Following the trail of oat crown rust: a UK isolate connects to the USA

Pathogen genomics often feels like a forward-looking field: new sequencing methods, larger datasets, and more powerful analysis. But some of the most useful insights can come from looking back.

A recent international collaborative study led by Prof. Melania Figueroa (CSIRO, Australia), recently published online (First Look) in Molecular Plant–Microbe Interactions, explores the global population structure of the oat crown rust pathogen (Puccinia coronata f. sp. avenae). The study uses haplotype-resolved, chromosome-scale genome assemblies from isolates collected across multiple continents over several decades.

One of the key findings is that some pathogen haplotypes can persist for a surprisingly long time and can move between continents with little change. In particular, one haplotype links a UK isolate collected in 1984 with isolates sampled in the USA in 1990 and again in 2017.

Why does this matter?

Oat crown rust is a fast-evolving pathogen. In some regions, especially where its alternate host (for example common buckthorn) is in abundance, sexual reproduction can generate high genetic diversity and rapid shifts in virulence. In other regions, populations are thought to be mostly asexual, dominated by clonal lineages that change more slowly.

This genome-wide analysis suggests these clonal lineages can be long-lived. Finding a nearly identical nuclear haplotype in isolates separated by more than 30 years, and thousands of miles, supports the idea that some clonal haplotypes persist globally. They may occasionally move between lineages through nuclear exchange and are only rarely reshuffled by sexual recombination.

This challenges the assumption that older isolates are necessarily “obsolete”, or that modern populations are always made up of recently evolved haplotypes.

The role of a UK historic isolate

Niab contributed pathotyping data for a UK oat crown rust isolate sampled in 1984 and well preserved in the Niab collection of cereal rust isolates, along with high-quality, high-molecular-weight genomic DNA suitable for long-read sequencing, and fungal spore preparations for high-throughput chromosome conformation capture (Hi-C) sequencing. These materials enabled a fully phased, chromosome-scale genome assembly for this old isolate. That assembly proved very informative. One of its two nuclear haplotypes is nearly identical to a haplotype found in North American isolates collected decades later. Without a phased genome from the 1984 UK isolate, this long-term persistence, and what it tells us about global population structure, would have been much harder to detect.

This is a good example of how well-curated archival material can greatly increase the value of modern sequencing.

Beyond a single result

More broadly, the study generated haplotype-resolved genomes from ten oat crown rust isolates originating from Europe, Africa, and the Middle East. This expanded the collection to 52 haplotypes from 26 isolates worldwide.

Together, these data point to a global population largely made up of long-lived clonal lineages, with occasional nuclear exchange events and rare sexual recombination.

The work also highlights how different evolutionary processes can operate side-by-side: long-term stability of whole haplotypes, alongside more dynamic changes in gene content, effector repertoires, and gene expression. For disease surveillance and resistance breeding, this combination of persistence and flexibility is both challenging and important to understand.

Additional take-home messages

This story is a useful reminder that historic isolates can be scientifically invaluable, and that maintaining pathogen collections can pay dividends decades later. It also reinforces that high-quality sample preparation remains critical for getting the most out of downstream sequencing and bioinformatics. And sometimes, even a single isolate can change how we think about an entire pathogen population.

Read the paper