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
Vvi3g736 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1070 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g737 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g738 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g739 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1069 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g740 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g741 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone8ag1068 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g742 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g743 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g744 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cone12ag1036 Cone8ag1067 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Vvi3g745 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
   
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Gene_GFF

Select Chromosome Start End Strand Old_gene Gene Num
8 9691283 9694403 + Conep08aG0109600.1 Cone8ag1067 1067
8 9696866 9699800 + Conep08aG0109700.1 Cone8ag1068 1068
8 9700799 9704419 + Conep08aG0109800.1 Cone8ag1069 1069
8 9706691 9710262 + Conep08aG0109900.1 Cone8ag1070 1070
12 8661014 8664634 - Conep12aG0106500.1 Cone12ag1036 1036
3 7855564 7864719 - Vvi3g736 Vvi3g736 736
3 7866656 7868625 - Vvi3g737 Vvi3g737 737
3 7888985 7890280 - Vvi3g738 Vvi3g738 738
3 7903957 7934080 - Vvi3g739 Vvi3g739 739
3 7935403 7950401 - Vvi3g740 Vvi3g740 740
3 7951097 7955705 - Vvi3g741 Vvi3g741 741
3 7987350 7989378 - Vvi3g742 Vvi3g742 742
3 7999218 8021041 - Vvi3g743 Vvi3g743 743
3 8035060 8039037 - Vvi3g744 Vvi3g744 744
3 8069855 8072937 - Vvi3g745 Vvi3g745 745
       

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