Resurgence of cucurbit downy mildew in the United States: Insights from comparative genomic analysis of .

, the causal agent of cucurbit downy mildew (CDM), is known to exhibit host specialization. The virulence of different isolates of the pathogen can be classified into pathotypes based on their compatibility with a differential set composed of specific cucurbit host types. However, the genetic basis of host specialization within is not yet known. Total genomic DNA extracted from nine isolates of collected from 2008 to 2013 from diverse cucurbit host types ( var. , , and ) in the United States were subjected to whole-genome sequencing. Comparative analysis of these nine genomes confirmed the presence of two distinct evolutionary lineages (lineages I and II) of . Many fixed polymorphisms separated lineage I comprising isolates from , and from lineage II comprising isolates from spp. and . Phenotypic characterization showed that lineage II isolates were of the A1 mating type and belonged to pathotypes 1 and 3 that were not known to be present in the United States prior to the resurgence of CDM in 2004. The association of lineage II isolates with the new pathotypes and a lack of genetic diversity among these isolates suggest that lineage II of is associated with the resurgence of CDM on cucumber in the United States.