DNA methylation, a conserved epigenetic modification, plays a crucial role in gene regulation and genome stability. Recently, a growing number of studies have investigated the role of DNA methylation in fruit development. Fruit size is an important indicator for measuring the yield and quality of horticultural plant fruits. However, the precise regulatory role of DNA methylation in the fruit swelling process remains poorly understood. Here, we completed the haploid genome assembly of Prunus persica ‘Zhong You 4’ (ZY4) and analyzed the changes in the methylome and transcriptome at the four fruit developmental stages of ZY4. DNA methylome analysis revealed that, compared to 31 days post-anthesis (DPA), CG and CHG methylation levels reduced at 46 DPA, 55 DPA, and 62 DPA, while CHH methylation levels increased. Further studies have found that changes in the methylation levels of CG and CHG may be associated with DNA demethylases, while the methylation levels of CHH may be regulated by DNA methyltransferases. The combined analysis of methylome and transcriptome identified three auxin-related genes, PpARF6 , PpARF16 , and PpTAR2 . qRT-PCR and bisulfite sequencing PCR (BSP) results showed that the CG DNA methylation levels of PpARF6 , PpARF16 , and PpTAR2 were negatively correlated with their expression level, which was further verified by the expression level changes in ‘Zaoyoutao’ calli treated with 5-Azacytidine (5-AzaC). Overall, this study reveals the dynamic variation of DNA methylation across fruit swelling and highlights the function of auxin metabolism-related genes in this process. • A chromosome-level genome assembly of ‘Zhong You 4’ (ZY4) was established. • The DNA methylation profile during the fruit swelling of ZY4 was constructed. • DNA methylation of PpARF6 , PpARF16 , and PpTAR2 was correlated with fruit swelling.
Hou et al. (2026) studied this question.