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Background  Insects use pheromones, chemical signals that underlie all animal behaviors, for communication and for attracting mates. Synthetic pheromones are widely used in pest control strategies because they are environmentally safe. The production of insect pheromones in transgenic plants, which could be more economical and effective in producing isomerically pure compounds, has recently been successfully demonstrated. This research requires information regarding the pheromone  biosynthetic pathways  and the characterization of pheromone biosynthetic enzymes (PBEs). We used Illumina sequencing to characterize the pheromone gland (PG) transcriptome of the Pyralid moth,  Ephestia cautella , a destructive storage pest, to reveal putative candidate genes involved in pheromone biosynthesis, release, transport and degradation.    Results  We isolated the  E. cautella  pheromone compound as ( Z,E )-9,12-tetradecadienyl acetate, and the major pheromone precursors 16:acyl, 14:acyl,  E 14-16:acyl,  E 12-14:acyl and  Z 9, E 12-14:acyl. Based on the abundance of precursors, two possible pheromone  biosynthetic pathways  are proposed. Both pathways initiate from C16:acyl-CoA, with one involving ∆14 and ∆9 desaturation to generate  Z 9, E 12-14:acyl, and the other involving the chain shortening of C16:acyl-CoA to C14:acyl-CoA, followed by ∆12 and ∆9 desaturation to generate  Z 9, E 12-14:acyl-CoA. Then, a final reduction and acetylation generates  Z 9, E 12-14:OAc. Illumina sequencing yielded 83,792 transcripts, and we obtained a PG transcriptome of ~49.5 Mb. A total of 191 PBE transcripts, which included pheromone biosynthesis activating neuropeptides, fatty acid transport proteins, acetyl-CoA carboxylases, fatty acid synthases, desaturases, β-oxidation enzymes, fatty acyl-CoA reductases (FARs) and fatty acetyltransferases (FATs), were selected from the dataset. A comparison of the  E. cautella  transcriptome data with three other Lepidoptera PG datasets revealed that 45 % of the sequences were shared. Phylogenetic trees were constructed for desaturases, FARs and FATs, and transcripts that clustered with the ∆14, ∆12 and ∆9 desaturases, PG-specific FARs and potential candidate FATs, respectively, were identified. Transcripts encoding putative pheromone degrading enzymes, and candidate pheromone carrier and receptor proteins expressed in the  E. cautella  PG, were also identified.    Conclusions  Our study provides important background information on the enzymes involved in pheromone biosynthesis. This information will be useful for the  in vitro  production of  E. cautella  sex pheromones and may provide potential targets for disrupting the pheromone-based communication system of  E. cautella  to prevent infestations.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1710-2) contains supplementary material, which is available to authorized users.

Genes involved in sex pheromone biosynthesis of Ephestia cautella, an important food storage pest, are determined by transcriptome sequencing