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Global genome and transcriptome analyses of Magnaporthe oryzae epidemic isolate 98-06 uncover novel effectors and pathogenicity-related genes, revealing gene gain and lose dynamics in genome evolution.

Dong Y, Li Y, Zhao M, Jing M, Liu X, Liu M, Guo X, Zhang X, Chen Y, Liu Y, Liu Y, Ye W, Zhang H, Wang Y, Zheng X, Wang P, Zhang Z - PLoS Pathog. (2015)

Bottom Line: A unique 1.4 Mb of genomic sequences was found in isolate 98-06 in comparison to reference strain 70-15.In addition, 134 candidate effectors with various segregation patterns were identified.Characterization of isolate-specific effector candidates Iug6 and Iug9 and PaR candidate Iug18 revealed that they have a role in fungal propagation and pathogenicity.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.

ABSTRACT
Genome dynamics of pathogenic organisms are driven by pathogen and host co-evolution, in which pathogen genomes are shaped to overcome stresses imposed by hosts with various genetic backgrounds through generation of a variety of isolates. This same principle applies to the rice blast pathogen Magnaporthe oryzae and the rice host; however, genetic variations among different isolates of M. oryzae remain largely unknown, particularly at genome and transcriptome levels. Here, we applied genomic and transcriptomic analytical tools to investigate M. oryzae isolate 98-06 that is the most aggressive in infection of susceptible rice cultivars. A unique 1.4 Mb of genomic sequences was found in isolate 98-06 in comparison to reference strain 70-15. Genome-wide expression profiling revealed the presence of two critical expression patterns of M. oryzae based on 64 known pathogenicity-related (PaR) genes. In addition, 134 candidate effectors with various segregation patterns were identified. Five tested proteins could suppress BAX-mediated programmed cell death in Nicotiana benthamiana leaves. Characterization of isolate-specific effector candidates Iug6 and Iug9 and PaR candidate Iug18 revealed that they have a role in fungal propagation and pathogenicity. Moreover, Iug6 and Iug9 are located exclusively in the biotrophic interfacial complex (BIC) and their overexpression leads to suppression of defense-related gene expression in rice, suggesting that they might participate in biotrophy by inhibiting the SA and ET pathways within the host. Thus, our studies identify novel effector and PaR proteins involved in pathogenicity of the highly aggressive M. oryzae field isolate 98-06, and reveal molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions.

No MeSH data available.


Related in: MedlinePlus

Clustering analysis of gene expression patterns of pathogenicity-related genes and effectors through RNA-Seq.(A) CAST assay shows 14 M. oryzae expression clusters of 64 reported pathogenicity genes and ten effectors of M. oryzae at different stages. The y-axis stands for the log2 average gene expression levels. The quantity of cluster member is marked at the right bottom of each pattern line. (B) Heat map showing expression levels of known pathogenicity genes and effectors of M. oryzae during compatible interactions. The color bar represents the log2 of (RPKM +1) value, ranging from blue (0.0) to red (10.0). Top, stage tree; left, gene tree. The pink rectangle indicates expression pattern of effectors. The blue rectangle indicates expression pattern relevant to pathogenicity.
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ppat.1004801.g003: Clustering analysis of gene expression patterns of pathogenicity-related genes and effectors through RNA-Seq.(A) CAST assay shows 14 M. oryzae expression clusters of 64 reported pathogenicity genes and ten effectors of M. oryzae at different stages. The y-axis stands for the log2 average gene expression levels. The quantity of cluster member is marked at the right bottom of each pattern line. (B) Heat map showing expression levels of known pathogenicity genes and effectors of M. oryzae during compatible interactions. The color bar represents the log2 of (RPKM +1) value, ranging from blue (0.0) to red (10.0). Top, stage tree; left, gene tree. The pink rectangle indicates expression pattern of effectors. The blue rectangle indicates expression pattern relevant to pathogenicity.

Mentions: Finally, to investigate how the M. oryzae genetic program is deployed during infection, we explored 64 known genes relevant to pathogenicity and 10 known effectors of M. oryzae in our interaction transcriptome (S10 Table), and determined their expression patterns by the clustering affinity search technique (CAST) assay through MultiExperiment Viewer 4.6 software package [31]. The distance metric is the default Pearson correlation, and the threshold affinity value is 0.8. Fourteen clusters were generated, and the cluster-a with the most members (23 genes) was illustrated, which provided the major expression pattern of pathogenesis-related genes (Fig 3A, a; S10 Table). The expression pattern-a represents high expression throughout the infection process, with the exception of sharp reduction at 24 hpi. In general, the virulence factors were up-regulated with different waves of expression during infection (Fig 3A). Interestingly, another expression pattern-b for effectors was also distinguished (Fig 3A and 3B; S10 Table).


