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
Vvi4g722 . . . . . . . . . . . . . . . . . . . . . . . . Cla01g00848 Cam01g0873 Cec01g0873 Cco01g0902 Clacu01g0864 Cmu01g0830 Cre09g1678 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g723 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g724 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g725 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g726 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g727 . . . . . . . . . . . . . . . Cpe07g00821 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g728 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g729 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g730 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g731 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
1 10198500 10199861 - CaPI482276_01g008730.1 Cam01g0873 873
1 10010060 10011470 - CcPI632755_01g009020.1 Cco01g0902 902
1 10054181 10055562 - CePI673135_01g008730.1 Cec01g0873 873
1 9849127 9850528 - ClG42_01g0086400.10 Clacu01g0864 864
1 10345393 10347133 - ClCG01G008640.1 Cla01g00848 848
1 9813818 9815187 - CmPI595203_01g008300.1 Cmu01g0830 830
7 7428581 7431862 + Cp4.1LG07g08180.1 Cpe07g00821 821
9 34540267 34541655 + CrPI670011_09g016780.1 Cre09g1678 1678
4 11299191 11300619 - Vvi4g722 Vvi4g722 722
4 11381697 11383195 + Vvi4g723 Vvi4g723 723
4 11384823 11386846 - Vvi4g724 Vvi4g724 724
4 11443795 11463685 - Vvi4g725 Vvi4g725 725
4 11494434 11499618 + Vvi4g726 Vvi4g726 726
4 11504980 11507297 - Vvi4g727 Vvi4g727 727
4 11555482 11560214 + Vvi4g728 Vvi4g728 728
4 11587679 11589305 - Vvi4g729 Vvi4g729 729
4 11595049 11598012 + Vvi4g730 Vvi4g730 730
4 11610027 11613129 - Vvi4g731 Vvi4g731 731
       

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