Sexual epigenetics: genome-wide analysis revealed differential DNA methylation in the vector tick Haemaphysalis longicornis

Abstract

Background: Haemaphysalis longicornis is an important vector that transmits a variety of pathogens to humans and animals. This tick species is unique for having two separate reproductive populations: bisexual and parthenogenetic populations. In bisexual populations, morphological differences exist between the males and females, with the females often larger than the males. DNA methylation, as a key epigenetic modification, plays a crucial role in biological processes such as the maintenance of normal cellular function, the regulation of gene expression, and embryonic development. However, the epigenetic mechanism underlying sex differentiation in the bisexual population of H. longicornis has been overlooked.

Methods: In the present study, the global DNA methylation profiles of the female and male H. longicornis ticks from the bisexual population were explored using whole-genome bisulfite sequencing. Differentially methylated regions (DMRs) were identified, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DMR-related genes.

Results: The results revealed that DNA methylation levels in H. longicornis varied by sex and sequence context (CG, CHG, and CHH). The 3' untranslated region (UTR) had the highest methylation in the CG context, followed by exons, introns, and CGI_shore regions. Female ticks generally exhibited higher methylation levels than males, particularly in gene body regions. A total of 10,460 DMRs were identified, with 5282 hypermethylated and 5178 hypomethylated. Further, GO and KEGG pathway analyses showed that differentially methylated genes (DMGs) were highly enriched in binding and metabolic pathways.

Conclusions: These results broaden our understanding of DNA methylation changes associated with the female and male of H. longicornis and provide an important theoretical basis for subsequent studies of epigenetic mechanisms of sex differences in ticks.

Keywords: Haemaphysalis longicornis; DNA methylation; Epigenetic regulation; Sexual dimorphism; Whole-genome bisulfite sequencing.

Fig. 1

Pearson correlation based on the CG/CHG/CHH context among the replicate groups. A Pearson correlation based on CG context among the replicate groups. B Pearson correlation based on CHG context among the replicate groups. C Pearson correlation based on CHH context among the replicate groups. D Sample CG context clustering dendrogram. E Sample CHG context clustering dendrogram. F Sample CHH context clustering dendrogram. R² Pearson's correlation coefficient; F female group; M male group

Fig. 2

Distribution of methylation levels of functional regions, and the gene upstream and downstream between the female group and male group. A Distribution of methylation level of functional regions between female group and male group in mCG/CG. B Distribution of methylation level of functional regions between female group and male group in mCHG/CHG. C Distribution of methylation level of functional regions between female group and male group in mCHH/CHH. D Distribution of methylation level of genes upstream and downstream between female group and male group in mCG/CG. E Distribution of methylation level of genes upstream and downstream between female group and male group in mCHG/CHG. F Distribution of methylation level of genes upstream and downstream between female group and male group in mCHH/CHH. TSS transcription start site, TES transcription end site

Fig. 3

Heat map of differences in methylation levels in different gene regions. A Heat map of differences in methylation levels in mCG/CG. B Heat map of differences in methylation levels in mCHG/CHG. C Heat map of differences in methylation levels in mCHH/CHH

Fig. 4

The methylation patterns between the female group and male group of H. longicornis. A Venn diagrams of female and male group DMGs under CG, CHG, and CHH contexts of the H. longicornis adults. B Significantly different methylation patterns between the female group and male group

Fig. 5

Violin plot analysis of the methylation level of DMRs in the female and male groups of H. longicornis adults. A Violin plot analysis of CG DMR methylation level. B Violin plot analysis of CHG DMR methylation level. C Violin plot analysis of CHH DMR methylation level

Fig. 6

GO and KEGG enrichment analyses of the female and male group CG DMGs of the H. longicornis adults. A GO enrichment analysis of DMGs. B KEGG pathway enrichment