Comparative genomic analysis of subspecies of Pantoea stewartii reveals distinct variations

Pantoea stewartii subsp. stewartii (Pnss) and P. stewartii subsp. indologenes (Pnsi) are closely related plant pathogens that differ in their host specificities. Pnss is the causal agent of Stewart’s wilt of corn, whereas Pnsi causes disease on millets but not corn. Comparative genomics is a valuable method for characterizing the differences between genomes, but there are few studies on this important quarantine pathogen. Here, we compared publicly available genomes of seven strains of Pnss and three strains of Pnsi. Pan- and core-genome analyses showed that strains isolated from close geographical regions are more similar in their genome structures. Gene content and collinearity analyses further revealed numerous strain-specific genes. In particular, the Pnss type strain DC283 contained over 1200 additional genes compared with other strains. Importantly, we also identified eleven genes that are only present in Pnsi genomes and thus may be useful to distinguish between Pnss and Pnsi strains. Overall, this study characterized the common and distinct genomic features of Pnss and Pnsi, which lay the foundation for future development of molecular methods to detect the Stewart’s wilt pathogen in maize for quarantine regulations and distinguish its two subspecies.