Serial analysis of gene expression reveals identifiable patterns in transcriptome profiles of Palaemonetes pugio...

Serial analysis of gene expression (SAGE) is a transcriptome-profiling technique that allows accurate gene expression profiles to be generated without any need for prior sequence knowledge, making it ideal for assaying toxicant-specific genetic responses in nonmodel species. We used SAGE to perform a large-scale survey of the Palaemonetes pugio transcriptome under different chemical xenobiotic stresses. Four libraries were constructed from fipronil-exposed, endosulfan-exposed, and cadmium-exposed shrimp, as well as from carrier-control-exposed shrimp. A total of 37,152 tags were sequenced from the four libraries, including 13,754 unique tags. Statistical analysis revealed that 117 tags were differentially expressed significantly in at least one of the three exposures. Cluster analyses of the altered tags showed that fipronil and endosulfan elicit transcriptome profiles that are more similar to each other than either one was to cadmium. Quantitative polymerase chain reaction (QPCR) was performed on a subset of 46 differentially expressed tags, and largely confirmed the SAGE results. The tags were filtered to identify tags for which both SAGE and QPCR agreed in regard to the direction and magnitude of affect, and which were informative about the exposure experienced. A subset of 16 tags was identified that represents a putative biomarker suite that is indicative of exposures to the three toxicants.