Transcriptome discovery in non-model wild fish species for the development of quantitative transcript abundance assays
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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.
| Publication type | Article |
|---|---|
| Publication Subtype | Journal Article |
| Title | Transcriptome discovery in non-model wild fish species for the development of quantitative transcript abundance assays |
| Series title | Comparative Biochemistry and Physiology, Part D: Genomics and Proteomics |
| DOI | 10.1016/j.cbd.2016.07.001 |
| Volume | 20 |
| Year Published | 2016 |
| Language | English |
| Publisher | Elsevier |
| Contributing office(s) | Leetown Science Center, Contaminant Biology Program |
| Description | 14 p. |
| First page | 27 |
| Last page | 40 |
| Google Analytic Metrics | Metrics page |