Figure 3.

Volcano plots showing differential expression of genes in the live attenuated strains. Log₂ ratio gene expression levels for the mutant strains (A) ∆cps/psaA and (B) ∆cps/proABC compared to the wild type strain. Fold change expression is represented in the X-axis, with negative values indicating genes that are under-expressed in the mutant versus the wild type, while positive fold change values indicate genes that are over-expressed in the mutant versus the wild type. The Y-axis shows the p values (as -log₁₀ values) for differentially expressed genes. Genes belonging to cps locus are shown in blue, while those belonging to the pilus are shown in green, other genes that are differentially expressed are represented in red and all other genes are represented in black. Differential gene expression and statistical significance were analysed using the DESeq2 method. The dashed line above the x axis marks the significance threshold of p = 0.01. A full list of the genes showing differential expression with their expression levels is shown in Table S2, with selected genes of interest shown in Table 1.