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In planta Identification of Putative Pathogenicity Factors from the Chickpea Pathogen Ascochyta rabiei by De novo Transcriptome Sequencing Using RNA-Seq and Massive Analysis of cDNA Ends.

Fondevilla S, Krezdorn N, Rotter B, Kahl G, Winter P - Front Microbiol (2015)

Bottom Line: Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins.MACE identified 596 transcripts that were up-regulated during infection.An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology, Institute for Molecular Bioscience, Goethe-University of Frankfurt Frankfurt am Main, Germany.

ABSTRACT
The most important foliar diseases in legumes worldwide are ascochyta blights. Up to now, in the Ascochyta-legume pathosystem most studies focused on the identification of resistance genes in the host, while very little is known about the pathogenicity factors of the fungal pathogen. Moreover, available data were often obtained from fungi growing under artificial conditions. Therefore, in this study we aimed at the identification of the pathogenicity factors of Ascochyta rabiei, causing ascochyta blight in chickpea. To identify potential fungal pathogenicity factors, we employed RNA-seq and Massive Analysis of cDNA Ends (MACE) to produce comprehensive expression profiles of A. rabiei genes isolated either from the fungus growing in absence of its host or from fungi infecting chickpea leaves. We further provide a comprehensive de novo assembly of the A. rabiei transcriptome comprising 22,725 contigs with an average length of 1178 bp. Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins. MACE identified 596 transcripts that were up-regulated during infection. An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.

No MeSH data available.


Related in: MedlinePlus

Percentage of A. rabiei transcripts belonging to over/under-represented (χ2, p < 0.05) GO Slim terms in the set of up-regulated genes in comparison to the complete transcriptome for the GO categories (A) Molecular Function (B) Biological process.
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Figure 6: Percentage of A. rabiei transcripts belonging to over/under-represented (χ2, p < 0.05) GO Slim terms in the set of up-regulated genes in comparison to the complete transcriptome for the GO categories (A) Molecular Function (B) Biological process.

Mentions: To identify the A. rabiei genes specifically involved in host infection, we compared the gene expression profiles of the “in medium” with the “in planta” growing pathogen at three relevant steps of the infection process. Statistical analysis of the transcriptome data with DEseq identified A. rabiei genes consistently differentially expressed during the infection process across three independent replicates. In total 596 transcripts were up-regulated at least at one time point after infection in comparison to the fungus grown in medium (Additional file 6). The largest number of up-regulated transcripts (431) was up-regulated at the earliest steps of infection at 12 hai, while 353 and 342 were up-regulated at 36 and 96 hai, respectively. A total of 179 transcripts were up-regulated under all infection conditions. A heat map showing nine clusters describing the expression pattern of these up-regulated transcripts at the different time points is shown in Additional file 7. The transcripts included in each cluster can be found in Additional file 8. GO term enrichment analysis revealed that genes categorized to the GO biological processes “secondary metabolic process,” “cell wall organization and biogenesis,” “symbiosis, encompassing mutualism through parasitism,” “DNA metabolic process,” “Chromosome organization,” and “Chromosome segregation” were overrepresented in up-regulated genes compared to the whole transcriptome (Figure 6). For the GO category “Molecular function,” an enrichment of genes showing “oxyreductase activity,” “helicase activity,” “hydrolase activity, acting on glycosyl bonds,” “isomerase activity,” “nuclease activity,” “DNA binding,” and “ion binding” was detected.


In planta Identification of Putative Pathogenicity Factors from the Chickpea Pathogen Ascochyta rabiei by De novo Transcriptome Sequencing Using RNA-Seq and Massive Analysis of cDNA Ends.

Fondevilla S, Krezdorn N, Rotter B, Kahl G, Winter P - Front Microbiol (2015)

Percentage of A. rabiei transcripts belonging to over/under-represented (χ2, p < 0.05) GO Slim terms in the set of up-regulated genes in comparison to the complete transcriptome for the GO categories (A) Molecular Function (B) Biological process.
© Copyright Policy
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC4664620&req=5

Figure 6: Percentage of A. rabiei transcripts belonging to over/under-represented (χ2, p < 0.05) GO Slim terms in the set of up-regulated genes in comparison to the complete transcriptome for the GO categories (A) Molecular Function (B) Biological process.
Mentions: To identify the A. rabiei genes specifically involved in host infection, we compared the gene expression profiles of the “in medium” with the “in planta” growing pathogen at three relevant steps of the infection process. Statistical analysis of the transcriptome data with DEseq identified A. rabiei genes consistently differentially expressed during the infection process across three independent replicates. In total 596 transcripts were up-regulated at least at one time point after infection in comparison to the fungus grown in medium (Additional file 6). The largest number of up-regulated transcripts (431) was up-regulated at the earliest steps of infection at 12 hai, while 353 and 342 were up-regulated at 36 and 96 hai, respectively. A total of 179 transcripts were up-regulated under all infection conditions. A heat map showing nine clusters describing the expression pattern of these up-regulated transcripts at the different time points is shown in Additional file 7. The transcripts included in each cluster can be found in Additional file 8. GO term enrichment analysis revealed that genes categorized to the GO biological processes “secondary metabolic process,” “cell wall organization and biogenesis,” “symbiosis, encompassing mutualism through parasitism,” “DNA metabolic process,” “Chromosome organization,” and “Chromosome segregation” were overrepresented in up-regulated genes compared to the whole transcriptome (Figure 6). For the GO category “Molecular function,” an enrichment of genes showing “oxyreductase activity,” “helicase activity,” “hydrolase activity, acting on glycosyl bonds,” “isomerase activity,” “nuclease activity,” “DNA binding,” and “ion binding” was detected.

Bottom Line: Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins.MACE identified 596 transcripts that were up-regulated during infection.An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology, Institute for Molecular Bioscience, Goethe-University of Frankfurt Frankfurt am Main, Germany.

ABSTRACT
The most important foliar diseases in legumes worldwide are ascochyta blights. Up to now, in the Ascochyta-legume pathosystem most studies focused on the identification of resistance genes in the host, while very little is known about the pathogenicity factors of the fungal pathogen. Moreover, available data were often obtained from fungi growing under artificial conditions. Therefore, in this study we aimed at the identification of the pathogenicity factors of Ascochyta rabiei, causing ascochyta blight in chickpea. To identify potential fungal pathogenicity factors, we employed RNA-seq and Massive Analysis of cDNA Ends (MACE) to produce comprehensive expression profiles of A. rabiei genes isolated either from the fungus growing in absence of its host or from fungi infecting chickpea leaves. We further provide a comprehensive de novo assembly of the A. rabiei transcriptome comprising 22,725 contigs with an average length of 1178 bp. Since pathogenicity factors are usually secreted, we predicted the A. rabiei secretome, yielding 550 putatively secreted proteins. MACE identified 596 transcripts that were up-regulated during infection. An analysis of these genes identified a collection of candidate pathogenicity factors and unraveled the pathogen's strategy for infecting its host.

No MeSH data available.


Related in: MedlinePlus