Gene expression analyses on Dickeya solani strains of diverse virulence levels unveil important pathogenicity factors for this species

Abstract

Dickeya solani causes soft rot and blackleg mainly on potato crops. High pathogenicity of this species results from efficient production of plant cell wall-degrading enzymes, especially pectate lyases, potent root colonization, and fast vascular movement. Despite genomic homogeneity, variations in virulence-related phenotypes suggest differences in the gene expression patterns between diverse strains. Therefore, the methylomes and transcriptomes of two strains (virulent IFB0099 and low virulent IFB0223), differing in tissue maceration capacity and virulence factors production, have been studied. Methylation analysis revealed no significant differences. However, the analysis of transcriptomes, studied under both non-induced and induced by polygalacturonic acid conditions (in order to mimic diverse stages of plant infection process), unveiled higher expression of pectate lyases (pelD, pelE, pelL), pectin esterase (pemA), proteases (prtE, prtD) and Vfm-associated quorum-sensing genes (vfmC, vfmD, vfmE) in IFB0099 strain compared to IFB0223. Additionally, the genes related to the secretion system II (T2SS) (gspJ, nipE) displayed higher induction of expression in IFB0099. Furthermore, IFB0099 showed more elevated expression of genes involved in flagella formation, which coincides with enhanced motility and pathogenicity of this strain compared to IFB0223. To sum up, differential expression analysis of genes important for the virulence of D. solani indicated candidate genes, which might be crucial for the pathogenicity of this species.

Keywords: Dickeya spp.; Blackleg; Methylomes; RNA-Seq; Soft rot; Transcriptoms.

Fig. 1

Genome-wide DNA methylome of IFB0099 and IFB0223 D. solani strains. The extent of methylation is shown, using a 10-kb sliding window, of the methylated sites across the D. solani IFB0099 (A to C) and IFB0223 (D to F) chromosomes. Data for each of the three methylated motifs are shown in separate panels for every strain, with the sequence of each motif provided within the panels. In the case of non-palindromic motifs, in which each strand is methylated, the data for these two strands are shown in black (top strand) and grey (bottom strand).

Fig. 2

Principal Component Analysis of the RNA-Seq data. The plot shows the two-dimensional similarity using the Bray-Curtis distance matrix. PC1 and PC2 represent the two principal components. Dots represent individual biological replicates and are colored according to the genotype and growth condition as shown within the in-figure legend.

Fig. 3

Differential expression of 30 genes showing the lowest adjusted p-value for D. solani IFB0099. Hierarchical clustering was used to generate the heatmap. The scale represents the normalized expression level of the genes, which have been transformed using the regularized log technique (normalized log2-transformed expression values (rlog)). The selection criterion for these genes was the adjusted p-value (p adj) < 0.05.

Fig. 4

Differential expression of 30 genes showing the lowest adjusted p-value for D. solani IFB0223. Hierarchical clustering was used to generate the heatmap. The scale represents the normalized expression level of the genes, which have been transformed using the regularized log technique (normalized log2-transformed expression values (rlog)). The selection criterion for these genes was the adjusted p-value (p adj) < 0.05.