Whole-Genome DNA Methylation Analysis of Inoculation with Trichothecium roseum in Harvested Muskmelons

DNA methylation is a crucial epigenetic marker linked to plant defense responses, but its significance in fungal infection of postharvest fruits remains poorly understood. This study indicated that <i>Trichothecium roseum</i> inoculation increased ROS production, enhanced phenylpropanoid metabolism-related enzyme activity, and promoted lignin accumulation in harvested muskmelon fruits <i>(Cucumis melo</i> cv. Yujinxiang) within 24 h post-inoculation (hpi). In addition, whole-genome bisulfite sequencing showed that genomic DNA methylation levels of muskmelon decreased by 6.15% at 24 hpi. Notably, CG sites exhibited a higher methylation level and the largest number of differentially methylated regions (DMRs). Moreover, 176 DMR-associated genes (DMGs) involved in the defense response, 134 DMGs in the ROS metabolic pathway, and 41 DMGs in phenylpropanoid metabolism were identified. The differentially expressed genes harboring differential methylation were mainly influenced by hypomethylation and exhibited elevated transcript levels, involved in phenylpropanoid biosynthesis and biosynthesis of secondary metabolites.