Population genomics of Puccinia graminis f.sp. tritici

Puccinia graminis f.sp. tritici (Pgt), the causal agent of stem rust disease in wheat, is one of the most destructive pathogens that can cause severe yield losses. The factors driving the evolution of its virulence and adaptation in distinct geographic regions remain poorly characterized. Here, we utilize a long-read sequencing technology to develop a haplotype-resolved genome assembly of a US isolate of Pgt. A collection of haplotype-resolved Pgt assemblies is used as a reference genome representation to characterize the structural variation and single nucleotide polymorphisms in a diverse panel of re-sequenced Pgt isolates. Our study highlights the adaptive role of genomic variants and processes affecting the Pgt effector repertoire and creates a resource for detecting pathogen avirulence factors that might be exploited to prevent future epidemic outbreaks.