Journal
GENOME BIOLOGY
Volume 16, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13059-015-0590-8
Keywords
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Funding
- Sustainable Crop Production Research for International Development (SCPRID) programme from the Biotechnology and Biological Sciences Research Council (BBSRC) [BB/J012017/1]
- BBSRC Institute Strategic Programme [BB/J004553/1]
- John Innes Foundation
- Gatsby Charitable Foundation
- Japanese Society for Promotion of Science (JSPS) fellowship
- Norwich Research Park PhD Studentship
- Genome Analysis Centre Funding and Maintenance Grant
- Genome Analysis Centre
- John Innes Centre
- BBSRC
- BBSRC [BBS/E/J/000C0659, BB/L018535/1, BB/M025497/1, BBS/E/J/000CA474, BB/M025519/1, BB/J012017/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/M025497/1, BB/J012017/1, BB/L018535/1, BBS/E/J/000C0659, BBS/E/J/000CA474, BB/M025519/1] Funding Source: researchfish
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Background: Emerging and re-emerging pathogens imperil public health and global food security. Responding to these threats requires improved surveillance and diagnostic systems. Despite their potential, genomic tools have not been readily applied to emerging or re-emerging plant pathogens such as the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici (PST). This is due largely to the obligate parasitic nature of PST, as culturing PST isolates for DNA extraction remains slow and tedious. Results: To counteract the limitations associated with culturing PST, we developed and applied a field pathogenomics approach by transcriptome sequencing infected wheat leaves collected from the field in 2013. This enabled us to rapidly gain insights into this emerging pathogen population. We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years. Population genetic structure analyses revealed four distinct lineages that correlated to the phenotypic groups determined through traditional pathology-based virulence assays. Furthermore, the genetic diversity between members of a single population cluster for all 2013 PST field samples was much higher than that displayed by historical UK isolates, revealing a more diverse population of PST. Conclusions: Our field pathogenomics approach uncovered a dramatic shift in the PST population in the UK, likely due to a recent introduction of a diverse set of exotic PST lineages. The methodology described herein accelerates genetic analysis of pathogen populations and circumvents the difficulties associated with obligate plant pathogens. In principle, this strategy can be widely applied to a variety of plant pathogens.
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