Phytopathogen emergence in the genomics era

• Next-generation sequencing has provided unprecedented insight into how new plant pathogens emerge.
• Horizontal gene transfer, genome plasticity, and hybridisation all play a role in phytopathogen emergence.
• Publicly-available genome sequences are crucial to rapidly identifying emerging pathogens and the mechanisms by which they emerged.

Phytopathogens are a global threat to plant agriculture and biodiversity. The genomics era has lead to an exponential rise in comparative gene and genome studies of both economically significant and insignificant microorganisms. In this review we highlight some recent comparisons and discuss how they identify shared genes or genomic regions associated with host virulence. The two major mechanisms of rapid genome adaptation – horizontal gene transfer and hybridisation – are reviewed and we consider how intra-specific pan-genome sequences encode alternative host specificity. We also discuss the power that access to expansive gene databases provides in aiding the study of phytopathogen emergence. These databases can rapidly enable the identification of an unknown pathogen and its origin, as well as genomic adaptations required for emergence.