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
Vvi18g1530 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1531 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1532 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1533 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1534 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1535 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1536 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1537 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1538 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1539 . . . . . . . . . . . . . . . . . . . . . . . . Cla08g00019 Cam08g0013 Cec08g0247 Cco08g0060 Clacu08g0032 Cmu08g0028 Cre08g0014 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lsi08g00013 . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 226063 235150 - CaPI482276_08g000130.1 Cam08g0013 13
8 620615 629668 - CcPI632755_08g000600.1 Cco08g0060 60
8 4729112 4738281 + CePI673135_08g002470.1 Cec08g0247 247
8 670277 679426 - ClG42_08g0003200.10 Clacu08g0032 32
8 476580 487238 - ClCG08G000190.1 Cla08g00019 19
8 593918 596809 - CmPI595203_08g000280.1 Cmu08g0028 28
8 378706 381588 - CrPI670011_08g000140.1 Cre08g0014 14
8 301505 311341 - Lsi08G000130.1 Lsi08g00013 13
18 24574673 24579669 - Vvi18g1530 Vvi18g1530 1530
18 24591354 24594186 - Vvi18g1531 Vvi18g1531 1531
18 24595026 24597973 - Vvi18g1532 Vvi18g1532 1532
18 24598422 24599846 - Vvi18g1533 Vvi18g1533 1533
18 24609786 24626801 + Vvi18g1534 Vvi18g1534 1534
18 24632903 24636927 - Vvi18g1535 Vvi18g1535 1535
18 24653599 24658199 + Vvi18g1536 Vvi18g1536 1536
18 24686321 24706873 + Vvi18g1537 Vvi18g1537 1537
18 24707444 24716860 - Vvi18g1538 Vvi18g1538 1538
18 24717584 24778463 + Vvi18g1539 Vvi18g1539 1539
       

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