A Population Genomics Approach to Understand the Diversity, Migration, and Reproduction of the Rice Pathogen

Cercospora janseana is the causal agent of narrow brown leaf spot (NBLS) on rice, an increasingly problematic disease in the southern United States. Historically, this disease was considered sporadic and a minor nuisance, however, recent NBLS epidemics and the resulting detrimental impacts on yield underscore the need for a deeper understanding of the pathogen population biology. In this study, we used whole-genome sequencing of 136 C. janseana isolates collected from Louisiana and Texas to investigate genetic diversity, population structure, and possible reproductive strategies. Our results revealed a high level of genetic diversity across sampling years and locations. Population structure and phylogenetic analyses identified two distinct lineages with most isolates belonging to a dominant lineage found in both states. Despite the disparity in observed lineage frequencies, overall population differentiation was minimal, indicating ongoing gene flow across regional boundaries. Linkage disequilibrium decay and index of association analyses revealed evidence for a population that predominately reproduces clonally with infrequent sexual reproduction. However, nearly equal frequencies of mating type idiomorphs in most sampled populations indicate ongoing or past sexual reproduction to some extent. Taken together, these results suggest that C. janseana populations are diverse, migrate between production regions, and exhibit a mixed mode of reproduction. These findings have important implications for the development of integrated disease management and pathogen monitoring practices to ultimately mitigate the impacts of this resurgent disease.