SmithRNAs: A Common Feature among Metazoa.

SmithRNAs are a novel class of small noncoding RNAs that are encoded in the mitochondrial genome and regulate the expression of nuclear transcripts. They have been recently described in the Manila clam Ruditapes philippinarum and their biological function has been confirmed in vivo. It is currently unclear whether smithRNAs are a unique feature of this species, possibly related to the peculiar mechanism of sex determination observed in bivalves, or a common feature of Metazoa. Aiming at a broader survey on the presence and biological features of smithRNAs across Metazoa, 14 species were selected to represent major lineages, and for each species small RNAseq data, as well as the transcriptome, mitochondrial and nuclear genomes, were collected from the literature or sequenced/assembled de novo. Data were analyzed using the SmithHunter pipeline, a recently published tool specifically designed to identify smithRNAs and their targets. Candidate smithRNAs were identified in all species studied, supporting the notion that smithRNAs are a common feature across Metazoa. SmithRNAs are generally encoded within other genes, on the same strand, and with a preference for mitochondrial rRNAs and tRNAs. Based on their strandedness and preferential position at the 5'-end of the encompassing gene, a transcription mechanism is proposed where smithRNAs are cleaved off from gene-specific transcripts after the maturation of the two primary mitochondrial transcripts. A substantial variability was identified concerning the possible nuclear targets of smithRNAs, with a preference for regulation/response terms, mitochondrial functions, and sex/germline associated terms.