Global genome and transcriptome analyses of Magnaporthe oryzae epidemic isolate 98-06 uncover novel effectors and pathogenicity-related genes, revealing gene gain and lose dynamics in genome evolution.

Dong Y, Li Y, Zhao M, Jing M, Liu X, Liu M, Guo X, Zhang X, Chen Y, Liu Y, Liu Y, Ye W, Zhang H, Wang Y, Zheng X, Wang P, Zhang Z - PLoS Pathog. (2015)

Clustering analysis of gene expression patterns of pathogenicity-related genes and effectors through RNA-Seq.(A) CAST assay shows 14 M. oryzae expression clusters of 64 reported pathogenicity genes and ten effectors of M. oryzae at different stages. The y-axis stands for the log2 average gene expression levels. The quantity of cluster member is marked at the right bottom of each pattern line. (B) Heat map showing expression levels of known pathogenicity genes and effectors of M. oryzae during compatible interactions. The color bar represents the log2 of (RPKM +1) value, ranging from blue (0.0) to red (10.0). Top, stage tree; left, gene tree. The pink rectangle indicates expression pattern of effectors. The blue rectangle indicates expression pattern relevant to pathogenicity.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383609&req=5

ppat.1004801.g003: Clustering analysis of gene expression patterns of pathogenicity-related genes and effectors through RNA-Seq.(A) CAST assay shows 14 M. oryzae expression clusters of 64 reported pathogenicity genes and ten effectors of M. oryzae at different stages. The y-axis stands for the log2 average gene expression levels. The quantity of cluster member is marked at the right bottom of each pattern line. (B) Heat map showing expression levels of known pathogenicity genes and effectors of M. oryzae during compatible interactions. The color bar represents the log2 of (RPKM +1) value, ranging from blue (0.0) to red (10.0). Top, stage tree; left, gene tree. The pink rectangle indicates expression pattern of effectors. The blue rectangle indicates expression pattern relevant to pathogenicity.
Mentions: Finally, to investigate how the M. oryzae genetic program is deployed during infection, we explored 64 known genes relevant to pathogenicity and 10 known effectors of M. oryzae in our interaction transcriptome (S10 Table), and determined their expression patterns by the clustering affinity search technique (CAST) assay through MultiExperiment Viewer 4.6 software package [31]. The distance metric is the default Pearson correlation, and the threshold affinity value is 0.8. Fourteen clusters were generated, and the cluster-a with the most members (23 genes) was illustrated, which provided the major expression pattern of pathogenesis-related genes (Fig 3A, a; S10 Table). The expression pattern-a represents high expression throughout the infection process, with the exception of sharp reduction at 24 hpi. In general, the virulence factors were up-regulated with different waves of expression during infection (Fig 3A). Interestingly, another expression pattern-b for effectors was also distinguished (Fig 3A and 3B; S10 Table).

Bottom Line: A unique 1.4 Mb of genomic sequences was found in isolate 98-06 in comparison to reference strain 70-15.In addition, 134 candidate effectors with various segregation patterns were identified.Characterization of isolate-specific effector candidates Iug6 and Iug9 and PaR candidate Iug18 revealed that they have a role in fungal propagation and pathogenicity.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, China; Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China.

ABSTRACT
Genome dynamics of pathogenic organisms are driven by pathogen and host co-evolution, in which pathogen genomes are shaped to overcome stresses imposed by hosts with various genetic backgrounds through generation of a variety of isolates. This same principle applies to the rice blast pathogen Magnaporthe oryzae and the rice host; however, genetic variations among different isolates of M. oryzae remain largely unknown, particularly at genome and transcriptome levels. Here, we applied genomic and transcriptomic analytical tools to investigate M. oryzae isolate 98-06 that is the most aggressive in infection of susceptible rice cultivars. A unique 1.4 Mb of genomic sequences was found in isolate 98-06 in comparison to reference strain 70-15. Genome-wide expression profiling revealed the presence of two critical expression patterns of M. oryzae based on 64 known pathogenicity-related (PaR) genes. In addition, 134 candidate effectors with various segregation patterns were identified. Five tested proteins could suppress BAX-mediated programmed cell death in Nicotiana benthamiana leaves. Characterization of isolate-specific effector candidates Iug6 and Iug9 and PaR candidate Iug18 revealed that they have a role in fungal propagation and pathogenicity. Moreover, Iug6 and Iug9 are located exclusively in the biotrophic interfacial complex (BIC) and their overexpression leads to suppression of defense-related gene expression in rice, suggesting that they might participate in biotrophy by inhibiting the SA and ET pathways within the host. Thus, our studies identify novel effector and PaR proteins involved in pathogenicity of the highly aggressive M. oryzae field isolate 98-06, and reveal molecular and genomic dynamics in the evolution of M. oryzae and rice host interactions.

No MeSH data available.


Related in: MedlinePlus