Abstract

Grapevine is extensively grown for fresh table grapes, wine, and other processed products worldwide. DNA methylation levels are regulated by DNA methylation maintenance and DNA methylation removal involved in the grapevine growth. We comprehensively analyzed the transcriptome and metabolome of the ‘Kyoho’ fruit with or without demethylation and screened for a large number of differential genes and metabolites. Color, hardness, and aroma are the most obvious traits reflecting the ripening of grapes. We used gas chromatography–mass spectrometry and high-performance liquid chromatography to understand the changes in metabolites during ripening. We cloned many key genes selected by transcriptome analysis and found that intron retention was observed in VvCHS, VvDFR, and VvGST. The imbalance of methylation levels affects the alternative splicing of pre-mRNA, which makes the translation process abnormal and affects gene expression. In addition, analyzing promoters of some genes, such as proVvGST4 and proVvUFGT, found that the promoters of these genes after demethylating were more difficult to methylate. Taken together, this study will provide new insights into comprehension of the molecular mechanism of methylation during ripening of grape berries. In addition, the study provides some genetic information to help guide our improvement, cultivation, and management of grapes in the future.