Genome-wide DNA hypermethylation enhances watermelon fruit ripening

Watermelon ( Citrullus lanatus ), an important member of the Cucurbitaceae family, has become one of the most popular economic crops in the world, and understanding its fruit development and ripening has always been a hot topic. Although DNA methylation is known to play an essential role in fruit ripening, its contribution to watermelon ripening remains unknown. Here, we found a global and conspicuous hypermethylation pattern during watermelon fruit development and ripening, which is opposite to the hypomethylation found in tomato and strawberry. Application of the DNA methylation inhibitor 5-azacytidine (5-Aza) delayed fruit ripening, confirming that the positive role of hypermethylation in this process. The hypermethylation mainly occurred in CHG and CHH types, and gene-body hypermethylation strongly correlated with the expression of genes that related to sugar metabolism and ABA (abscisic acid) response. We also found an overall hypermethylation pattern in domesticated watermelon. ClROS1 ( Repressor Of Silencing 1 ), a gene encoding the DNA demethylase, was under selection; its expression was negatively correlated with DNA methylation levels, suggesting that it contributes to the hypermethylation during ripening. Collectively, our research illuminates the genome-wide DNA methylation dynamics during watermelon ripening and provides an invaluable genetic resource that will greatly benefit the molecular breeding and quality improvement of this important crop. • ●Genome-wide DNA hypermethylation accompanies watermelon fruit ripening, exhibiting preferential enrichment in CHG and CHH methylation. • ●Multi-dimensional analyses demonstrated the functional significance of DNA hypermethylation in watermelon fruit ripening. • ● ClROS1 was evolutionarily selected and potentially driving genome-wide hypermethylation during watermelon fruit ripening.