Deep sequencing-based transcriptome profiling analysis of Chlamys farreri exposed to benzo[a]pyrene

• Dynamic transcriptome responses to BaP exposure of Chlamys farreri were examined.
• Genes involved in detoxification, oxidative stress and innate immunity were altered.
• GO and KEGG enrichment analysis of differentially expressed genes were conducted.
• Ten detoxification-related genes were selected for qRT-PCR analysis for validation.

Whole-genome transcriptome measurements are pivotal for characterizing molecular mechanisms of chemicals and predicting toxic classes, such as genotoxicity and carcinogenicity, from in vitro and in vivo assays. We analyzed the dynamic defense transcriptome responsive to Chlamys farreri upon exposure to benzo[a]pyrene (BaP) using a digital gene expression (DGE) approach. Following exposure, 251 and 177 genes were up-regulated, and 142 and 300 genes were down-regulated at 3 days post-exposure and 10 days post-exposure, respectively. The differentially expressed genes were related to toxicological response, oxidative stress and the metabolism of proteins and fats. Of these genes, most genes up-regulated at the early stage of exposure tended to be constantly down-regulated at the later stage whereas the landscape of the up- or down-regulated genes differed significantly at the two time points investigated. Functional enrichment analyses show that RNA-seq yields more insight into the biological mechanisms related to the toxic effects caused by BaP, i.e., two to fivefold more affected pathways and biological processes. Besides, we observed a change in the expression of ten genes which are important and differentially-expressed detoxification-related genes, and this was subsequently confirmed via quantitative real-time PCR. Our results provide evidence that RNA-seq is a powerful tool for toxicology and is capable of generating novel and valuable information at the transcriptome level for characterizing deleterious effects caused by BaP.