Development and Application of Quantitative Gene Expression Assays in Wild-Caught, Non-Model Fish Species

The Great Lakes Basin is the most significant freshwater resource in North America. It is a central location for diverse anthropogenic enterprises and consequently has been heavily impacted by the release of toxic substances. 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. To address this issue, the U.S. Fish and Wildlife Service Environmental Contaminants Programs initiated a multiagency, collaborative study which included chemical analysis of water and benthic sediment, assessment of caged fathead minnows and assessment of wild fish health using a suite of biological endpoints. In an effort to accurately and efficiently assess the ecological risks of complex chemical mixtures through the integration and synthesis of data from many levels of biological organization, sequence databases for non-model, resident fish species were required. This dissertation contains chapters that describe; 1.) The development of partial transcriptomes for three wild-caught, resident fish species 2.) The utilization of these sequence databases in the development of quantitative gene expression assays 3.) The application of these assays in both laboratory and environmental analyses and 4.) The use of transcriptome sequence databases in the identification of a novel virus