Wolbachia-derived small non-coding RNAs exhibit cross-kingdom regulatory effects on host reproduction of a polyphagous mite

<i>Wolbachia</i> is a ubiquitous endosymbiont in arthropods that produces small non-coding RNAs, which function as regulators in both the bacterium and its host. Although recent studies have shown cross-kingdom communication between <i>Wolbachia</i> and its host through <i>Wolbachia</i>-derived small non-coding RNAs (<i>W</i>snRNAs), the functions of <i>W</i>snRNAs have not been systematically examined. Here, we identify <i>W</i>snRNAs in <i>Wolbachia</i>-infected <i>Tetranychus truncatus</i> Ehara via RNA-seq and investigate their impacts on host reproductive fitness. A total of 12 <i>W</i>snRNAs were identified, along with their predicted precursors and hairpin structures. The predicted target genes of five highly expressed <i>W</i>snRNAs are involved in reproductive development, as revealed by enrichment analysis. Inhibition of <i>W</i>snRNA-744 and <i>W</i>snRNA-3640 reduced fecundity, whereas inhibition of <i>W</i>snRNA-6108 promoted it, indicating that different <i>W</i>snRNAs exert opposing effects on host fecundity. These findings suggest that <i>W</i>snRNAs mediate host-endosymbiont communication across species and could represent promising targets for <i>Wolbachia</i>-based pest control strategies.