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Background    Trichinella spiralis  is a parasite with unique features. It is a multicellular organism but with an intracellular parasitization and development stage.  T. spiralis  is the helminthic pathogen that causes zoonotic trichinellosis and afflicts more than 10 million people worldwide, whereas the parasite's biology, especially the developmental regulation is largely unknown. In other organisms, small non-coding RNAs, such as microRNAs (miRNA) and small interfering RNAs (siRNA) execute post-transcriptional regulation by translational repression or mRNA degradation, and a large number of miRNAs have been identified in diverse species. In  T. spiralis , the profile of small non-coding RNAs and their function remains poorly understood.    Methodology and Principal Findings  Here, the transcriptional profiles of miRNA and siRNA in three developmental stages of  T. spiralis  in the rat host were investigated, and compared by high-throughput cDNA sequencing technique (“RNA-seq”). 5,443,641 unique sequence tags were obtained. Of these, 21 represented conserved miRNAs related to 13 previously identified metazoan miRNA families and 213 were novel miRNAs so far unique to  T. spiralis . Some of these miRNAs exhibited stage-specific expression. Expression of miRNAs was confirmed in three stages of the life cycle by qRT-PCR and northern blot analysis. In addition, endogenous siRNAs (endo-siRNAs) were found mainly derived from natural antisense transcripts (NAT) and transposable elements (TE) in the parasite.    Conclusions and Significance  We provide evidence for the presence of miRNAs and endo-siRNAs in  T. spiralis . The miRNAs accounted for the major proportion of the small regulatory RNA population of  T. spiralis , while fewer endogenous siRNAs were found. The finding of stage-specific expression patterns of the miRNAs in different developmental stages of  T. spiralis  suggests that miRNAs may play important roles in parasite development. Our data provide a basis for further understanding of the molecular regulation and functional evolution of miRNAs in parasitic nematodes.

Transcriptome of Small Regulatory RNAs in the Development of the Zoonotic Parasite Trichinella spiralis