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Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors.

Sperschneider J, Ying H, Dodds PN, Gardiner DM, Upadhyaya NM, Singh KB, Manners JM, Taylor JM - Front Plant Sci (2014)

Bottom Line: We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialized gene families.In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving.This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification.

View Article: PubMed Central - PubMed

Affiliation: Plant Industry, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation Perth, WA, Australia.

ABSTRACT
Plant pathogens cause severe losses to crop plants and threaten global food production. One striking example is the wheat stem rust fungus, Puccinia graminis f. sp. tritici, which can rapidly evolve new virulent pathotypes in response to resistant host lines. Like several other filamentous fungal and oomycete plant pathogens, its genome features expanded gene families that have been implicated in host-pathogen interactions, possibly encoding effector proteins that interact directly with target host defense proteins. Previous efforts to understand virulence largely relied on the prediction of secreted, small and cysteine-rich proteins as candidate effectors and thus delivered an overwhelming number of candidates. Here, we implement an alternative analysis strategy that uses the signal of adaptive evolution as a line of evidence for effector function, combined with comparative information and expression data. We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialized gene families. In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving. One of our top candidates has recently been shown to induce genotype-specific hypersensitive cell death in wheat. This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification. Our system can be applied to a wide range of pathogens and will give insight into host-pathogen dynamics, ultimately leading to progress in strategies for disease control.

No MeSH data available.


Related in: MedlinePlus

Highly significant in planta expression for predicted clusters of the fungal gene families and pathogen-associated gene families in wheat stem rust. For each cluster, the enriched sequence-derived features and number of highly significant up-regulated genes are shown (p < 0.00001). Note that for clarity, only clusters which have more than 20 up-regulated proteins are shown. The pathogen-associated cluster C6 sits at the top with 78 proteins that are up-regulated with high significance and has enrichment in features that are associated with effector proteins (secreted, small size, cysteine-rich).
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Figure 3: Highly significant in planta expression for predicted clusters of the fungal gene families and pathogen-associated gene families in wheat stem rust. For each cluster, the enriched sequence-derived features and number of highly significant up-regulated genes are shown (p < 0.00001). Note that for clarity, only clusters which have more than 20 up-regulated proteins are shown. The pathogen-associated cluster C6 sits at the top with 78 proteins that are up-regulated with high significance and has enrichment in features that are associated with effector proteins (secreted, small size, cysteine-rich).

Mentions: At significance threshold p < 0.05, up-regulation was found for 1476 of 8851 (16.6%) genes in the pathogen-associated gene family clusters, whereas up-regulation was detected for 1295 of 6536 (19.8%) genes in the fungal gene family clusters (Figure 2). A striking difference in the distribution of up-regulated stem rust genes with high significance (p < 0.00001) can be observed across the clusters (Figure 3). The pathogen-associated, secreted, cysteine-rich cluster C6 contains the highest number of genes that are up-regulated. However, we do observe highly significant up-regulation during infection also across the fungal gene families. This can be expected as the stem rust activates a diverse number of proteins during infection and not all of these will act as an effector or have a function directly related to pathogenesis. For example, haustoria play a major role in nutrient uptake from the host during infection and show high expression of sugar and amino acid transporters (Garnica et al., 2013). Furthermore, not all fungal effector proteins can be expected to be part of the small, cysteine-rich cluster C6. Additional pathogen-associated clusters show potential of containing effector candidates, with elevated levels of highly significant up-regulation during infection in clusters C1, C7, and C11 (Table 1, Figure 3). 9.7, 4.7, and 14.4% of proteins in clusters C1, C7, and C11, respectively, are predicted to be secreted by SignalP 4.1 and could thus contain putative effector candidates. Therefore, signatures of diversifying selection are used in the following as an additional line of evidence for pathogenicity function.


Diversifying selection in the wheat stem rust fungus acts predominantly on pathogen-associated gene families and reveals candidate effectors.

