Abstract
BackgroundMicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in a wide variety of physiological processes. They can control both temporal and spatial gene expression and are believed to regulate 30 to 70 % of the genes. Data are however limited for fish species, with only 9 out of the 30,000 fish species present in miRBase. The aim of the current study was to discover and characterize rainbow trout (Oncorhynchus mykiss) miRNAs in a large number of tissues using next-generation sequencing in order to provide an extensive repertoire of rainbow trout miRNAs.ResultsA total of 38 different samples corresponding to 16 different tissues or organs were individually sequenced and analyzed independently in order to identify a large number of miRNAs with high confidence. This led to the identification of 2946 miRNA loci in the rainbow trout genome, including 445 already known miRNAs. Differential expression analysis was performed in order to identify miRNAs exhibiting specific or preferential expression among the 16 analyzed tissues. In most cases, miRNAs exhibit a specific pattern of expression in only a few tissues. The expression data from sRNA sequencing were confirmed by RT-qPCR. In addition, novel miRNAs are described in rainbow trout that had not been previously reported in other species.ConclusionThis study represents the first characterization of rainbow trout miRNA transcriptome from a wide variety of tissue and sets an extensive repertoire of rainbow trout miRNAs. It provides a starting point for future studies aimed at understanding the roles of miRNAs in major physiological process such as growth, reproduction or adaptation to stress. These rainbow trout miRNAs repertoire provide a novel resource to advance genomic research in salmonid species.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2505-9) contains supplementary material, which is available to authorized users.
Highlights
MicroRNAs have emerged as important post-transcriptional regulators of gene expression in a wide variety of physiological processes
All the pre-miRNA predicted loci were annotated against non-coding RuboNucleic acid (RNA) (ncRNAs) databases including miRBase 21.0 [11], RFAM 11.0 [18, 19], Silva [20, 21] and GtRNAdb [22]. miRNA from miRBase and RFAM were merged before annotation in order to have a unique miRNA database
In conclusion, this study represents the first characterization of rainbow trout miRNA transcriptome from a wide variety of organs/tissues and describes an extensive repertoire of rainbow trout miRNAs
Summary
MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in a wide variety of physiological processes. They can control both temporal and spatial gene expression and are believed to regulate 30 to 70 % of the genes. The aim of the current study was to discover and characterize rainbow trout (Oncorhynchus mykiss) miRNAs in a large number of tissues using next-generation sequencing in order to provide an extensive repertoire of rainbow trout miRNAs. MicroRNAs (miRNAs) have emerged as important posttranscriptional regulators of gene expression in a wide variety of physiological processes. MiRNAs are often expressed in a tissue-enriched manner [8] They can control both temporal and spatial gene expression and are believed to regulate 30 to 70 % of the proteincoding genes [3]
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