Fig. 7

Summary of the metabolites, genes, and DNA methylation involved in pear flesh development. a The numbers of metabolites and genes were calculated between two adjacent stages during pear flesh development. DAM was calculated from metabolome data, while DEG was calculated from transcriptome data. Genes correlated with DAMs between adjacent stages was isolated from the gene-metabolite database and referred to as “correlated genes”. The intersection of DEGs and correlated genes is referred to as “Correlated DEGs.” Correlated DEGs that were modified by DNA methylation are denoted as “DMR-modified correlated DEG.” S1 to S11 indicate the different stages of pear flesh development. b A model shows the molecular pathway through which development-induced DNA methylation affects pear flesh development. During flesh development, TFs induce the expression of catalytic genes, leading to increased accumulation of catalytic enzymes that convert metabolite from one type (metabolite A) to another (metabolite B), thereby promoting the flesh development process. However, this process also represses the expression of demethylase, RdDM pathway, and methyltransferase genes, resulting in increased DNA methylation. This elevated DNA methylation affects the transcription of TFs and downstream catalytic genes, thereby influencing pear flesh development