Chromosome-level, haplotype-phased genome assembly of an Australian isolate of the oat crown rust fungus Puccinia coronata f. sp. avenae provides insights into population structure and genomics

Abstract

Puccinia coronata f. sp. avenae (Pca), the causal agent of oat crown rust, is one of the most damaging pathogens of oat worldwide. Rapid evolution and extensive virulence variation continually erode host resistance, posing major challenges for disease management and breeding. This thesis investigated the genomic architecture, population structure, and molecular basis of virulence evolution in Pca through integrated genomic analyses. A chromosome-scale, haplotype-phased reference genome was generated for OCR_502, a representative Australian isolate, using PacBio HiFi sequencing and Hi-C scaffolding. The resulting high-quality assembly provides a valuable genomic resource and a foundation for downstream analyses. Using this reference genome, whole-genome resequencing data from Australian isolates collected over multiple decades were analysed to examine population structure and evolutionary dynamics. The population exhibited high genetic diversity and consisted of several distinct lineages. Temporal shifts in lineage composition suggested that mutation, somatic recombination, and/or the introduction of exotic lineages contribute to diversification despite predominantly clonal reproduction. To investigate the genetic basis of virulence, genome-wide association studies (GWAS) and haplotype-resolved comparative genomics were conducted using 361 isolates phenotyped on five oat crown rust resistance genes (Pc38, Pc39, Pc50, Pc56, and Pc68). Comparative analyses indicated that virulence evolution is more likely driven by allelic variation than gene presence–absence variation. Four high-confidence candidate avirulence genes associated with AvrPc50 and AvrPc56 were identified. Overall, this study provides important genomic resources and advances understanding of the mechanisms underlying virulence evolution and population diversification in Pca.