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
Vvi18g1680 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1681 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1682 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1683 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla11g00805 Cam11g0842 Cec11g0828 . Clacu11g1015 Cmu11g0878 Cre11g1288 . . . .
Vvi18g1684 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1685 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1686 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1687 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi18g1688 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cmo09g01262 . . . . . . Bhi06g00166 . . . . . . . . . . . . . . . . .
Vvi18g1689 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
6 3879120 3883884 + XM_039034069.1 Bhi06g00166 166
11 10992717 10993076 - CaPI482276_11g008420.1 Cam11g0842 842
11 10083868 10089430 - CePI673135_11g008280.1 Cec11g0828 828
11 12321642 12328903 + ClG42_11g0101500.10 Clacu11g1015 1015
11 11878659 11884531 - ClCG11G008400.2 Cla11g00805 805
9 11031083 11034747 - CmoCh09G012620.1 Cmo09g01262 1262
11 11650910 11657961 + CmPI595203_11g008780.1 Cmu11g0878 878
11 11677338 11677697 - CrPI670011_11g012880.1 Cre11g1288 1288
18 27443175 27445765 - Vvi18g1680 Vvi18g1680 1680
18 27461822 27467042 - Vvi18g1681 Vvi18g1681 1681
18 27468330 27468644 - Vvi18g1682 Vvi18g1682 1682
18 27481318 27483541 + Vvi18g1683 Vvi18g1683 1683
18 27491473 27505772 - Vvi18g1684 Vvi18g1684 1684
18 27505817 27508135 - Vvi18g1685 Vvi18g1685 1685
18 27514536 27525652 - Vvi18g1686 Vvi18g1686 1686
18 27560395 27577010 - Vvi18g1687 Vvi18g1687 1687
18 27592347 27597480 - Vvi18g1688 Vvi18g1688 1688
18 27602437 27608757 + Vvi18g1689 Vvi18g1689 1689
       

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