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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.

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