Micro-RNA Expression Profiles and Gene Target Prediction in Atlantic Salmon Infected with Caligus rogercresseyi

Caligus rogercresseyi represents one of the major issues for the Chilean salmon aquaculture. This ectoparasite causes tissue damages and immunosuppression in infected fish. Among the immune responses previously reported, inflammatory responses, protease activity and changes in iron modulation genes have mainly been observed. However, how these responses are modulated at molecular level and which molecules are involved, represent pivotal questions still unresolved. Post-transcriptional regulators of gene expression such as microRNAs (miRNAs) have been associated with important biological processes in model species. Herein, miRNAs reveal transcriptional modulations in infected fish, showing putative roles in the host/pathogen interaction. The aim of this study was to evaluate the miRNA expression profiles in Atlantic salmon infested with the sea louse C. rogercresseyi. Illumina small RNA sequencing was conducted in samples of skin and head kidney obtained from Atlantic salmon at 0, 7 and 14 days post-infestation. A total of 2,787 miRNAs were annotated using miRBase database, and differences of miRNA expression patterns in infected salmons were observed. MiRNAs linked to immune related-genes such as miR-126, miR-146 and let7 were upregulated after infestation. Furthermore, miR-21, a negative regulator of Th1 response, was downregulated after infestation. Moreover, a correlation analysis among miRNAs and coding genes evidenced strong relationships with immune-related genes and iron regulation genes. From this analysis, the most up and down-regulated miRNA were used to discover novel putative target genes. This study is the first to identify small RNAs in Atlantic salmon in response to C. rogercresseyi infestation, providing novel molecular knowledge in the complexity of the host/parasite interactions.

Funding: FONDAP 15110027 and FONDECYT 1150077 awarded by CONICYT-Chile