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Background  Despite a number of recent reports of insect resistance to transgenic crops expressing insecticidal toxins from  Bacillus thuringiensis  (Bt), little is known about the mechanism of resistance to these toxins. The purpose of this study is to identify genes associated with the mechanism of Cry1F toxin resistance in European corn borer ( Ostrinia nubilalis  Hübner). For this, we compared the global transcriptomic response of laboratory selected resistant and susceptible  O. nubilalis  strain to Cry1F toxin. We further identified constitutive transcriptional differences between the two strains.    Results  An  O. nubilalis  midgut transcriptome of 36,125 transcripts was assembled  de novo  from 106 million Illumina HiSeq and Roche 454 reads and used as a reference for estimation of differential gene expression analysis. Evaluation of gene expression profiles of midgut tissues from the Cry1F susceptible and resistant strains after toxin exposure identified a suite of genes that responded to the toxin in the susceptible strain ( n  = 1,654), but almost 20-fold fewer in the resistant strain ( n  = 84). A total of 5,455 midgut transcripts showed significant constitutive expression differences between Cry1F susceptible and resistant strains. Transcripts coding for previously identified Cry toxin receptors, cadherin and alkaline phosphatase and proteases were also differentially expressed in the midgut of the susceptible and resistant strains.    Conclusions  Our current study provides a valuable resource for further molecular characterization of Bt resistance and insect response to Cry1F toxin in  O. nubilalis  and other pest species.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1751-6) contains supplementary material, which is available to authorized users.

Transcriptional analysis of susceptible and resistant European corn borer strains and their response to Cry1F protoxin