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Small RNA pathways play key and diverse regulatory roles in  C. elegans , but our understanding of their conservation and contributions in other nematodes is limited. We analyzed small RNA pathways in the divergent parasitic nematode  Ascaris. Ascaris  has ten Argonautes with five worm-specific Argonautes (WAGOs) that associate with secondary 5’-triphosphate 22-24G-RNAs. These small RNAs target repetitive sequences or mature mRNAs and are similar to the  C. elegans  mutator, nuclear, and CSR-1 small RNA pathways. Even in the absence of a piRNA pathway,  Ascaris  CSR-1 may still function to “license” as well as fine-tune or repress gene expression.  Ascaris  ALG-4 and its associated 26G-RNAs target and likely repress specific mRNAs during testis meiosis.  Ascaris  WAGO small RNAs demonstrate target plasticity changing their targets between repeats and mRNAs during development. We provide a unique and comprehensive view of mRNA and small RNA expression throughout spermatogenesis. Overall, our study illustrates the conservation, divergence, dynamics, and flexibility of small RNA pathways in nematodes.

Small RNA pathways in the nematode Ascaris in the absence of piRNAs