Genome-wide demethylation and targeted remethylation during metamorphosis in the jewel wasp Nasonia vitripennis

DNA methylation plays a critical regulatory role during insect development, yet the underlying mechanisms remain poorly understood. Here, we provide a comprehensive profile of DNA methylation dynamics across the developmental stages of the parasitoid wasp Nasonia vitripennis, a key insect model with functional methylation machinery. Using whole-genome bisulfite sequencing, we identify stage-specific methylation levels, including substantial genome-wide demethylation during the embryonic-to-larval transition and remethylation during subsequent metamorphic stages. Differential methylation analyses reveal significant enrichment of developmentally relevant Gene Ontology terms, highlighting roles in gastrulation, embryogenesis, larval development, regionalisation and morphogenesis. Analysis of protein binding motifs at differentially methylated sites further suggests DNA methylation may directly modulate transcription factor activity, a regulatory mechanism previously underappreciated in insects methylomics. RNA sequencing reveals coordinated expression of methylation-associated enzymes, including high embryonic expression of the demethylase tet and the methylation reader mbd, consistent with methylation dynamics. Although the regulatory relationship between DNA methylation and gene expression is complex, we observed that methylation may contribute to developmental transitions by influencing transcription factor accessibility and chromatin state. Our results suggest that DNA methylation levels are dynamic across Nasonia metamorphosis, and may modulate transcription factor binding across development. These findings refine current models of epigenetic regulation in holometabolous insects and establish a Nasonia vitripennis methylome across metamorphosis for the first time.