Limits...
Field pathogenomics reveals the emergence of a diverse wheat yellow rust population.

Hubbard A, Lewis CM, Yoshida K, Ramirez-Gonzalez RH, de Vallavieille-Pope C, Thomas J, Kamoun S, Bayles R, Uauy C, Saunders DG - Genome Biol. (2015)

Bottom Line: We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years.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.

View Article: PubMed Central - PubMed

ABSTRACT

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.

Show MeSH

Related in: MedlinePlus

PST field isolates belong to a diverse emergent lineage. (a) A total of 219 samples of wheat and triticale infected with PST were collected from 17 different counties across the United Kingdom (UK) in the spring and summer of 2013. Transcriptome sequencing was carried out on 39 samples to generate transcript data from both the pathogen and host. For the pathogen, the data were used to assess the pathogen population diversity and differential gene expression. For the host, the data were used to confirm the host variety within a particular sample. SNP, single nucleotide polymorphism. (b) 2013 field isolates (dark blue squares) are distinct and highly diverse when compared with the older UK population (light blue squares). Phylogenetic analysis was undertaken using the third codon position of 5,610 PST-130 gene models (2,496,679 sites) with ≥80% breadth of coverage for all PST isolates using a maximum likelihood model. Stars indicate samples in which both the genome and transcriptome were sequenced from the same PST isolate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4342793&req=5

Fig1: PST field isolates belong to a diverse emergent lineage. (a) A total of 219 samples of wheat and triticale infected with PST were collected from 17 different counties across the United Kingdom (UK) in the spring and summer of 2013. Transcriptome sequencing was carried out on 39 samples to generate transcript data from both the pathogen and host. For the pathogen, the data were used to assess the pathogen population diversity and differential gene expression. For the host, the data were used to confirm the host variety within a particular sample. SNP, single nucleotide polymorphism. (b) 2013 field isolates (dark blue squares) are distinct and highly diverse when compared with the older UK population (light blue squares). Phylogenetic analysis was undertaken using the third codon position of 5,610 PST-130 gene models (2,496,679 sites) with ≥80% breadth of coverage for all PST isolates using a maximum likelihood model. Stars indicate samples in which both the genome and transcriptome were sequenced from the same PST isolate.

Mentions: To characterize the genotypic diversity of PST at the field level, we collected 219 samples of wheat and triticale infected with PST from 17 different counties across the UK in the spring and summer of 2013 (Figure 1a; Table S1 in Additional file 1). From these, we selected 35 PST-infected wheat samples from wheat varieties that spanned the resistance spectrum, and 4 PST-infected triticale samples (Table S1 in Additional file 1). Total RNA was extracted from each sample and subjected to RNA-seq analysis (Figure 1a). After filtering, an average of 37% (standard deviation 12.7%) reads aligned to the PST-130 reference genome [18], indicating that fungal transcripts account for a high percentage of the transcripts in PST-infected plant tissue (Table S2 in Additional file 1). To address whether each sample comprised a single PST genotype without considerable bias in allele-specific expression, we calculated the distribution of read counts for biallelic single nucleotide polymorphisms (SNPs), determined from alignment to the PST-130 genome. As a dikaryon, the PST mean of read counts at heterokaryotic positions is expected to have a single mode at 0.5, with two alternative alleles each representing one of the two haploid nuclei (Additional file 2) [22]. Based on the presence of only two alleles and the shape of the distribution being comparable to purified isolates when heterokaryotic SNPs were considered, we concluded that all samples likely represent a predominantly single genotype with little bias in allele expression (Additional files 3 and 4).Figure 1


Field pathogenomics reveals the emergence of a diverse wheat yellow rust population.

Hubbard A, Lewis CM, Yoshida K, Ramirez-Gonzalez RH, de Vallavieille-Pope C, Thomas J, Kamoun S, Bayles R, Uauy C, Saunders DG - Genome Biol. (2015)

PST field isolates belong to a diverse emergent lineage. (a) A total of 219 samples of wheat and triticale infected with PST were collected from 17 different counties across the United Kingdom (UK) in the spring and summer of 2013. Transcriptome sequencing was carried out on 39 samples to generate transcript data from both the pathogen and host. For the pathogen, the data were used to assess the pathogen population diversity and differential gene expression. For the host, the data were used to confirm the host variety within a particular sample. SNP, single nucleotide polymorphism. (b) 2013 field isolates (dark blue squares) are distinct and highly diverse when compared with the older UK population (light blue squares). Phylogenetic analysis was undertaken using the third codon position of 5,610 PST-130 gene models (2,496,679 sites) with ≥80% breadth of coverage for all PST isolates using a maximum likelihood model. Stars indicate samples in which both the genome and transcriptome were sequenced from the same PST isolate.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4342793&req=5

Fig1: PST field isolates belong to a diverse emergent lineage. (a) A total of 219 samples of wheat and triticale infected with PST were collected from 17 different counties across the United Kingdom (UK) in the spring and summer of 2013. Transcriptome sequencing was carried out on 39 samples to generate transcript data from both the pathogen and host. For the pathogen, the data were used to assess the pathogen population diversity and differential gene expression. For the host, the data were used to confirm the host variety within a particular sample. SNP, single nucleotide polymorphism. (b) 2013 field isolates (dark blue squares) are distinct and highly diverse when compared with the older UK population (light blue squares). Phylogenetic analysis was undertaken using the third codon position of 5,610 PST-130 gene models (2,496,679 sites) with ≥80% breadth of coverage for all PST isolates using a maximum likelihood model. Stars indicate samples in which both the genome and transcriptome were sequenced from the same PST isolate.
Mentions: To characterize the genotypic diversity of PST at the field level, we collected 219 samples of wheat and triticale infected with PST from 17 different counties across the UK in the spring and summer of 2013 (Figure 1a; Table S1 in Additional file 1). From these, we selected 35 PST-infected wheat samples from wheat varieties that spanned the resistance spectrum, and 4 PST-infected triticale samples (Table S1 in Additional file 1). Total RNA was extracted from each sample and subjected to RNA-seq analysis (Figure 1a). After filtering, an average of 37% (standard deviation 12.7%) reads aligned to the PST-130 reference genome [18], indicating that fungal transcripts account for a high percentage of the transcripts in PST-infected plant tissue (Table S2 in Additional file 1). To address whether each sample comprised a single PST genotype without considerable bias in allele-specific expression, we calculated the distribution of read counts for biallelic single nucleotide polymorphisms (SNPs), determined from alignment to the PST-130 genome. As a dikaryon, the PST mean of read counts at heterokaryotic positions is expected to have a single mode at 0.5, with two alternative alleles each representing one of the two haploid nuclei (Additional file 2) [22]. Based on the presence of only two alleles and the shape of the distribution being comparable to purified isolates when heterokaryotic SNPs were considered, we concluded that all samples likely represent a predominantly single genotype with little bias in allele expression (Additional files 3 and 4).Figure 1

Bottom Line: We found that the PST population across the United Kingdom (UK) underwent a major shift in recent years.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.

View Article: PubMed Central - PubMed

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus