Comparative transcriptomics reveals an extracellular worm argonaute as an ancestral regulator of LTR retrotransposons

Safeguarding the genome from non-self elements is essential for reproduction, development, and ageing. One of the major threats to genome integrity are Transposable Elements (TEs), which can be post-transcriptionally silenced through small RNAs (sRNAs) and argonaute proteins. While TE-derived sRNAs are known to mediate post-transcriptional silencing, recent work suggests they may also act as virulence factors in host-pathogen interactions. During infection, the intestinal parasite Heligmosomoides bakeri secretes a single argonaute protein (exWAGO) and a wide variety of transposon-derived sRNAs. Although exWAGO is highly expressed, conserved, and secreted by parasitic nematodes, its evolutionary function and sRNA guide preferences remain unclear. Using comparative transcriptomics of the sRNA guides bound by exWAGO across nematodes of rodents, livestock and humans, and its orthologs in C. elegans, we propose that the ancestral endogenous function of exWAGO is linked to LTR-retrotransposon regulation. To gain insight into the extracellular role of exWAGO, we characterized its associated sRNAs inside and outside extracellular vesicles (EVs) from H. bakeri secretion. We found that while vesicular exWAGO prefers guides from divergent, lineage-specific soloLTRs, the non-vesicular exWAGO prefers guides from longer, non-autonomous LTR retrotransposons, suggesting that fragmented LTR retrotransposons act as adaptable reservoirs of regulatory sRNAs with potential roles in cross-species RNA communication. Together, our results show that exWAGO is part of an evolutionarily conserved pathway for LTR retrotransposon regulation, underscoring its dual role in TE-regulation while selectively utilising degenerated elements as sources of secreted sRNAs.