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
Vvi3g0873 . . . . . . Aed1g2041 . . . . . . . . . . . Apr8g2391 . . . Bach11g00370 . . . Bva13g00421 Bva14g00511 Car04g01392 . Cca02g02469 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lapu7g02249 . Lasa6g04386 . . . . . . . . . Lja5g0465 . . Mal1g0610 Mepo4g04496 . Mesa1g04922 . . . . Mtr1g3997 . . Phco6g02723 . . . . . Pste4g01302 . . . . . Pumo3g00702 . Pvu7g0484 . Rops6g03023 . Seca8g07657 . Spst10g01226 . Ssu7g0541 . . Sto10g0393 . Tpr1g0511 Trre1g05739 . . Tsu01g04674 Vian3g00439 . Vifa3g03256 . Vimu3g03324 . Viun7g03549 . Vivi1g04014 . Vra8g2375 .
Vvi3g0874 . . . . . . Aed1g2042 . . Aev05g1247 . Ahy15g1312 . Aip05g01384 . . . Amo15g0067 Apr8g2390 . . . Bach11g00371 . . . Bva13g00422 Bva14g00512 Car04g01391 . Cca02g02468 . . . . Dod02g1389 . . . . . . . . . . . . . . . . . . . . . . . . Lapu7g02248 . Lasa6g04383 . . . . . . . . . Lja5g0466 . . Mal1g0611 Mepo4g04495 . Mesa1g04921 . . . . Mtr1g3996 . . Phco6g02722 . . . Psa6g4860 . Pste4g01303 . . . . . Pumo3g00704 . Pvu7g0485 . Rops6g03022 . Seca8g07656 . Spst10g01224 . Ssu7g0542 . . . . Tpr1g0512 Trre1g05738 . . Tsu01g04673 Vian3g00440 . Vifa3g03255 . Vimu3g03323 . Viun7g03547 . Vivi1g04015 . Vra8g2374 .
Vvi3g0875 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0876 . . . . . Adu05g01340 . Aed11g1940 . Aev05g1245 . Ahy15g1310 . Aip05g01382 . . . Amo15g0069 . . . Arst5g01713 . . . . . Bva14g00514 . Car08g00040 . Cca06g02025 . . . Dod02g1387 . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa2g02534 . . . . . . . . . . . . . Mepo5g00048 . Mesa17g00044 . . . . . . . Phco4g00047 . . . . . . . . . Pte19g00454 . . . Pvu2g0514 . . . . . . . Ssu2g3139 Sto2g0472 . . . . Trre9g00044 . . . . . . . . . . . Vivi2g04245 . Vra11g0050
Vvi3g0877 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0878 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0879 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lal3g0053 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Psa6g4857 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0880 . . . . . . . . . . . . . . . . . . . . . . . . . . Bva13g00424 Bva14g00515 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g0881 . . . . Adu09g02571 . Aed1g2046 . . . Ahy19g3356 . Aip09g03824 . . . . . Apr8g2388 . Arst9g03402 . . . . . . . Car04g01386 . Cca02g02466 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasa6g04379 . . . . . . . . . Lja5g0468 . . . . . . . . . . Mtr1g3992 . . Phco6g02719 . . . Psa6g4853 . . . . . . . . . Pvu7g0487 . Rops6g03020 . . . Spst10g01222 . . . . Sto10g0394 . . . . . . . . Vifa3g03251 . Vimu3g03320 . . . Vivi1g04019 . Vra8g2372 .
