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RNA interference (RNAi) or RNA silencing is a gene regulatory system, widely conserved in eukaryotes, that represses gene expression through a homology-dependent mechanism. This repressive effect is mediated by small non-coding RNAs (sRNAs) of about 20–30 nucleotides, derived from double-stranded RNA (dsRNA) precursors that are recognized and processed by the RNaseIII Dicer. These sRNAs are loaded into an RNA-induced silencing complex (RISC), where the Argonaute protein plays a main role. Upon loading, the sRNAs selectively guide RISC to the target RNAs, causing their degradation or preventing their translation. In certain organisms, including fungi and parasitic protozoa, the silencing mechanism requires RNA-dependent RNA polymerases (RdRPs) to generate dsRNA from single-stranded RNA (ssRNA) or to amplify sRNA signals [1,2]. Originally described as a defense mechanism against invasive nucleic acids and viruses, RNAi and related pathways play many fundamental roles in metazoans, including regulation of mRNA accumulation and translation, chromatin silencing, programmed DNA rearrangements, and genome surveillance.

Loss and Retention of RNA Interference in Fungi and Parasites