Doc-Alignment

  Inter-genomic and intra-genomic comparisons can help reveal the structural complexity of Cucurbitales genomes. We used V.vinifera as a reference, and by comparing homologous gene locus maps and Ks values between V.vinifera and other Cucurbitales, we could separate orthologous and paralogous genes produced by different polyploidization in the species genomes. We created a hierarchical lists of homologous genes using V.vinifera as a reference.
  The relevant gene ids can be obtained from the Cucurbitales blast and match under the Tools module. This link is Cucurbitales blast and match.

Orthogroup analysis platform
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Select Vvi1 Blo1 Blo2 Bda1 Bda2 Bpe1 Bpe2 Bma1 Bma2 Cmo1 Cmo2 Cma1 Cma2 Car1 Car2 Sed1 Cpe1 Cpe2 Bhi1 Tan1 Cmetu1 Lac1 Hepe1 Mch1 Lcy1 Cla1 Cam1 Cec1 Cco1 Clacu1 Cmu1 Cre1 Cone1 Cone2 Cone3 Cone4 Lsi1 Csa1 Chy1 Cme1 Blo3 Blo4 Bda3 Bda4 Bpe3 Bpe4 Bma3 Bma4 Sed2 Cmo3 Cmo4 Cma3 Cma4 Car3 Car4 Cpe3 Cpe4 Bhi2 Tan2 Cmetu2 Lac2 Hepe2 Mch2 Lcy2 Cla2 Cam2 Cec2 Cco2 Clacu2 Cmu2 Cre2 Lsi2 Csa2 Chy2 Cme2
Vvi4g412 . . . . . . . . . . . Cma05g00408 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g413 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g414 . . Bda01g00727 . . . . . . . . . . . . . . . . . . . . . Cla05g01759 Cam05g1873 Cec05g1886 Cco05g1950 Clacu05g1865 Cmu05g1746 Cre05g1876 . . . Cone20ag0657 . . Chy04g00346 . . . . . . . . . . . . . . . . . Cpe02g00466 . . . . . . . . . . . . . . . . . Cme04g00385
Vvi4g415 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g416 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone17ag1044 . . . . . Blo17g00030 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g417 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g418 . . . Bda03g00059 . . Bma04g00058 . . . Cma01g01476 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe04g00046 . . . Cmo01g01531 . . . . . . Cpe02g00477 . . . . . . . . . . . . . . . . . .
Vvi4g419 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g420 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g421 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 34575149 34576566 + Bda002764.1 Bda01g00727 727
3 700402 701831 - Bda015995.1 Bda03g00059 59
17 170237 171976 - BLOR15851 Blo17g00030 30
4 544434 545866 - Bma018509.1 Bma04g00058 58
4 430599 432027 - Bpe014770.1 Bpe04g00046 46
5 27674346 27675692 + CaPI482276_05g018730.1 Cam05g1873 1873
5 28559093 28560457 + CcPI632755_05g019500.1 Cco05g1950 1950
5 30914013 30915305 + CePI673135_05g018860.1 Cec05g1886 1886
4 3091120 3092467 + Chy4G070640.1 Chy04g00346 346
5 27870995 27872340 + ClG42_05g0186500.10 Clacu05g1865 1865
5 29416695 29424195 + ClCG05G017160.2 Cla05g01759 1759
1 10405178 10407747 + CmaCh01G014760.1 Cma01g01476 1476
5 1796639 1800228 - CmaCh05G004080.1 Cma05g00408 408
4 3091602 3093967 + MELO3C003677.2.1 Cme04g00385 385
1 11828449 11830638 + CmoCh01G015310.1 Cmo01g01531 1531
5 27589216 27590561 + CmPI595203_05g017460.1 Cmu05g1746 1746
17 7876242 7879261 - Conep17aG0107200.1 Cone17ag1044 1044
20 4002259 4004514 + Conep20aG0067700.1 Cone20ag0657 657
2 2640372 2642295 - Cp4.1LG02g03960.1 Cpe02g00466 466
2 2707191 2709704 - Cp4.1LG02g03940.1 Cpe02g00477 477
5 30909828 30911181 + CrPI670011_05g018760.1 Cre05g1876 1876
4 4185432 4190152 - Vvi4g412 Vvi4g412 412
4 4190724 4193303 + Vvi4g413 Vvi4g413 413
4 4193360 4196318 - Vvi4g414 Vvi4g414 414
4 4206513 4209963 - Vvi4g415 Vvi4g415 415
4 4215068 4225087 + Vvi4g416 Vvi4g416 416
4 4227018 4234518 - Vvi4g417 Vvi4g417 417
4 4241392 4244043 - Vvi4g418 Vvi4g418 418
4 4258542 4265236 + Vvi4g419 Vvi4g419 419
4 4265751 4286094 + Vvi4g420 Vvi4g420 420
4 4286127 4295628 + Vvi4g421 Vvi4g421 421
       

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