Genome-Enabled Analysis of Pathogen Migration and Evolution

Genomics-based genetic marker discovery is leading to unprecedented collection of population genetic data for pathogens. Genomics-based data can be used for detailed analysis of the ancestry of population samples for studying pathogen molecular epidemiology and evolution. Population genomics studies of agricultural pathogens are increasing in number as the costs of sequencing continue to go down. Genomics-enabled markers are valuable for rapidly changing populations and for emerging and clonal pathogens that exhibit little genetic variation. International trade and continued globalization of agriculture has had major effects on plant pathogen populations and their interactions with crop hosts. Increased long-distance movement of pathogens has made disease management particularly challenging. Genomic information is providing data for disease management strategies. We are using whole genome sequencing to examine the processes underlying shifts in the Xanthomonas perforans population causing bacterial spot of tomato in Florida. We have found gain and loss of effectors not previously recognized as being under R gene selection, as well as variation in effector gene content correlated with strain genetic background, indicating multiple introductions of strains with different effector profiles. For understanding the role of strain movement in pathogen population shifts, national and international cooperative efforts are needed. Rapid monitoring of population variation using genomics-informed markers would benefit disease management in many pathosystems.