MicroRNAs (miRNAs) are small, highly conserved, non-coding RNAs that regulate gene expression of target mRNAs through cleavage or translational inhibition. miRNAs are most often identified through computational prediction from genome sequences. The rainbow trout genome sequence is not available yet, which does not allow miRNA prediction for this species which is of great economic interest for aquaculture and sport fisheries, and is a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. To identify miRNAs from rainbow trout, we constructed a miRNA library from a pool of nine somatic tissues. Analysis of the library identified 210 unique sequences representing 54 distinct miRNAs; 50 with conserved sequences matching previously identified miRNAs and four novel miRNAs. In addition, 13 miRNAs were computationally predicted from the rainbow trout transcriptome. Real-time PCR was used to measure miRNA expression patterns in adult somatic tissues and unfertilized eggs. The majority of the miRNAs showed characteristic tissue-specific expression patterns suggesting potential roles in maintaining tissue identity. Potential miRNA-target interactions were computationally predicted and single nucleotide polymorphisms (SNPs) were identified in the miRNAs and their target sites in the rainbow trout transcripts. The rainbow trout miRNAs identified and characterized in this study provide a new tool for functional genome research in salmonids. Tissue-specific miRNAs may serve as molecular markers, predictive of specific functional and diagnostic implications. The data on genetic polymorphisms in miRNA-target interactions is particularly useful for rainbow trout breeding programs.
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