Evolutionary Patterns of small RNA Pathway Genes in Hymenopteran Insects

Small RNAs are short noncoding RNA sequences of 20-30 nucleotides. There are three classes of small RNAs: small interfering RNA (siRNA), microRNA (miRNA), and Piwi- interacting RNA (piRNA). There is a comprehensive understanding of the small RNA pathways in D. melanogaster and how these pathways function, due to D. melanogaster being a widely studied model organism. From studies of the small RNA pathways in D. melanogaster, it is known that the small RNA pathways are extremely important in defending the host genome against viruses and retrotransposons and regulating target genes. However, very little is known about small RNA pathways outside of D. melanogaster and whether or not small RNA pathways are highly conserved in distantly related insects. The objective of this study was to identify the small RNA pathway genes in representative hymenopteran insects and determine the level of conservation across this diverse group. By BLAST searching small RNA pathway proteins against the genomes of five bees, two wasps, three ants, and two sawflies, I found there are more small RNA pathway genes present in hymenopteran insects than in D. melanogaster. By constructing Bayesian gene trees using BEAST v1.10.4 to determine how the identified homologs are related, I found that the piRNA pathway genes Piwi and Aubergine have undergone dramatic duplication in most hymenopteran lineages, whereas AGO1, AGO2, and especially AGO3 are less dynamic in expansion. Finally, alignment of small RNA protein sequences revealed large-scale length differences between certain genes, suggesting functional diversification of these genes