The Caligus rogercresseyi miRNome: Discovery and transcriptome profiling during the sea lice ontogeny

Small RNA sequencing in the copepod ectoparasite Caligus rogercresseyi was conducted to evidence putative roles of non-coding RNAs during the sea louse ontogeny. Here, differentially expressed miRNAs and mRNAs for each developmental stage were analyzed in parallel with bioinformatic gene target predictions. Based on sequence analysis, C. rogercresseyi miRNome comprises 673 conserved miRNAs, including precursors, 5′ and 3′ isomiRs. The conserved miRNAs include 40 families found in twelve different arthropods species. The results also showed that C. rogercresseyi miRNome exhibit stage-specific expression patterns, with miRNA-996-4 and miRNA-124 displaying sex-biased expression. Target prediction of these miRNAs identifies possible silencing mechanism of sex-related genes. Furthermore, bantam isomiRs were highly transcribed during the infective stage of copepodid and target prediction using differentially expressed genes in Atlantic salmon infested with sea lice, suggests a putative role of these miRNAs in the host-pathogen interaction. This is the first study reporting a miRNA repertoire in a marine copepod ectoparasite that affects the salmon aquaculture worldwide

Integrative testis transcriptome analysis reveals differentially expressed miRNAs and their mRNA targets during early puberty in Atlantic salmon

Background: Our understanding of the molecular mechanisms implementing pubertal maturation of the testis in vertebrates is incomplete. This topic is relevant in Atlantic salmon aquaculture, since precocious male puberty negatively impacts animal welfare and growth. We hypothesize that certain miRNAs modulate mRNAs relevant for the initiation of puberty. To explore which miRNAs regulate mRNAs during initiation of puberty in salmon, we performed an integrated transcriptome analysis (miRNA and mRNA-seq) of salmon testis at three stages of development: an immature, long-term quiescent stage, a prepubertal stage just before, and a pubertal stage just after the onset of single cell proliferation activity in the testis. Results: Differentially expressed miRNAs clustered into 5 distinct expression profiles related to the immature, prepubertal and pubertal salmon testis. Potential mRNA targets of these miRNAs were predicted with miRmap and filtered for mRNAs displaying negatively correlated expression patterns. In summary, this analysis revealed miRNAs previously known to be regulated in immature vertebrate testis (miR-101, miR-137, miR-92b, miR-18a, miR-20a), but also miRNAs first reported here as regulated in the testis (miR-new289, miR-30c, miR-724, miR-26b, miR-new271, miR-217, miR-216a, miR-135a, miR-new194 and the novel predicted n268). By KEGG enrichment analysis, progesterone signaling and cell cycle pathway genes were found regulated by these differentially expressed miRNAs. During the transition into puberty we found differential expression of miRNAs previously associated (let7a/b/c), or newly associated (miR-15c, miR-2184, miR-145 and the novel predicted n7a and b) with this stage. KEGG enrichment analysis revealed that mRNAs of the Wnt, Hedgehog and Apelin signaling pathways were potential regulated targets during the transition into puberty. Likewise, several regulated miRNAs in the pubertal stage had earlier been associated (miR-20a, miR-25, miR-181a, miR-202, let7c/d/a, miR-125b, miR-222a/b, miR-190a) or have now been found connected (miR-2188, miR-144, miR-731, miR-8157 and the novel n2) to the initiation of puberty. Conclusions: This study has - for the first time - linked testis maturation to specific miRNAs and their inversely correlated expressed targets in Atlantic salmon. The study indicates a broad functional conservation of already known miRNAs and associated pathways involved in the transition into puberty in vertebrates. The analysis also reveals miRNAs not previously associated with testis tissue or its maturation, which calls for further functional studies in the testis