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
Vvi4g742 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cla03g01101 Cam03g1149 Cec03g1167 Cco03g1155 Clacu03g1120 Cmu03g1707 Cre03g1421 . . . Cme02g00942
Vvi4g743 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g744 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g745 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g746 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g747 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe14g00067 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g748 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g749 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe14g00054 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g750 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone10ag0655 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi4g751 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
14 881585 884955 - Bpe006712.1 Bpe14g00054 54
14 1077870 1080909 + Bpe006722.1 Bpe14g00067 67
3 22498060 22501979 - CaPI482276_03g011490.1 Cam03g1149 1149
3 22004166 22007675 - CcPI632755_03g011550.1 Cco03g1155 1155
3 25690423 25693492 - CePI673135_03g011670.1 Cec03g1167 1167
3 21303266 21307170 - ClG42_03g0112000.10 Clacu03g1120 1120
3 22218829 22223205 - ClCG03G011470.1 Cla03g01101 1101
2 13329780 13333712 + MELO3C010087.2.1 Cme02g00942 942
3 21689225 21693129 - CmPI595203_03g017070.1 Cmu03g1707 1707
10 3164573 3174134 + Conep10aG0067200.1 Cone10ag0655 655
3 26740139 26744027 - CrPI670011_03g014210.1 Cre03g1421 1421
4 12136528 12197093 + Vvi4g742 Vvi4g742 742
4 12716998 12717535 + Vvi4g743 Vvi4g743 743
4 12779376 12797933 + Vvi4g744 Vvi4g744 744
4 12797954 12843528 + Vvi4g745 Vvi4g745 745
4 12956303 12969259 - Vvi4g746 Vvi4g746 746
4 13006927 13017295 + Vvi4g747 Vvi4g747 747
4 13017350 13019076 + Vvi4g748 Vvi4g748 748
4 13197212 13217334 + Vvi4g749 Vvi4g749 749
4 13311388 13319110 + Vvi4g750 Vvi4g750 750
4 13328947 13333387 - Vvi4g751 Vvi4g751 751
       

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