1107 Chr2 17515272 17517964 +
Aed Aed11g1050 Chr11 16247057 16249607 +
Aev Aev05g0251 Chr05 1836932 1840182 +
Aip Aip05g00214 Chr05 2282047 2287765 +
Apr Apr7g1863 Chr7 25904868 25908412 +
Apr Apr3g0474 Chr3 9856538 9859442 -
Bva Bva08g01035 Chr08 5295295 5297875 -
Cca Cca06g01102 Chr06 25099911 25104223 +
Gma Gma01g01554 Chr01 51039118 51043730 +
Gma Gma09g02009 Chr09 45687097 45690966 +
Gso Gso1g1288 Chr1 49322951 49328826 +
Gso Gso1g1288 Chr1 49322951 49328826 +
Lal Lal15g0340 Chr15 2296752 2299622 -
Lan Lan18g0833 Chr18 13687571 13692840 +
Lja Lja2g0715 Chr2 6521650 6525482 -
Mal Mal6g0769 Chr6 11333207 11336676 +
Mtr Mtr5g1088 Chr5 10866292 10868604 -
Psa Psa2g3263 Chr2 370265852 370268137 +
Ssu Ssu2g2080 Chr2 75672666 75677961 +
Tpr Tpr2g1336 Chr2 15619028 15621991 -
Tsu Tsu05g01081 Chr05 9481099 9483740 -
Vvi Vvi2g1108 Chr2 17518996 17520471 -
Mal Mal5g3167 Chr5 92549533 92551011 +
Mtr Mtr8g2258 Chr8 32806437 32808249 +
Tpr Tpr4g4439 Chr4 52078851 52080746 -
Tsu Tsu04g03053 Chr04 37772750 37774219 +
Vvi Vvi2g1109 Chr2 17546386 17549931 +
Vvi Vvi2g1110 Chr2 17566264 17566545 -
Vvi Vvi2g1111 Chr2 17582981 17584459 -
Aev Aev05g0252 Chr05 1842624 1844129 +
Aip Aip05g00215 Chr05 2289632 2291253 +
Apr Apr7g1864 Chr7 25910432 25911886 +
Apr Apr3g0473 Chr3 9837679 9840652 -
Bach Bach4g00888 Chr4 5959047 5960546 -
Bva Bva08g01034 Chr08 5290963 5292600 -
Gma Gma01g01555 Chr01 51044896 51046356 +
Gma Gma09g02010 Chr09 45691980 45693457 +
Gso Gso1g1289 Chr1 49328845 49330448 +
Gso Gso1g1289 Chr1 49328845 49330448 +
Lapu Lapu3g02114 Chr3 41040068 41041770 -
Lapu Lapu3g02114 Chr3 41040068 41041770 -
Lasa Lasa2g03644 Chr2 545917566 545919032 -
Lasa Lasa4g01965 Chr4 399831091 399832584 -
Lja Lja2g0714 Chr2 6519055 6520569 -
Mal Mal6g0770 Chr6 11338403 11339854 +
Mepo Mepo5g01217 Chr5 12362038 12363599 -
Mepo Mepo1g02312 Chr1 23867522 23868988 -
Mesa Mesa17g01296 Chr17 16879303 16880493 -
Mesa Mesa29g02449 Chr29 33511160 33512611 -
Mtr Mtr5g1087 Chr5 10862819 10864560 -
Phac Phac2g01997 Chr2 21972082 21973545 -
Phco Phco4g00679 Chr4 5128033 5129493 +
Phco Phco8g00247 Chr8 2313846 2315360 -
Psa Psa2g3264 Chr2 370268575 370270445 +
Pste Pste7g00532 Chr7 4933695 4935206 +
Pvu Pvu2g1285 Chr2 25088917 25090380 -
Pvu Pvu3g2852 Chr3 50261078 50262883 +
Spst Spst2g01107 Chr2 9746935 9748398 -
Spst Spst3g03630 Chr3 86361735 86363249 -
Sto Sto6g4097 Chr6 44525858 44531739 -
Tpr Tpr2g1335 Chr2 15616189 15617817 -
Trre Trre9g01594 Chr9 13954080 13955537 -
Trre Trre15g02431 Chr15 20190732 20192198 +
Tsu Tsu05g01080 Chr05 9478560 9480017 -
Vimu Vimu7g03292 Chr7 27947525 27948988 -
Vimu Vimu11g00977 Chr11 10138999 10140450 +
Vivi Vivi2g02595 Chr2 117339905 117341987 +