Abstract
BackgroundEmerging 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.ResultsTo 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0590-8) contains supplementary material, which is available to authorized users.
Highlights
Emerging and re-emerging pathogens imperil public health and global food security
Our field pathogenomics approach circumvents the difficulties associated with less-tractable filamentous plant pathogens and can be applied to other emerging populations of pathogens. Genotyping pathogens and their hosts using RNA sequencing (RNA-seq) of field-collected infected leaves To characterize the genotypic diversity of Puccinia striiformis f. sp. tritici (PST) at the field level, we collected 219 samples of wheat and triticale infected with PST from 17 different counties across the United Kingdom (UK) in the spring and summer of 2013 (Figure 1a; Table S1 in Additional file 1)
To address whether each sample comprised a single PST genotype without considerable bias in allelespecific expression, we calculated the distribution of read counts for biallelic single nucleotide polymorphisms (SNPs), determined from alignment to the PST isolate 130 (PST-130) genome
Summary
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. Traditional diagnostic tools for pathogens have been based on targeted cultures, PCR-based approaches and/ or phenotypic evaluation of disease response in specific plant genotypes [7]. These methods detect only known pathogenic agents, can introduce bias, and can fail to recognize novel variants or races due to their narrow
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