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.