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Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses.

Mathioni SM, Beló A, Rizzo CJ, Dean RA, Donofrio NM - BMC Genomics (2011)

Bottom Line: We identified 4,973 genes that were differentially expressed in at least one of the in planta and in vitro stress conditions when compared to fungal mycelia grown in complete medium, which was used as reference.Functional categorization of the 55 induced genes revealed that most were either related to carbon metabolism, membrane proteins, or were involved in oxidoreduction reactions.The 129 repressed genes showed putative roles in vesicle trafficking, signal transduction, nitrogen metabolism, or molecular transport.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.

ABSTRACT

Background: Rice blast is the most threatening disease to cultivated rice. Magnaporthe oryzae, its causal agent, is likely to encounter environmental challenges during invasive growth in its host plants that require shifts in gene expression to establish a compatible interaction. Here, we tested the hypothesis that gene expression patterns during in planta invasive growth are similar to in vitro stress conditions, such as nutrient limitation, temperature up shift and oxidative stress, and determined which condition most closely mimicked that of in planta invasive growth. Gene expression data were collected from these in vitro experiments and compared to fungal gene expression during the invasive growth phase at 72 hours post-inoculation in compatible interactions on two grass hosts, rice and barley.

Results: We identified 4,973 genes that were differentially expressed in at least one of the in planta and in vitro stress conditions when compared to fungal mycelia grown in complete medium, which was used as reference. From those genes, 1,909 showed similar expression patterns between at least one of the in vitro stresses and rice and/or barley. Hierarchical clustering of these 1,909 genes showed three major clusters in which in planta conditions closely grouped with the nutrient starvation conditions. Out of these 1,909 genes, 55 genes and 129 genes were induced and repressed in all treatments, respectively. Functional categorization of the 55 induced genes revealed that most were either related to carbon metabolism, membrane proteins, or were involved in oxidoreduction reactions. The 129 repressed genes showed putative roles in vesicle trafficking, signal transduction, nitrogen metabolism, or molecular transport.

Conclusions: These findings suggest that M. oryzae is likely primarily coping with nutrient-limited environments at the invasive growth stage 72 hours post-inoculation, and not with oxidative or temperature stresses.

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Hierarchical clustering of M. oryzae treatments. (A) Hierarchical clustering of gene expression in each of seven M. oryzae treatments based on the transcription profile of the 1,909 genes differentially expressed. The distance method used to cluster the treatments was 1 - correlation (y-axis). The red and green values in each node of the dendrogram represent the percentage confidence of the cluster estimated by 10,000 bootstrap re-samplings. (B) Heatmap of the set of 1,909 genes from panel (A), where red and green represent induced and repressed gene expression versus the reference sample, respectively. (C) Heatmap of the "meta-dataset" of 4,793 genes (red and green colors as above). Acronyms stand for fungal gene expression during the following conditions: R = rice at 72 hpi; B = barley at 72 hpi; PQ = paraquat (oxidative); TS = temperature up-shift (heat shock); MM = minimal media; MM-C = carbon limitation; MM-N = nitrogen limitation.
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Figure 1: Hierarchical clustering of M. oryzae treatments. (A) Hierarchical clustering of gene expression in each of seven M. oryzae treatments based on the transcription profile of the 1,909 genes differentially expressed. The distance method used to cluster the treatments was 1 - correlation (y-axis). The red and green values in each node of the dendrogram represent the percentage confidence of the cluster estimated by 10,000 bootstrap re-samplings. (B) Heatmap of the set of 1,909 genes from panel (A), where red and green represent induced and repressed gene expression versus the reference sample, respectively. (C) Heatmap of the "meta-dataset" of 4,793 genes (red and green colors as above). Acronyms stand for fungal gene expression during the following conditions: R = rice at 72 hpi; B = barley at 72 hpi; PQ = paraquat (oxidative); TS = temperature up-shift (heat shock); MM = minimal media; MM-C = carbon limitation; MM-N = nitrogen limitation.

Mentions: In order to identify fungal gene expression patterns from the in vitro treatments that were most similar to gene expression in planta, we further sorted the 4,973 differentially expressed gene set. Genes were grouped together if they had significant expression in rice and/or barley and at least one other in vitro condition, which resulted in 1,909 genes. Hierarchical clustering of this subset of genes revealed three major clusters (Figure 1A). The first grouped the in vitro treatments PQ, TS and MM, the second grouped the in planta treatments rice and barley, and the third grouped the nutrient-limited treatments MM-C and MM-N. Overall, we found that fungal gene expression in rice and barley more closely grouped with MM-C and MM-N, than the other in vitro stress conditions. Heat maps are shown for the smaller 1,909-gene dataset, as well as the "meta-dataset" of 4,973 genes (Figures 1B and 1C, respectively). Clustering of the meta-dataset revealed that fungal gene expression in planta was more disparate from any of the in vitro conditions, but was still closer to the nutrient-limited conditions, as indicated by the length of the tree branch.


Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses.

Mathioni SM, Beló A, Rizzo CJ, Dean RA, Donofrio NM - BMC Genomics (2011)

Hierarchical clustering of M. oryzae treatments. (A) Hierarchical clustering of gene expression in each of seven M. oryzae treatments based on the transcription profile of the 1,909 genes differentially expressed. The distance method used to cluster the treatments was 1 - correlation (y-axis). The red and green values in each node of the dendrogram represent the percentage confidence of the cluster estimated by 10,000 bootstrap re-samplings. (B) Heatmap of the set of 1,909 genes from panel (A), where red and green represent induced and repressed gene expression versus the reference sample, respectively. (C) Heatmap of the "meta-dataset" of 4,793 genes (red and green colors as above). Acronyms stand for fungal gene expression during the following conditions: R = rice at 72 hpi; B = barley at 72 hpi; PQ = paraquat (oxidative); TS = temperature up-shift (heat shock); MM = minimal media; MM-C = carbon limitation; MM-N = nitrogen limitation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3037901&req=5

Figure 1: Hierarchical clustering of M. oryzae treatments. (A) Hierarchical clustering of gene expression in each of seven M. oryzae treatments based on the transcription profile of the 1,909 genes differentially expressed. The distance method used to cluster the treatments was 1 - correlation (y-axis). The red and green values in each node of the dendrogram represent the percentage confidence of the cluster estimated by 10,000 bootstrap re-samplings. (B) Heatmap of the set of 1,909 genes from panel (A), where red and green represent induced and repressed gene expression versus the reference sample, respectively. (C) Heatmap of the "meta-dataset" of 4,793 genes (red and green colors as above). Acronyms stand for fungal gene expression during the following conditions: R = rice at 72 hpi; B = barley at 72 hpi; PQ = paraquat (oxidative); TS = temperature up-shift (heat shock); MM = minimal media; MM-C = carbon limitation; MM-N = nitrogen limitation.
Mentions: In order to identify fungal gene expression patterns from the in vitro treatments that were most similar to gene expression in planta, we further sorted the 4,973 differentially expressed gene set. Genes were grouped together if they had significant expression in rice and/or barley and at least one other in vitro condition, which resulted in 1,909 genes. Hierarchical clustering of this subset of genes revealed three major clusters (Figure 1A). The first grouped the in vitro treatments PQ, TS and MM, the second grouped the in planta treatments rice and barley, and the third grouped the nutrient-limited treatments MM-C and MM-N. Overall, we found that fungal gene expression in rice and barley more closely grouped with MM-C and MM-N, than the other in vitro stress conditions. Heat maps are shown for the smaller 1,909-gene dataset, as well as the "meta-dataset" of 4,973 genes (Figures 1B and 1C, respectively). Clustering of the meta-dataset revealed that fungal gene expression in planta was more disparate from any of the in vitro conditions, but was still closer to the nutrient-limited conditions, as indicated by the length of the tree branch.

Bottom Line: We identified 4,973 genes that were differentially expressed in at least one of the in planta and in vitro stress conditions when compared to fungal mycelia grown in complete medium, which was used as reference.Functional categorization of the 55 induced genes revealed that most were either related to carbon metabolism, membrane proteins, or were involved in oxidoreduction reactions.The 129 repressed genes showed putative roles in vesicle trafficking, signal transduction, nitrogen metabolism, or molecular transport.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA.

ABSTRACT

Background: Rice blast is the most threatening disease to cultivated rice. Magnaporthe oryzae, its causal agent, is likely to encounter environmental challenges during invasive growth in its host plants that require shifts in gene expression to establish a compatible interaction. Here, we tested the hypothesis that gene expression patterns during in planta invasive growth are similar to in vitro stress conditions, such as nutrient limitation, temperature up shift and oxidative stress, and determined which condition most closely mimicked that of in planta invasive growth. Gene expression data were collected from these in vitro experiments and compared to fungal gene expression during the invasive growth phase at 72 hours post-inoculation in compatible interactions on two grass hosts, rice and barley.

Results: We identified 4,973 genes that were differentially expressed in at least one of the in planta and in vitro stress conditions when compared to fungal mycelia grown in complete medium, which was used as reference. From those genes, 1,909 showed similar expression patterns between at least one of the in vitro stresses and rice and/or barley. Hierarchical clustering of these 1,909 genes showed three major clusters in which in planta conditions closely grouped with the nutrient starvation conditions. Out of these 1,909 genes, 55 genes and 129 genes were induced and repressed in all treatments, respectively. Functional categorization of the 55 induced genes revealed that most were either related to carbon metabolism, membrane proteins, or were involved in oxidoreduction reactions. The 129 repressed genes showed putative roles in vesicle trafficking, signal transduction, nitrogen metabolism, or molecular transport.

Conclusions: These findings suggest that M. oryzae is likely primarily coping with nutrient-limited environments at the invasive growth stage 72 hours post-inoculation, and not with oxidative or temperature stresses.

Show MeSH
Related in: MedlinePlus