Diversity and Structure of Diaporthe humulicola Populations from Eastern North America

Hop (Humulus lupulus) production in the eastern United States has increased in recent years, prompting the need to understand emerging fungal pathogens in this region. This study is the first population genetics analysis of Diaporthe humulicola, a recently described pathogen causing halo blight. A total of 71 D. humulicola isolates from Michigan, New York, Minnesota, and Canada were sequenced and analyzed using Illumina 150 × 150-bp reads with 10× coverage. Single-nucleotide polymorphisms were discovered and filtered using the Genome Analysis Toolkit. After filtering and clone correction, 63 isolates remained for downstream analysis. Population structure was determined to have three clusters and was supported using STRUCTURE, principal component analysis, and discriminant analysis of principal components. Analyses showed that Michigan isolates closely clustered with isolates from Canada and New York, as well as one isolate from Minnesota. The rest of the Minnesota isolates clustered in an independent cluster. Minnesota isolates appear to have high levels of population differentiation when compared with the different populations exhibiting a high fixation index, a measure of population differentiation and low nucleotide diversity. Mating type was determined for each isolate, with Mat1-2-1 present in 61.9% of the whole population. We also detected signals of recombination in each of the fungal populations, with higher levels in Michigan and Canada. These findings highlight the genetic complexity and regional differentiation of D. humulicola populations, with implications for disease management and hop breeding programs.