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Comparative transcriptome analysis of Arabidopsis thaliana infested by diamond back moth (Plutella xylostella) larvae reveals signatures of stress response, secondary metabolism, and signalling.

Ehlting J, Chowrira SG, Mattheus N, Aeschliman DS, Arimura G, Bohlmann J - BMC Genomics (2008)

Bottom Line: Among DBM-induced genes associated with plant signal molecules or phytohormones, genes associated with octadecanoid signalling were clearly overrepresented.We identified a substantial number of differentially expressed genes associated with signal transduction in response to DBM feeding, and we compared there expression profiles with those of previously reported transcriptome responses induced by other insect herbivores, specifically Pieris rapae, Frankliniella occidentalis, Bemisia tabaci,Myzus persicae, and Brevicoryne brassicae.Based on a meta-analysis of microarray data we identified groups of transcription factors that are either affected by multiple forms of biotic or abiotic stress including DBM feeding or, alternatively, were responsive to DBM herbivory but not to most other forms of stress.

View Article: PubMed Central - HTML - PubMed

Affiliation: Michael Smith Laboratories, University of British Columbia, 2185 East Mall Vancouver, BC, V6T 1Z4, Canada. je@uvic.ca

ABSTRACT

Background: Plants are exposed to attack from a large variety of herbivores. Feeding insects can induce substantial changes of the host plant transcriptome. Arabidopsis thaliana has been established as a relevant system for the discovery of genes associated with response to herbivory, including genes for specialized (i.e. secondary) metabolism as well as genes involved in plant-insect defence signalling.

Results: Using a 70-mer oligonucleotide microarray covering 26,090 gene-specific elements, we monitored changes of the Arabidopsis leaf transcriptome in response to feeding by diamond back moth (DBM; Plutella xylostella) larvae. Analysis of samples from a time course of one hour to 24 hours following onset of DBM feeding revealed almost three thousand (2,881) array elements (including 2,671 genes with AGI annotations) that were differentially expressed (>2-fold; p[t-test] < 0.05) of which 1,686 also changed more than twofold in expression between at least two time points of the time course with p(ANOVA) < 0.05. While the majority of these transcripts were up-regulated within 8 h upon onset of insect feeding relative to untreated controls, cluster analysis identified several distinct temporal patterns of transcriptome changes. Many of the DBM-induced genes fall into ontology groups annotated as stress response, secondary metabolism and signalling. Among DBM-induced genes associated with plant signal molecules or phytohormones, genes associated with octadecanoid signalling were clearly overrepresented. We identified a substantial number of differentially expressed genes associated with signal transduction in response to DBM feeding, and we compared there expression profiles with those of previously reported transcriptome responses induced by other insect herbivores, specifically Pieris rapae, Frankliniella occidentalis, Bemisia tabaci,Myzus persicae, and Brevicoryne brassicae.

Conclusion: Arabidopsis responds to feeding DBM larvae with a drastic reprogramming of the transcriptome, which has considerable overlap with the response induced by other insect herbivores. Based on a meta-analysis of microarray data we identified groups of transcription factors that are either affected by multiple forms of biotic or abiotic stress including DBM feeding or, alternatively, were responsive to DBM herbivory but not to most other forms of stress.

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Expression profiles based on K-means clustering. Mean log2-expression ratios for genes that are differentially expressed in at least one time point (p[t-test] < 0.05 with more than two-fold change of transcript abundance between treatment and control) and which are also changing more than two-fold over time with p(ANOVA) < 0.05 were used for K-means clustering. Each gene within a given cluster is shown with a grey line and the mean expression profile from all genes in a given cluster is indicated with a single blue line. Cluster designation and the number of genes in each cluster are shown above each panel.
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Figure 2: Expression profiles based on K-means clustering. Mean log2-expression ratios for genes that are differentially expressed in at least one time point (p[t-test] < 0.05 with more than two-fold change of transcript abundance between treatment and control) and which are also changing more than two-fold over time with p(ANOVA) < 0.05 were used for K-means clustering. Each gene within a given cluster is shown with a grey line and the mean expression profile from all genes in a given cluster is indicated with a single blue line. Cluster designation and the number of genes in each cluster are shown above each panel.

Mentions: To estimate the number of genes that were changing in expression between at least two time points we performed an analysis of variance (ANOVA), and found 3,111 genes that changed more than twofold with p(ANOVA) < 0.05 (Table 1). However, of these only 1,686 were also differentially expressed between treatment and control in at least one time point. These 1,686 genes, which met our most stringent definition of differential expression in response to DBM feeding over the 24 hour time course, were placed into nine expression clusters based on their temporal patterns of expression profiles identified by K-means clustering (Figure 2; identification of genes belonging to each cluster is provided in Additional File 1). While 71 genes displayed a rapid transient up-regulation within 1 h upon onset of herbivory (Cluster A), a total of 779 genes peaked at 8 h (cluster B and cluster C). Another group of differentially expressed genes showed up-regulation of transcript abundance mainly at late time-points (cluster D), while 234 genes were up-regulated early during the treatment and maintained high expression levels relative to control plants (cluster E).