Sperschneider J, Ying H, Dodds PN, Gardiner DM, Upadhyaya NM, Singh KB, Manners JM, Taylor JM - Front Plant Sci (2014)

Highly significant in planta expression for predicted clusters of the fungal gene families and pathogen-associated gene families in wheat stem rust. For each cluster, the enriched sequence-derived features and number of highly significant up-regulated genes are shown (p < 0.00001). Note that for clarity, only clusters which have more than 20 up-regulated proteins are shown. The pathogen-associated cluster C6 sits at the top with 78 proteins that are up-regulated with high significance and has enrichment in features that are associated with effector proteins (secreted, small size, cysteine-rich).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150398&req=5

Figure 3: Highly significant in planta expression for predicted clusters of the fungal gene families and pathogen-associated gene families in wheat stem rust. For each cluster, the enriched sequence-derived features and number of highly significant up-regulated genes are shown (p < 0.00001). Note that for clarity, only clusters which have more than 20 up-regulated proteins are shown. The pathogen-associated cluster C6 sits at the top with 78 proteins that are up-regulated with high significance and has enrichment in features that are associated with effector proteins (secreted, small size, cysteine-rich).
Mentions: At significance threshold p < 0.05, up-regulation was found for 1476 of 8851 (16.6%) genes in the pathogen-associated gene family clusters, whereas up-regulation was detected for 1295 of 6536 (19.8%) genes in the fungal gene family clusters (Figure 2). A striking difference in the distribution of up-regulated stem rust genes with high significance (p < 0.00001) can be observed across the clusters (Figure 3). The pathogen-associated, secreted, cysteine-rich cluster C6 contains the highest number of genes that are up-regulated. However, we do observe highly significant up-regulation during infection also across the fungal gene families. This can be expected as the stem rust activates a diverse number of proteins during infection and not all of these will act as an effector or have a function directly related to pathogenesis. For example, haustoria play a major role in nutrient uptake from the host during infection and show high expression of sugar and amino acid transporters (Garnica et al., 2013). Furthermore, not all fungal effector proteins can be expected to be part of the small, cysteine-rich cluster C6. Additional pathogen-associated clusters show potential of containing effector candidates, with elevated levels of highly significant up-regulation during infection in clusters C1, C7, and C11 (Table 1, Figure 3). 9.7, 4.7, and 14.4% of proteins in clusters C1, C7, and C11, respectively, are predicted to be secreted by SignalP 4.1 and could thus contain putative effector candidates. Therefore, signatures of diversifying selection are used in the following as an additional line of evidence for pathogenicity function.

Bottom Line: We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialized gene families.In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving.This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification.

View Article: PubMed Central - PubMed

Affiliation: Plant Industry, Centre for Environment and Life Sciences, Commonwealth Scientific and Industrial Research Organisation Perth, WA, Australia.

ABSTRACT
Plant pathogens cause severe losses to crop plants and threaten global food production. One striking example is the wheat stem rust fungus, Puccinia graminis f. sp. tritici, which can rapidly evolve new virulent pathotypes in response to resistant host lines. Like several other filamentous fungal and oomycete plant pathogens, its genome features expanded gene families that have been implicated in host-pathogen interactions, possibly encoding effector proteins that interact directly with target host defense proteins. Previous efforts to understand virulence largely relied on the prediction of secreted, small and cysteine-rich proteins as candidate effectors and thus delivered an overwhelming number of candidates. Here, we implement an alternative analysis strategy that uses the signal of adaptive evolution as a line of evidence for effector function, combined with comparative information and expression data. We demonstrate that in planta up-regulated genes that are rapidly evolving are found almost exclusively in pathogen-associated gene families, affirming the impact of host-pathogen co-evolution on genome structure and the adaptive diversification of specialized gene families. In particular, we predict 42 effector candidates that are conserved only across pathogens, induced during infection and rapidly evolving. One of our top candidates has recently been shown to induce genotype-specific hypersensitive cell death in wheat. This shows that comparative genomics incorporating the evolutionary signal of adaptation is powerful for predicting effector candidates for laboratory verification. Our system can be applied to a wide range of pathogens and will give insight into host-pathogen dynamics, ultimately leading to progress in strategies for disease control.

No MeSH data available.


Related in: MedlinePlus