MicroRNAs are ubiquitous, short, non‐coding RNA molecules that function as post‐transcriptional regulators of gene expression in a variety of biological processes. In order to further our understanding of the microRNA hierarchy in the reproductive axis of male teleosts, four small RNA libraries were constructed, and sequenced from the testis and brain of sexually mature adults and immature juvenile rainbow trout (Oncorhynchus mykiss) using Illumina small‐RNA deep sequencing. We obtained 56,632,987; 39,870,661; 82,454,370; and 53,143,465 high‐quality, filtered reads for immature testis, mature testis, immature brain, and mature brain, respectively. Among the libraries, 433 known mature piscine miRNAs were identified, with 124 and 116 significantly differentially expressed miRNAs found between sexually immature/mature testes and immature/mature brain tissues, respectively. Among these differentially expressed miRNAs, miR‐129, ‐130c, ‐135b, ‐140, ‐146a, ‐192, ‐199a, ‐16, and, ‐19b showed higher abundance in the testis whereas miR‐10b, ‐183, ‐199, ‐375, ‐1937, and miR‐nov210 were more abundant in the brain. In silico target prediction of these differentially expressed miRNAs suggested their putative roles in the sexual maturation of male rainbow trout. Mol. Reprod. Dev. 82: 651–662, 2015. © 2015 Wiley Periodicals, Inc.

The IPN virus (IPNV) causes a highly contagious disease that affects farmed salmonids. IPNV isolates have been phylogenetically classified into seven genogroups, of which two are present in Chile, genogroups 1 and 5. This study aimed to compare the transcriptomic response of rainbow trout fry challenged with two Chilean isolates of IPNV, RTTX (genogroup 1), and ALKA (genogroup 5). Tissue samples from challenged individuals and controls were taken at 1, 7, and 20 days post-challenge and analyzed by RNA-Seq. The results revealed that infection with RTTX elicited a greater modulation of the trout transcriptome compared to ALKA infection, generating a greater number of highly differentially expressed genes in relation to the control fish. Gene Ontology enrichment indicated that functions related to the inflammatory and immune responses were modulated in fish challenged with both isolates throughout the trial, but with different regulation patterns. On day 1 post challenge, these functions were activated in those challenged with ALKA, but suppressed in RTTX-challenged fish. These results suggest that rainbow trout exhibit a differential transcriptomic response to infection with the two genetically distinct IPNV isolates, especially at early times post-infection.