The available high resolution of genome information and transcriptomes data allows the understanding of complex biological processes. However, the analysis of complex experimental designs involving different tissues, times-points or environment represents the main obstacle . This study proposes a novel approach to analyze complex data sets combining coding and non-coding RNAs at the chromosome-level genome.
Therein, Atlantic salmon smolts were transferred to SW under two strategies. (i) Fish group exposed to gradual salinity changes (GSC), and ( ii) exposed to a salinity shock (SS). Gills, intestine, and head kidney samples were used for total RNA extraction, followed by mRNAs and small RNAs Illumina sequencing.
Through a whole-genome transcriptomic approach, different expression patterns among the tissues and treatments were observed. A mRNAs and miRNAs correlations expression were observed at chromosome levels. Chromosome regions highly expressed between experimental conditions included a high abundance of transposable elements. In addition, differential expression analysis showed a higher number of transcripts modulated in response to SS in gills and head kidney. miRNAs expression analysis suggested a low number of miRNAs involved in the smoltification process. However, the target analysis of these miRNAs showed a regulatory role in growth, stress response, and immunity. This study is the first evidencing the interplaying among the mRNAs/ miRNAs and the structural relationship at genome level during Atlantic salmon smoltification.
Funding: ANID-Chile funded this study through the Postdoctoral grant FONDECYT (3190320), grants FONDAP (15110027) and FONDECYT (1210852).