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Bacteria belonging to the genera  Dickeya  and  Pectobacterium  are responsible for significant economic losses in a wide variety of crops and ornamentals. During last years, increasing losses in potato production have been attributed to the appearance of  Dickeya solani . The  D. solani  strains investigated so far share genetic homogeneity, although different virulence levels were observed among strains of various origins. The purpose of this study was to investigate the genetic traits possibly related to the diverse virulence levels by means of comparative genomics. First, we developed a new genome assembly pipeline which allowed us to complete the  D. solani  genomes. Four  de novo  sequenced and ten publicly available genomes were used to identify the structure of the  D. solani  pangenome, in which 74.8 and 25.2% of genes were grouped into the core and dispensable genome, respectively. For  D. solani  panregulon analysis, we performed a binding site prediction for four transcription factors, namely CRP, KdgR, PecS and Fur, to detect the regulons of these virulence regulators. Most of the  D. solani  potential virulence factors were predicted to belong to the accessory regulons of CRP, KdgR, and PecS. Thus, some differences in gene expression could exist between  D. solani  strains. The comparison between a highly and a low virulent strain, IFB0099 and IFB0223, respectively, disclosed only small differences between their genomes but significant differences in the production of virulence factors like pectinases, cellulases and proteases, and in their mobility. The  D. solani  strains also diverge in the number and size of prophages present in their genomes. Another relevant difference is the disruption of the adhesin gene  fhaB2  in the highly virulent strain. Strain IFB0223, which has a complete adhesin gene, is less mobile and less aggressive than IFB0099. This suggests that in this case, mobility rather than adherence is needed in order to trigger disease symptoms. This study highlights the utility of comparative genomics in predicting  D. solani  traits involved in the aggressiveness of this emerging plant pathogen.

Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species