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
Vvi5g869 . . . . . . . . . . . . . . . Cpe08g00417 . . . . . . . . . . . . . . . . . . . Lsi05g01869 . . . . . . Bda13g00019 . . Bma02g00734 . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g870 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g871 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g872 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g873 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g874 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Bpe13g00903 . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g875 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g876 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g877 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi5g878 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
13 360968 362466 - Bda000861.1 Bda13g00019 19
2 37559291 37561396 + Bma015434.1 Bma02g00734 734
13 15064913 15070017 + Bpe010587.1 Bpe13g00903 903
8 2671282 2674819 - Cp4.1LG08g02580.1 Cpe08g00417 417
5 25912314 25915116 + Lsi05G018690.1 Lsi05g01869 1869
5 12253153 12259771 - Vvi5g869 Vvi5g869 869
5 12262125 12304003 - Vvi5g870 Vvi5g870 870
5 12315751 12321473 + Vvi5g871 Vvi5g871 871
5 12321476 12325195 + Vvi5g872 Vvi5g872 872
5 12427631 12428669 - Vvi5g873 Vvi5g873 873
5 13037454 13039809 + Vvi5g874 Vvi5g874 874
5 13060764 13061268 - Vvi5g875 Vvi5g875 875
5 13190068 13190368 + Vvi5g876 Vvi5g876 876
5 13295413 13296045 + Vvi5g877 Vvi5g877 877
5 13298066 13301005 - Vvi5g878 Vvi5g878 878
       

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