Sex‐specific changes in the aphid DNA methylation landscape

Abstract

Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome bisulphite sequencing and transcriptome sequencing of the green peach aphid (Myzus persicae), we present the first detailed analysis of cytosine methylation in an aphid and investigate differences in the methylation and transcriptional landscapes of male and asexual female morphs. We found that methylation primarily occurs in a CG dinucleotide (CpG) context and that exons are highly enriched for methylated CpGs, particularly at the 3′ end of genes. Methylation is positively associated with gene expression, and methylated genes are more stably expressed than unmethylated genes. Male and asexual female morphs have distinct methylation profiles. Strikingly, these profiles are divergent between the sex chromosome and the autosomes; autosomal genes are hypomethylated in males compared to asexual females, whereas genes belonging to the sex chromosome, which is haploid in males, are hypermethylated. Overall, we found correlated changes in methylation and gene expression between males and asexual females, and this correlation was particularly strong for genes located on the sex chromosome. Our results suggest that differential methylation of sex‐biased genes plays a role in aphid sexual differentiation.

DNA Methylation and Demethylation Are Regulated by Functional DNA Methyltransferases and DnTET Enzymes in Diuraphis noxia

“…The sequence reads were analyzed for contexts of DNA methylation within the genome and the results revealed that RWA has methylation in all contexts (CpG, CHG and CHH), with the majority of methylation within the CpG context (±5.19%), but still notable methylation in the other contexts (CHG-± 0.27%; CHH-± 0.34%), with most of the methylation located in the genic regions. A similar finding was recently reported by Mathers et al (2019) in the green peach aphid, Myzus persicae. The authors found that exons are highly enriched for methylated CpGs, particularly at the 3 ′ end of genes.…”

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

“…We identified the aphid sex (X) chromosome in our new assemblies of M. persicae clone O and A. pisum JIC1 based on the ratio of male (M) to asexual female (FA) coverage of Illumina genomic DNA reads. For M. persicae, we used whole genome bisulphite sequencing (BS-seq) reads from Mathers et al (2019), merging biological replicates by morph. These data are derived from the same clonal population (clone O) as used for the genome assembly.…”

Population epigenetic divergence exceeds genetic divergence in the Eastern oyster Crassostrea virginica in the Northern Gulf of Mexico

“…Benjamini-Hochberg adjusted p-value (q-value) less than or equal to .05 (Mathers et al, 2019). (Gavery & Roberts, 2013;Keller, Han, & Yi, 2016;Song et al, 2017).…”