Luke R. Iwanowicz Robert S. Cornman Patricia M. Mazik Vicki S. Blazer Cassidy M. Hahn 2016 <p><span>Environmental studies increasingly identify the presence of both contaminants of emerging concern (CECs) and legacy contaminants in aquatic environments; however, the biological effects of these compounds on resident fishes remain largely unknown. High throughput methodologies were employed to establish partial transcriptomes for three wild-caught, non-model fish species; smallmouth bass (</span><i>Micropterus dolomieu</i><span>), white sucker (</span><i>Catostomus commersonii</i><span>) and brown bullhead (</span><i>Ameiurus nebulosus</i><span>). Sequences from these transcriptome databases were utilized in the development of a custom nCounter CodeSet that allowed for direct multiplexed measurement of 50 transcript abundance endpoints in liver tissue. Sequence information was also utilized in the development of quantitative real-time PCR (qPCR) primers. Cross-species hybridization allowed the smallmouth bass nCounter CodeSet to be used for quantitative transcript abundance analysis of an additional non-model species, largemouth bass (</span><i>Micropterus salmoides</i><span>). We validated the nCounter analysis data system with qPCR for a subset of genes and confirmed concordant results. Changes in transcript abundance biomarkers between sexes and seasons were evaluated to provide baseline data on transcript modulation for each species of interest.</span></p> application/pdf 10.1016/j.cbd.2016.07.001 en Elsevier Transcriptome discovery in non-model wild fish species for the development of quantitative transcript abundance assays article