Vvi3g0882 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Select Species Gene Chromosome Start End Strand
Vvi Vvi3g0873 Chr3 8427168 8430686 -
Aed Aed1g2041 Chr1 17169805 17172071 -
Apr Apr8g2391 Chr8 34190599 34193761 +
Bach Bach11g00370 Chr11 2493558 2496278 -
Bva Bva13g00421 Chr13 1945433 1947799 -
Bva Bva14g00511 Chr14 2437025 2439440 -
Car Car04g01392 Chr04 14179122 14182870 +
Cca Cca02g02469 Chr02 45839327 45842786 +
Lapu Lapu7g02249 Chr7 38819981 38825822 +
Lasa Lasa6g04386 Chr6 638068918 638071877 +
Lja Lja5g0465 Chr5 4101409 4105413 -
Mal Mal1g0610 Chr1 7038097 7040944 -
Mepo Mepo4g04496 Chr4 54712601 54716141 +
Mesa Mesa1g04922 Chr1 76091305 76093025 +
Mtr Mtr1g3997 Chr1 51588409 51590629 +
Phco Phco6g02723 Chr6 48725884 48729664 +
Pste Pste4g01302 Chr4 9529875 9533749 -
Pumo Pumo3g00702 Chr3 10374886 10378358 -
Pvu Pvu7g0484 Chr7 3823318 3827445 -
Rops Rops6g03023 Chr6 53279687 53282715 +
Seca Seca8g07657 Chr8 173879852 173882898 +
Spst Spst10g01226 Chr10 13052797 13054934 +
Ssu Ssu7g0541 Chr7 9909899 9912700 -
Sto Sto10g0393 Chr10 3158131 3162699 -
Tpr Tpr1g0511 Chr1 4290982 4294258 -
Trre Trre1g05739 Chr1 62348284 62351145 +
Tsu Tsu01g04674 Chr01 54092004 54095334 +
Vian Vian3g00439 Chr3 4131063 4134555 -
Vifa Vifa3g03256 Chr3 932782549 932785339 +
Vimu Vimu3g03324 Chr3 46683680 46686791 +
Viun Viun7g03549 Chr7 36910811 36913999 +
Vivi Vivi1g04014 Chr1 84716775 84720539 -
Vra Vra8g2375 Chr8 41940633 41945221 +
Vvi Vvi3g0874 Chr3 8432236 8436227 -
Aed Aed1g2042 Chr1 17173035 17177064 -
Aev Aev05g1247 Chr05 8786817 8793021 +
Ahy Ahy15g1312 Chr15 21471528 21474612 +
Aip Aip05g01384 Chr05 20694238 20697347 +
Amo Amo15g0067 Chr15 2289341 2292389 -
Apr Apr8g2390 Chr8 34185322 34189175 +
Bach Bach11g00371 Chr11 2497370 2500407 -
Bva Bva13g00422 Chr13 1948556 1952690 -
Bva Bva14g00512 Chr14 2439977 2444158 -
Car Car04g01391 Chr04 14172967 14177342 +
Cca Cca02g02468 Chr02 45833510 45838268 +
Dod Dod02g1389 Chr02 16771740 16775399 +
Lapu Lapu7g02248 Chr7 38815091 38819217 +
Lasa Lasa6g04383 Chr6 638025068 638028064 +
Lja Lja5g0466 Chr5 4107457 4111232 -
Mal Mal1g0611 Chr1 7042856 7046614 -
Mepo Mepo4g04495 Chr4 54703389 54707388 +
Mesa Mesa1g04921 Chr1 76081799 76085878 +
Mtr Mtr1g3996 Chr1 51580919 51585011 +
Phco Phco6g02722 Chr6 48720730 48724504 +
Psa Psa6g4860 Chr6 425431569 425435452 +
Pste Pste4g01303 Chr4 9535903 9539158 -
Pumo Pumo3g00704 Chr3 10382847 10384120 -
Pvu Pvu7g0485 Chr7 3828585 3832663 -
Rops Rops6g03022 Chr6 53273016 53276904 +
Seca Seca8g07656 Chr8 173873108 173878029 +
Spst Spst10g01224 Chr10 13035466 13040348 +
Ssu Ssu7g0542 Chr7 9915281 9920019 -
