AbstractBackgroundChilo suppressalisis a widespread rice pest that poses a major threat to food security in China. This pest can develop resistance to Cry toxins fromBacillus thuringiensis(Bt), threatening the sustainable use of insect-resistant transgenicBtrice. However, the molecular basis for the resistance mechanisms ofC. suppressalisto Cry1C toxin remains unknown. This study aimed to identify genes associated with the mechanism of Cry1C resistance inC. suppressalisby comparing the midgut transcriptomic responses of resistant and susceptibleC. suppressalisstrains to Cry1C toxin and to provide information for insect resistance management.ResultsAC. suppressalismidgut transcriptome of 139,206 unigenes was de novo assembled from 373 million Illumina HiSeq and Roche 454 clean reads. Comparative analysis identified 5328 significantly differentially expressed unigenes (DEGs) betweenC. suppressalisCry1C-resistant and -susceptible strains. DEGs encoding Bt Cry toxin receptors, aminopeptidase-P like protein, the ABC subfamily and alkaline phosphatase were downregulated, suggesting an association withC. suppressalisCry1C resistance. Additionally, Cry1C resistance inC. suppressalismay be related to changes in the transcription levels of enzymes involved in hydrolysis, digestive, catalytic and detoxification processes.ConclusionOur study identified genes potentially involved in Cry1C resistance inC. suppressalisby comparative transcriptome analysis. The assembled and annotated transcriptome data provide valuable genomic resources for further study of the molecular mechanisms ofC. suppressalisresistance to Cry toxins.