Whole-Genome Transcript Expression Profiling Reveals Novel Insights into Transposon Genes and Non-Coding RNAs during Atlantic Salmon Seawater Adaptation

SIMPLE SUMMARY: This study proposes a novel approach to analyze transcriptome data sets using the Atlantic salmon seawater adaptation process as a model. Salmon salar smolts were transferred to seawater under two strategies: (i) fish group exposed to gradual salinity changes (GSC) and (ii) fish group exposed to a salinity shock (SS). mRNA and miRNAs sequencing were performed for gills, intestine, and head kidney tissues. The whole-genome transcript expression profiling revealed specific gene expression patterns among the tissues and treatments. A great abundance of transposable elements was observed in chromosome regions differentially expressed under experimental conditions. Moreover, small RNA expression analysis suggested fewer of miRNAs associated with the smoltification process. However, target analysis of these miRNAs suggests a regulatory role of process such as growth, stress response, and immunity. The findings uncover whole-transcriptome modulation during seawater adaptation of Atlantic salmon, evidencing the interplaying among mRNAs and miRNAs. ABSTRACT: The growing amount of genome information and transcriptomes data available allows for a better understanding of biological processes. However, analysis of complex transcriptomic experimental designs involving different conditions, tissues, or times is relevant. This study proposes a novel approach to analyze complex data sets combining transcriptomes and miRNAs at the chromosome-level genome. Atlantic salmon smolts were transferred to seawater under two strategies: (i) fish group exposed to gradual salinity changes (GSC) and (ii) fish group exposed to a salinity shock (SS). Gills, intestine, and head kidney samples were used for total RNA extraction, followed by mRNA and small RNA illumina sequencing. Different expression patterns among the tissues and treatments were observed through a whole-genome transcriptomic approach. Chromosome regions highly expressed between experimental conditions included a great abundance of transposable elements. In addition, differential expression analysis showed a greater number of transcripts modulated in response to SS in gills and head kidney. miRNA expression analysis suggested a small number of miRNAs involved in the smoltification process. However, target analysis of these miRNAs showed a regulatory role in growth, stress response, and immunity. This study is the first to evidence the interplaying among mRNAs and miRNAs and the structural relationship at the genome level during Atlantic salmon smoltification.