Tpr Tpr1g0512 Chr1 4295426 4299196 -
Trre Trre1g05738 Chr1 62342881 62346642 +
Tsu Tsu01g04673 Chr01 54086683 54089503 +
Vian Vian3g00440 Chr3 4136186 4139915 -
Vifa Vifa3g03255 Chr3 932568100 932571450 +
Vimu Vimu3g03323 Chr3 46678332 46682039 +
Viun Viun7g03547 Chr7 36905444 36909652 +
Vivi Vivi1g04015 Chr1 84756318 84759426 -
Vra Vra8g2374 Chr8 41935302 41939452 +
Vvi Vvi3g0875 Chr3 8443429 8444643 +
Vvi Vvi3g0876 Chr3 8486865 8618518 -
Adu Adu05g01340 Chr05 20204094 20229722 +
Aed Aed11g1940 Chr11 22154609 22188736 +
Aev Aev05g1245 Chr05 8752400 8774978 +
Ahy Ahy15g1310 Chr15 21408551 21435620 +
Aip Aip05g01382 Chr05 20650592 20677120 +
Amo Amo15g0069 Chr15 2305273 2332222 -
Arst Arst5g01713 Chr5 20252297 20278678 +
Bva Bva14g00514 Chr14 2451966 2480267 -
Car Car08g00040 Chr08 337762 373568 -
Cca Cca06g02025 Chr06 35475122 35509323 +
Dod Dod02g1387 Chr02 16695717 16742358 +
Lasa Lasa2g02534 Chr2 504093998 504130715 -
Mepo Mepo5g00048 Chr5 447412 482092 -
Mesa Mesa17g00044 Chr17 413356 449599 -
Phco Phco4g00047 Chr4 295223 325565 -
Pte Pte19g00454 Chr19 3657209 3686963 -
Pvu Pvu2g0514 Chr2 4636513 4648787 +
Ssu Ssu2g3139 Chr2 93512023 93515775 +
Sto Sto2g0472 Chr2 4108864 4109427 +
Trre Trre9g00044 Chr9 500168 506897 -
Vivi Vivi2g04245 Chr2 156052836 156105084 +
Vra Vra11g0050 Chr11 361328 393613 -
Vvi Vvi3g0877 Chr3 8630875 8631114 -
Vvi Vvi3g0878 Chr3 8631356 8631469 -
Vvi Vvi3g0879 Chr3 8654539 8658460 -
Lal Lal3g0053 Chr3 311305 314843 +
Psa Psa6g4857 Chr6 425280446 425281721 +
Vvi Vvi3g0880 Chr3 8660792 8679292 +
Bva Bva13g00424 Chr13 1961540 1966809 +
Bva Bva14g00515 Chr14 2481342 2486441 +
Vvi Vvi3g0881 Chr3 8696026 8697570 +
Adu Adu09g02571 Chr09 113299745 113301636 +
Aed Aed1g2046 Chr1 17197567 17198049 +
Ahy Ahy19g3356 Chr19 156475688 156476761 -
Aip Aip09g03824 Chr09 144834824 144835525 -
Apr Apr8g2388 Chr8 34167030 34167746 -
Arst Arst9g03402 Chr9 111196529 111197308 +
Car Car04g01386 Chr04 14114695 14115396 -
Cca Cca02g02466 Chr02 45814131 45814727 -
Lasa Lasa6g04379 Chr6 637603782 637604495 -
Lja Lja5g0468 Chr5 4127122 4127649 +
Mtr Mtr1g3992 Chr1 51537116 51537829 -
Phco Phco6g02719 Chr6 48700528 48701307 -
Psa Psa6g4853 Chr6 422065882 422067934 -
Pvu Pvu7g0487 Chr7 3852475 3853233 -
Rops Rops6g03020 Chr6 53241879 53242451 -
Spst Spst10g01222 Chr10 12985578 12990814 +
Sto Sto10g0394 Chr10 3169932 3179228 +
Vifa Vifa3g03251 Chr3 928894403 928895117 -
Vimu Vimu3g03320 Chr3 46661919 46662233 +
Vivi Vivi1g04019 Chr1 84950733 84951446 +
Vra Vra8g2372 Chr8 41918652 41920262 +
Vvi Vvi3g0882 Chr3 8736929 8743307 -
Vifa Vifa3g03251 Chr3 928894403 928895117 -
Lal Lal3g0053 Chr3 311305 314843 +