Whole-genome DNA methylation profile of the jewel wasp (Nasonia vitripennis)

Abstract

The epigenetic mark of DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, has been extensively studied in many mammalian genomes and, although it is commonly found at the promoter regions of genes, it is also involved in a number of different biological functions. In other complex animals, such as social insects, DNA methylation has been determined to be involved in caste differentiation and to occur primarily in gene bodies. The role of methylation in nonsocial insects, however, has not yet been explored thoroughly. Here, we present the whole-genome DNA methylation profile of the nonsocial hymenopteran, the jewel wasp (Nasonia vitripennis). From high-throughput sequencing of bisulfite-converted gDNA extracted from male Nasonia thoraces, we were able to determine which cytosine residues are methylated in the entire genome. We found that an overwhelming majority of methylated sites (99.7%) occur at cytosines followed by a guanine in the 3' direction (CpG sites). Additionally, we found that a majority of methylation in Nasonia occurs within exonic regions of the genome (more than 62%). Overall, methylation is sparse in Nasonia, occurring only at 0.18% of all sites and at 0.63% of CpGs. Our analysis of the Nasonia methylome revealed that in contrast to the methylation profile typically seen in mammals, methylation is sparse and is constrained primarily to exons. This methylation profile is more similar to that of the social hymenopteran species, the honey bee (Apis mellifera). In presenting the Nasonia methylome, we hope to promote future investigation of the regulatory function of DNA methylation in both social and nonsocial hymenoptera.

Keywords: DNA methylation; Nasonia; epigenetics.

Figure 1

Sequencing coverage over all cytosines in male Nasonia thorax. (Left) Cumulative coverage, e.g., approximately 20% of sites are covered by 11 or more reads. (Right) The proportion of sites that have a certain level of coverage, e.g., approximately 2% of sites have coverage of 14 reads. Note that every read can trace its origin to a bisulfite conversion event that happened on one strand or the other. Here, we only counted reads that were on the correct strand to be informative at a particular cytosine.

Figure 2

Annotations of methylation patterns for the top 20 most methylated genes by proportion. Black bars represent exonic regions and red circles represent methylated sites. Genes are presented in order of ranking from left to right and then top to bottom. The three isoforms of NV12835 are presented as a single annotation.

Figure 3

Gene Ontology (GO) categories associated with the top 20 methylated genes by proportion of gene.