One clonal lineage of Calonectria pseudonaviculata is primarily responsible for the boxwood blight epidemic in the United States.

Boxwood blight caused by Calonectria pseudonaviculata (Cps) and C. henricotiae (Che) is destroying cultivated and native boxwood worldwide, with profound negative economic impacts on the horticulture industry. First documented in the U.S. in 2011, the disease has now occurred in 28 states. Previous research showed that global Cps populations prior to 2014 had a clonal structure, and only the MAT1-2 idiomorph was observed. In this study, we examined the Cps genetic diversity and population structure in the U.S. after 2014, following the expansion of the disease across the country over the past five years. Two hundred eighteen isolates from 21 states were genotyped by sequencing 11 simple sequence repeat (SSR) loci and by MAT1 idiomorph typing. All isolates presented Cps-specific alleles, indicating that Che is still absent in the U.S. states sampled. The presence of only the MAT1-2 idiomorph and gametic linkage disequilibrium suggests the prevalence of asexual reproduction. The contemporary Cps population is characterized by a clonal structure and composed of 13 multilocus genotypes (SSR-MLGs) unevenly distributed across the U.S. These SSR-MLGs grouped into two clonal lineages (CL). The predominant lineage CL2 (93% of isolates) is the primary contributor to U.S. disease expansion. The contemporary U.S. Cps population is not geographically subdivided and not genetically differentiated from the U.S. population prior to 2014, but is significantly differentiated from the main European population, which is largely composed of CL1. Our findings provide insights into the boxwood blight epidemic that are critical for disease management and breeding of resistant boxwood cultivars.