LAUSR

Dickeya dianthicola has caused an outbreak of blackleg and soft rot of potato in the eastern half of the USA since 2015. To investigate genetic diversity of the pathogen, a comparative analysis was conducted on genomes of D. dianthicola strains. Whole genomes of 16 strains from the USA outbreak were assembled and compared to 16 previously sequenced genomes of D. dianthicola isolated from potato or carnation. Among the 32 strains, eight distinct clades were distinguished based on phylogenomic analysis. The outbreak strains were grouped into three clades, with the majority of the strains in clade I. Clade I strains were unique and homogeneous, suggesting a recent incursion of this strain into potato production from alternative hosts or environmental sources. Pangenome of the 32 strains contained 6693 genes, 3377 of which were core genes. By screening primary protein subunits associated with virulence from all USA strains, we found many virulence-related gene clusters, such as plant cell wall degrading enzyme genes, flagellar and chemotaxis related genes, two-component regulatory genes, and type I/II/III secretion system genes were highly conserved but type IV and type VI secretion system genes varied. The virulent clade I strains encoded two clusters of type IV secretion systems, while clade II and III strains encoded only one cluster. Clade I and II strains encoded one more VgrG/PAAR spike protein than clade III. Thus, we predicted that the presence of additional virulence-related genes may have enabled the unique clade I strain to become predominant source in the USA outbreak.