We revisited the Roche 454 pyrosequencing data of transcripts from the gills and digestive glands of C. gasar, which had been exposed to three prevalent environmental contaminants: diesel fuel water-accommodated fraction (WAF), phenanthrene (PHE), and domestic sewage (SWG). For each pollutant, a corresponding control group was also examined. Using updated assemblers, we adhered to the pipeline proposed by the National Center for Genome Analysis Support (NCGAS) to generate a combined de novo transcriptome (CDTA).