Comparative transcriptome analysis between the short-term stress and long-term adaptation of the Ruditapes philippinarum in response to benzo[a]pyrene

In order to monitor the pollution of polycyclic aromatic hydrocarbons (PAHs) in the seawater environment, screening biomarkers capable of monitoring PAHs is the focus of many studies. The transcriptomic profiles of the digestive gland tissue from the R. philippinarum groups after the exposure to BaP (4 μg/L) at four time points (0, 0.5, 6 and 15 days) were investigated to globally screen the key genes and pathways involved in the responses to short-term stress and long-term adaptation of BaP resistance. By comparative transcriptome analysis, 233, 282 and 58 differentially expressed genes (DEGs) were identified at 0.5 day, 6 day and 15 day (vs 0 day). The differential expression genes were related to stress response, detoxification metabolic process and innate immunity. DEGs of each group at different stages were clustered in six profiles based on gene expression pattern. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis were used on all genes to determine the biological functions and processes. We selected Multidrug resistance protein 3 (MRP3), transcriptional regulator ATRX-like isoform X2 (ATRX) as biomarker indicator genes for short-term pollution monitoring and NADH dehydrogenase [ubiquinone] 1 (NQO1), Complement C1q-like protein 4 (C1q), Glutathione-S-transferase theta (GST), E3 ubiquitin-protein ligase (E3) for long-term pollution monitoring based on the different expression patterns and the function in detoxification and antioxidant defense system. Besides, the expression of seven genes was measured through Quantitative real-time PCR (qPCR) according to their gene expression patterns which was confirmed by the DGE analysis. Taken together, adoption of transcriptomic analysis to explore the bivalves' mRNA abundance changes and detoxification metabolic mechanism under the BaP stress at different time points can aid the development of sensitive and informed molecular endpoints for application towards ecotoxicogenomic monitoring of bivalves.