From genes to epidemics: Genomic insights into bacterial plant pathogen emergence

Bacterial phytopathogens are major causal agents of newly emerging plant diseases. The roles of both agricultural practices and the alteration of bacterial genomic content are well understood in the evolution of novel pathogens. However, translating this knowledge into effective tools for the comparison, prediction and understanding of current outbreaks remains challenging. To be pathogenic bacteria must be able to avoid plant immune responses, colonize host tissue and cause disease. Recent advances in both sequencing technologies and imaging techniques have provided fascinating insights into how bacterial interactions with each other and mobile genetic elements play a role in virulence evolution. This review explores these interactions, with a focus on the role of mobile genetic elements in plant pathogen evolution. Special consideration is given to how recent technologies can be applied to allow the observation of these interactions in the field and the future directions required to integrate these tools in field-based monitoring to further understand and enhance early management practices.