Abstract
Basidiomycetes like rust fungi have complex reproductive cycles and dikaryotic life stages which influence their population structure and evolution. Puccinia coronata f. sp. avenae (Pca), the causal agent of oat crown rust, is a pathogen of global economic importance. To investigate the genetic diversity of the species, as well as the role of mating type system and nuclear exchange (somatic hybridization) in host adaptation of Pca we acquired whole genome sequencing data of Taiwanese and Australian isolates, adding to existing data for USA and South African populations. An atlas of 30 chromosome-level, fully-phased nuclear haplotypes from six USA isolates and nine Australian isolates was generated to capture the genomic composition of key oat crown rust lineages. This study provides evidence of nuclear exchange and recombination of haplotypes in both the USA and Australian Pca populations as mechanisms for the introduction of genetic diversity. The limitations of assuming clonal evolutionary history from virulence phenotyping is demonstrated by the detection of either sexual or cryptic genetic recombination in the Pca Australian population. Overall, the characterization of intercontinental migration of Pca at the haplotype level provides further impetus for molecular monitoring of rust pathogen populations on a global scale.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Funding This project was supported by the Bioplatforms Australia Plant Pathogen ‘Omics Initiative, GRDC project CSP2204 007RTX, USDA-NIFA BBSRC award 2022-67013-36505, the CSIRO Research Office, and grant 109-2313-B-002-028-MY3 from the National Science and Technology Council of Taiwan. ECH was supported by the ANU University Research Scholarship and ANU/CSIRO Digital Agriculture PhD Supplementary Scholarship.