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Background  5-Azacytidine (5-azaC) promotes the development of ‘Kyoho’ grape berry but the associated changes in gene expression have not been reported. In this study, we performed transcriptome analysis of grape berry at five developmental stages after 5-azaC treatment to elucidate the gene expression networks controlling berry ripening.    Results  The expression patterns of most genes across the time series were similar between the 5-azaC treatment and control groups. The number of differentially expressed genes (DEGs) at a given developmental stage ranged from 9 (A3_C3) to 690 (A5_C5). The results indicated that 5-azaC treatment had not very great influences on the expressions of most genes. Functional annotation of the DEGs revealed that they were mainly related to fruit softening, photosynthesis, protein phosphorylation, and heat stress. Eight modules showed high correlation with specific developmental stages and hub genes such as  PEROXIDASE 4 ,  CAFFEIC ACID 3-O-METHYLTRANSFERASE 1 , and  HISTONE-LYSINE N-METHYLTRANSFERASE EZA1  were identified by weighted gene correlation network analysis.    Conclusions  5-AzaC treatment alters the transcriptional profile of grape berry at different stages of development, which may involve changes in DNA methylation.

Transcriptome profiling of ‘Kyoho’ grape at different stages of berry development following 5-azaC treatment