Field pathogenomics reveals the emergence of a diverse wheat yellow rust population.
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.
Amelia
A
Hubbard
Clare M
CM
Lewis
Kentaro
K
Yoshida
Ricardo H
RH
Ramirez-Gonzalez
Claude
C
de Vallavieille-Pope
Jane
J
Thomas
Sophien
S
Kamoun
Rosemary
R
Bayles
Cristobal
C
Uauy
Diane G O
DG
Saunders
D000595:Amino Acid Sequence; D001487:Basidiomycota / Q000145:classification* / Q000235:genetics*; D016681:Genome, Fungal; D023281:Genomics; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D008969:Molecular Sequence Data; D058889:Molecular Typing; D010641:Phenotype; D010802:Phylogeny; D058974:Phylogeography; D010935:Plant Diseases / Q000382:microbiology*; D018515:Plant Leaves; D012331:RNA, Fungal; D016415:Sequence Alignment; D014908:Triticum / Q000382:microbiology*; D006113:United Kingdom; D014774:Virulence / Q000235:genetics
D012331:RNA, Fungal