title: Characterization of an extensive rainbow trout miRNA transcriptome by next generation sequencing.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  A 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: INRA, UR1037 LPGP, Campus de Beaulieu, F-35000, Rennes, France. amelie.juanchich@tours.inra.fr.
authors.forename: Amelie
authors.initials: A
authors.lastname: Juanchich
authors.affiliation: INRA, UMR1388, Plate-forme SIGENAE/GenPhySE, Chemin de Borde Rouge, Auzeville CS 52627, F-31326, Castanet-Tolosan, France. philippe.bardou@toulouse.inra.fr.
authors.forename: Philippe
authors.initials: P
authors.lastname: Bardou
authors.affiliation: INRA, UR875 Plate-forme GenoToul Bioinfo, Chemin de Borde Rouge, Auzeville CS 52627, F-31326, Castanet-Tolosan, France. olivier.rue@toulouse.inra.fr.
authors.forename: Olivier
authors.initials: O
authors.lastname: Rué
authors.affiliation: INRA, UR1037 LPGP, Campus de Beaulieu, F-35000, Rennes, France. jean-charles.gabillard@rennes.inra.fr.
authors.forename: Jean-Charles
authors.initials: JC
authors.lastname: Gabillard
authors.affiliation: INRA, UR875 Plate-forme GenoToul Bioinfo, Chemin de Borde Rouge, Auzeville CS 52627, F-31326, Castanet-Tolosan, France. christine.gaspin@toulouse.inra.fr.
authors.forename: Christine
authors.initials: C
authors.lastname: Gaspin
authors.affiliation: INRA, UR1037 LPGP, Campus de Beaulieu, F-35000, Rennes, France. julien.bobe@rennes.inra.fr.
authors.forename: Julien
authors.initials: J
authors.lastname: Bobe
authors.affiliation: INRA, UR1037 LPGP, Campus de Beaulieu, F-35000, Rennes, France. yann.guiguen@rennes.inra.fr.
authors.forename: Yann
authors.initials: Y
authors.lastname: Guiguen
mesh_terms: D000818:Animals; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D017686:Oncorhynchus mykiss / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D035683:MicroRNAs