Fig. 3

Overall differences in gene expression between different groups of lice. a Correspondence analysis (CA) plot showing the overall gene expression of the samples analysed in this study (pink and turquoise dots) in comparison with other chalimus I and chalimus II larvae divided into various instar ages taken from Eichner et al. [27]. b MA plots for DESeq2 comparing the different conditions (lice sampled from gills versus lice sampled from skin at 10 days post-infestation (dpi) and 18 dpi, respectively) in the samplings: Experiment (Exp) 1, sampled at 10 dpi, Experiment 2 sampled at 10 dpi and Experiment 2 sampled at 18 dpi. The average binary logarithm of the expression across all samples is shown on the x-axis and the binary logarithm of fold change is shown on the y-axis. Red dots indicate differentially expressed genes (DESeq2, Padj < 0.05) while grey dots are not differentially expressed between the two groups. c Principal components analysis (PCA) plots of the same data