Repeated Duplication of Argonaute2 Is Associated with Strong Selection and Testis Specialization in Drosophila

Abstract

Argonaute2 (Ago2) is a rapidly evolving nuclease in the Drosophila melanogaster RNA interference (RNAi) pathway that targets viruses and transposable elements in somatic tissues. Here we reconstruct the history of Ago2 duplications across the D. obscura group and use patterns of gene expression to infer new functional specialization. We show that some duplications are old, shared by the entire species group, and that losses may be common, including previously undetected losses in the lineage leading to D. pseudoobscura. We find that while the original (syntenic) gene copy has generally retained the ancestral ubiquitous expression pattern, most of the novel Ago2 paralogs have independently specialized to testis-specific expression. Using population genetic analyses, we show that most testis-specific paralogs have significantly lower genetic diversity than the genome-wide average. This suggests recent positive selection in three different species, and model-based analyses provide strong evidence of recent hard selective sweeps in or near four of the six D. pseudoobscura Ago2 paralogs. We speculate that the repeated evolution of testis specificity in obscura group Ago2 genes, combined with their dynamic turnover and strong signatures of adaptive evolution, may be associated with highly derived roles in the suppression of transposable elements or meiotic drive. Our study highlights the lability of RNAi pathways, even within well-studied groups such as Drosophila, and suggests that strong selection may act quickly after duplication in RNAi pathways, potentially giving rise to new and unknown RNAi functions in nonmodel species.

Recurrent Amplification of the Heterochromatin Protein 1 (HP1) Gene Family across Diptera

“…2016 ). A detailed phylogenomic analysis of Argonautes in the Drosophila obscura clade revealed pervasive male germline restriction of young Argonaute2 (Ago2) paralogs ( Lewis, Webster, et al. 2016 ).…”

Selfish genetic elements and male fertility

“…The proliferation of certain testes-specific gene families-for example, the argonautes in Drosophila-is suggested to have evolved to suppress the activity of transposable elements during spermatogenesis [70,71]. The impact of SGE-fuelled genomic conflict could therefore contribute new testes-specific genes and promote diversification of gene families associated with generally suppressing a variety of SGEs during spermatogenesis [72,73]. Haploid silencing of many genes during spermatogenesis has been implicated as management by the diploid genome to avoid such intra-genomic conflict, (see Sutter & Immler 2020 in this issue [74]).…”

Natural Variation in Resistance to Virus Infection in Dipteran Insects

“…These patterns are also apparent in some immune genes, and are most striking in the RNAi pathway, which evolves rapidly due to adaptive evolution, particularly in genes mediating defense against transposons and viruses, including antiviral effectors Dcr-2 and Ago2 [ 159 , 160 , 161 ]. In addition, RNAi genes are more likely to show diversity patterns consistent with positive selection driving new mutations to fixation [ 161 , 162 , 163 , 164 ]. Although less likely to be virus-mediated selection, genes in the Toll and IMD signaling pathways may also have elevated levels of positive selection, with the most convincing evidence in Relish and its interactors [ 165 , 166 , 167 ].…”