Male-Biased microRNA Discovery in the Pea Aphid

SIMPLE SUMMARY: Males and females develop from a genome that is largely similar, yet the sexes have dramatically different traits. How this happens has driven interest in the role of epigenetic mechanisms—i.e., changes in gene function that are not due to changes in the DNA—in regulating sexual dimorphisms. Our focus here is on differences between the sexes in one epigenetic mechanism, the downregulation of gene expression by small RNAs called microRNAs. Typical genomes code for hundreds of microRNAs and each one can target many protein-coding RNAs, ultimately causing them to produce fewer protein copies. Here, we focus on microRNAs in male versus female pea aphids. We use small RNA sequence data to identify all the microRNAs in the pea aphid genome and to find microRNAs that are highly biased towards expression in males. This work is foundational for future studies of the epigenetic basis of sex differences in the pea aphid. ABSTRACT: Epigenetic mechanisms modulate gene expression levels during development, shaping how a single genome produces a diversity of phenotypes. Here, we begin to explore the epigenetic regulation of sexual dimorphism in pea aphids (Acyrthosiphon pisum) by focusing on microRNAs. Previous analyses of microRNAs in aphids have focused solely on females, so we performed deep sequencing of a sample containing early-stage males. We used this sample, plus samples from Genbank, to find 207 novel pea aphid microRNA coding loci. We localized microRNA loci to a chromosome-level assembly of the pea aphid genome and found that those on the X chromosome have lower overall expression compared to those on autosomes. We then identified a set of 19 putative male-biased microRNAs and found them enriched on the X chromosome. Finally, we performed protein-coding RNA-Seq of first instar female and male pea aphids to identify genes with lower expression in males. 10 of these genes were predicted targets of the 19 male-biased microRNAs. Our study provides the most complete set of microRNAs in the pea aphid to date and serves as foundational work for future studies on the epigenetic control of sexual dimorphism.