Allele-specific methylome analysis reveals cis-regulation of DNA methylation in Nasonia [WGBS-seq]

Wasps of the genus Nasonia are non-social parasitoids that are emerging as a model for studies of epigenetic processes in insects. To study the transmission pattern of DNA methylation and changes of methylation during species divergence, we scored genome-wide methylation and allele-specific methylation (ASM) percentages at single CpG level in both parental and reciprocal F1s of Nv and Ng. These closely related cross-fertile species are genetically tractable and inbred in nature, allowing accurate estimation of ASM. Among the ~7000 differentially methylated CpGs (DMCpGs) between Nv and Ng parents, 4364 were covered with >8x for both Nv and Ng alleles in reciprocal F1s and they clustered in 178 genes (DM-genes) with >4 DMCpGs per gene. Surprisingly, all 178 DM-genes are differentially methylated between the two alleles in F1s, remembering the parental methylation status with nearly 100% fidelity, suggesting the presence of strong cis-elements driving the target of gene body methylation. The 100% cis-regulation in F1 suggests the methylation machinery is conserved and DNA methylation is targeted by cis-motifs in Nasonia. In addition, we discovered that total and allele-specific expression is positively correlated with ASM in a subset of the DM-genes. Unlike in mammals, we did not find any parent-of-origin DMRs in Nasonia, with paternal or maternal-specific methylation, and there seemed to be no epigenetic reprogramming with two waves of de- and re-methylation. These results will shed light on the mechanism of DNA methylation in insects and the evolution of methylation in animals. Whole-genome bisulfite sequencing of 24-hour reciprocal F1 adults of Nasonia vitripennis and Nasonia giraulti using Illumina sequencing.