FIG 2 .

Expression levels of PhcA-responsive genes in planta. A scatter plot shows the relationship between the average transcript expression level and log fold change (log₂FC) for each coding sequence in the R. solanacearum genome, based on sequencing of RNA extracted from stems of tomato plants infected with either wild-type or ΔphcA bacteria. Log2FC data represent log₂-transformed values corresponding to reads per kilobase of million mapped reads (RPKM) of the ΔphcA mutant versus the wild type. Each circle represents a single coding sequence; black circles indicate genes that are differentially expressed (DE) at a false discovery rate (FDR) of ≤0.005; gray circles indicate non-DE genes. Colored circles indicate DE genes encoding traits of interest: green, extracellular polysaccharide (EPS); yellow, plant cell wall-degrading enzymes (CWDE); blue, structural proteins and effectors of the type III secretion system (T3SS); pink, uptake or catabolism of carbon, nitrogen, sulfur, or iron sources (C/N/S/Fe); red, type VI secretion system (T6SS); orange, hemagglutinin-like proteins and adhesins.