Comparative transcriptome analysis of Arabidopsis thaliana infested by diamond back moth (Plutella xylostella) larvae reveals signatures of stress response, secondary metabolism, and signalling.

Ehlting J, Chowrira SG, Mattheus N, Aeschliman DS, Arimura G, Bohlmann J - BMC Genomics (2008)

Expression profiles based on K-means clustering. Mean log2-expression ratios for genes that are differentially expressed in at least one time point (p[t-test] < 0.05 with more than two-fold change of transcript abundance between treatment and control) and which are also changing more than two-fold over time with p(ANOVA) < 0.05 were used for K-means clustering. Each gene within a given cluster is shown with a grey line and the mean expression profile from all genes in a given cluster is indicated with a single blue line. Cluster designation and the number of genes in each cluster are shown above each panel.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2375910&req=5

Figure 2: Expression profiles based on K-means clustering. Mean log2-expression ratios for genes that are differentially expressed in at least one time point (p[t-test] < 0.05 with more than two-fold change of transcript abundance between treatment and control) and which are also changing more than two-fold over time with p(ANOVA) < 0.05 were used for K-means clustering. Each gene within a given cluster is shown with a grey line and the mean expression profile from all genes in a given cluster is indicated with a single blue line. Cluster designation and the number of genes in each cluster are shown above each panel.
Mentions: To estimate the number of genes that were changing in expression between at least two time points we performed an analysis of variance (ANOVA), and found 3,111 genes that changed more than twofold with p(ANOVA) < 0.05 (Table 1). However, of these only 1,686 were also differentially expressed between treatment and control in at least one time point. These 1,686 genes, which met our most stringent definition of differential expression in response to DBM feeding over the 24 hour time course, were placed into nine expression clusters based on their temporal patterns of expression profiles identified by K-means clustering (Figure 2; identification of genes belonging to each cluster is provided in Additional File 1). While 71 genes displayed a rapid transient up-regulation within 1 h upon onset of herbivory (Cluster A), a total of 779 genes peaked at 8 h (cluster B and cluster C). Another group of differentially expressed genes showed up-regulation of transcript abundance mainly at late time-points (cluster D), while 234 genes were up-regulated early during the treatment and maintained high expression levels relative to control plants (cluster E).

Bottom Line: Among DBM-induced genes associated with plant signal molecules or phytohormones, genes associated with octadecanoid signalling were clearly overrepresented.We identified a substantial number of differentially expressed genes associated with signal transduction in response to DBM feeding, and we compared there expression profiles with those of previously reported transcriptome responses induced by other insect herbivores, specifically Pieris rapae, Frankliniella occidentalis, Bemisia tabaci,Myzus persicae, and Brevicoryne brassicae.Based on a meta-analysis of microarray data we identified groups of transcription factors that are either affected by multiple forms of biotic or abiotic stress including DBM feeding or, alternatively, were responsive to DBM herbivory but not to most other forms of stress.

View Article: PubMed Central - HTML - PubMed

Affiliation: Michael Smith Laboratories, University of British Columbia, 2185 East Mall Vancouver, BC, V6T 1Z4, Canada. je@uvic.ca

ABSTRACT

Background: Plants are exposed to attack from a large variety of herbivores. Feeding insects can induce substantial changes of the host plant transcriptome. Arabidopsis thaliana has been established as a relevant system for the discovery of genes associated with response to herbivory, including genes for specialized (i.e. secondary) metabolism as well as genes involved in plant-insect defence signalling.

Results: Using a 70-mer oligonucleotide microarray covering 26,090 gene-specific elements, we monitored changes of the Arabidopsis leaf transcriptome in response to feeding by diamond back moth (DBM; Plutella xylostella) larvae. Analysis of samples from a time course of one hour to 24 hours following onset of DBM feeding revealed almost three thousand (2,881) array elements (including 2,671 genes with AGI annotations) that were differentially expressed (>2-fold; p[t-test] < 0.05) of which 1,686 also changed more than twofold in expression between at least two time points of the time course with p(ANOVA) < 0.05. While the majority of these transcripts were up-regulated within 8 h upon onset of insect feeding relative to untreated controls, cluster analysis identified several distinct temporal patterns of transcriptome changes. Many of the DBM-induced genes fall into ontology groups annotated as stress response, secondary metabolism and signalling. Among DBM-induced genes associated with plant signal molecules or phytohormones, genes associated with octadecanoid signalling were clearly overrepresented. We identified a substantial number of differentially expressed genes associated with signal transduction in response to DBM feeding, and we compared there expression profiles with those of previously reported transcriptome responses induced by other insect herbivores, specifically Pieris rapae, Frankliniella occidentalis, Bemisia tabaci,Myzus persicae, and Brevicoryne brassicae.

Conclusion: Arabidopsis responds to feeding DBM larvae with a drastic reprogramming of the transcriptome, which has considerable overlap with the response induced by other insect herbivores. Based on a meta-analysis of microarray data we identified groups of transcription factors that are either affected by multiple forms of biotic or abiotic stress including DBM feeding or, alternatively, were responsive to DBM herbivory but not to most other forms of stress.

Show MeSH