3.2 Gene expression patterns in contrasted salinity treatments
RNAseq yielded 282 282 453 bp Illumina single-end reads, with an average of 28 228 245 single-end reads by library. After quality control and alignment, an average of 25 225 360 (89.35 %) reads per library was uniquely mapped (Table 2S) and only the uniquely aligned reads were submitted for subsequent analyses. The dendrogram obtained from VST-transformed count data showed clustering of biological replicates and separation of biological conditions (Fig. 3A). Principal component analysis (PCA) based on gene expression patterns (Fig. 3B) showed a clear clustering of samples according to salinity conditions, indicating very distinct expression patterns between salinity conditions. Striking differences between salinity treatments were observed along the PC1-axis that explained 40 % of the variance (except FW-4, that does not contribute to the first axis). Fish from both salinity treatments distributed equally along the PC2-axis that explained 21 % of the variance. Fig 1S shows the global gene expression profiles among all individuals using a heatmap.