Argonaute protein and small RNA expression patterns in Spodoptera frugiperda (Lepidoptera, Noctuidae)

PIWI-interacting RNAs (piRNAs) and PIWI proteins were initially described as playing a role in gametogenesis and maintaining genome integrity by controlling transposable elements (TEs). Expressed also in the soma and able to regulate protein coding gene expression, they are involved in multiple biological pathways, including host-pathogens interaction, sex determination and reproductive isolation. Spodoptera frugiperda (Sf) is a major invasive insect pest species consisting of two strains with distinct host-plant ranges. To identify which pathway was regulated by piRNAs in this species, we characterized proteins and genomic regions involved in their biogenesis, as well as TE and gene transcripts regulated. By phylogenetic analysis, we identified two new Piwi genes conserved in the genus Spodoptera, compared to the Lepidopteran model Bombyx mori, one more than in Drosophila. One of them, more expressed in the gonads than in the soma, could be a functional homolog of Drosophila PIWI or replace AGO3. A pool of 11 sRNA-Seq libraries was used to annotate piRNA clusters with ShortStack in the genomes of the two Sf strains. Identification of TE targeted by putative piRNAs revealed that active transposons may differ between the two Sf strains, despite a similar TE content, as a putative cause or consequence of reproductive isolation. GO analysis of genes targeted by piRNAs shows that some are involved in protein translation initiation. A piRNA cluster in the Masc gene suggests that sex determination is regulated by piRNAs. Our analysis contributes to functional annotation of the Sf strains genomes and supports additional roles than silencing of transposable elements for piRNAs.