Dynamic Birth and Death of Argonaute Gene Family Functional Repertoire Across Caenorhabditis Nematodes

Diverse small RNA pathways, composed of Argonaute effector proteins and their bound small RNA molecules, define critical systems for regulating gene expression in all domains of life. Some small RNA pathways have experienced significant evolutionary change across metazoans, including gains of novel Argonaute genes and losses of entire pathways. Differences in Argonaute functional complement among species therefore profoundly influence the available repertoire of mechanisms for gene regulation. Despite intensive study of Argonaute function in the nematode roundworm Caenorhabditis elegans, the extent of Argonaute gene family dynamism and functional breadth remains unknown. We therefore comprehensively surveyed Argonautes across 51 Caenorhabditis species, yielding over 1,200 genes from 11 subfamilies. We documented multiple cases of diversification, including the birth of a potentially novel Argonaute subfamily and the origin of the ALG-5 microRNA Argonaute near the base of the Caenorhabditis phylogeny, as well as evidence of adaptive sequence evolution and gain of a new CSR-1 splice isoform in a clade of 31 species. We detected repeated independent losses of multiple piRNA pathway components, mirroring within this one genus other instances of piRNA pathway loss across the phylum. We experimentally verified several Argonaute gene gains and losses, supporting their validity. Gene gain and loss occur significantly faster than expected within several Argonaute subfamilies, potentially associated with transposable element proliferation coevolving with WAGO-9/10/12 copy number variation. Our characterization of Argonaute diversity across Caenorhabditis demonstrates exceptional functional dynamism in the evolution of gene regulation, with broad implications for mechanisms of control over ontogenetic development and genome integrity.