title: Transcriptome discovery in non-model wild fish species for the development of quantitative transcript abundance assays.
abstract: 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 (Micropterus dolomieu), white sucker (Catostomus commersonii) and brown bullhead (Ameiurus nebulosus). 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 (Micropterus salmoides). 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.
authors: West Virginia University, School of Natural Resources, 322 Percival Hall, Morgantown, WV 26506, USA; US Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430, USA. Electronic address: cmhahn@usgs.gov.
authors: Cassidy M
authors: CM
authors: Hahn
authors: US Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430, USA.
authors: Luke R
authors: LR
authors: Iwanowicz
authors: US Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430, USA.
authors: Robert S
authors: RS
authors: Cornman
authors: West Virginia University, School of Natural Resources, 322 Percival Hall, Morgantown, WV 26506, USA.
authors: Patricia M
authors: PM
authors: Mazik
authors: US Geological Survey, Leetown Science Center, 11649 Leetown Road, Kearneysville, WV 25430, USA.
authors: Vicki S
authors: VS
authors: Blazer
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D005399:Fishes / Q000145:classification / Q000235:genetics* / Q000254:growth & development; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D045483:Rivers; D012621:Seasons; D059467:Transcriptome / Q000235:genetics*