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Background  Stripe rust ( Puccinia striiformis  f. sp.  tritici ;  Pst ) and powdery mildew ( Blumeria graminis  f. sp.  tritici ;  Bgt ) are important diseases of wheat ( Triticum aestivum ) worldwide. Similar mechanisms and gene transcripts are assumed to be involved in the host defense response because both pathogens are biotrophic fungi. The main objective of our study was to identify co-regulated mRNAs that show a change in expression pattern after inoculation with  Pst  or  Bgt , and to identify mRNAs specific to the fungal stress response.    Results  The transcriptome of the hexaploid wheat line N9134 inoculated with the Chinese  Pst  race CYR 31 was compared with that of the same line inoculated with  Bgt  race E09 at 1, 2, and 3 days post-inoculation. Infection by  Pst  and  Bgt  affected transcription of 23.8% of all  T. aestivum  genes. Infection by  Bgt  triggered a more robust alteration in gene expression in N9134 compared with the response to  Pst  infection. An array of overlapping gene clusters with distinctive expression patterns provided insight into the regulatory differences in the responses to  Bgt  and  Pst  infection. The differentially expressed genes were grouped into seven enriched Kyoto Encyclopedia of Genes and Genomes pathways in  Bgt -infected leaves and four pathways in  Pst -infected leaves, while only two pathways overlapped. In the plant–pathogen interaction pathway, N9134 activated a higher number of genes and pathways in response to  Bgt  infection than in response to  Pst  invasion. Genomic analysis revealed that the wheat genome shared some microbial genetic fragments, which were specifically induced in response to  Bgt  and  Pst  infection.    Conclusions  Taken together, our findings indicate that the responses of wheat N9134 to infection by  Bgt  and  Pst  shows differences in the pathways and genes activated. The mass sequence data for wheat–fungus interaction generated in this study provides a powerful platform for future functional and molecular research on wheat–fungus interactions.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-898) contains supplementary material, which is available to authorized users.

Large-scale transcriptome comparison reveals distinct gene activations in wheat responding to stripe rust and powdery mildew