The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. Despite, the wealth of toxicological data for this organism, until recently genome scale information was lacking for the species, which limited the utility of the species for pathway-based toxicity testing and research. As part of a EPA Pathfinder Innovation Project, next generation sequencing was applied to generate a draft genome assembly, which was published in 2016. However, application of those genome-scale sequencing resources was still limited by the lack of available gene annotations for fathead minnow. Here we report on development of a first generation genome annotation for fathead minnow and the dissemination of that information through a web-based browser that makes it easy to search for genes of interest, extract the corresponding sequence, identify intron and exon boundaries and regulatory regions, and align the computationally predicted genes with other supporting evidence. This work greatly enhances the utility of the genome assemblies that were developed and makes it accessible to the ecotoxicology community world-wide, opening up a wide array of new research opportunities with the species. The URL associated with this data set provides access to the genome browser that was developed as well as the current gene models and evidence tracks.
This dataset is associated with the following publication:
Saari, T., A. Schroeder, G. Ankley, and D. Villeneuve. First generation annotations for the fathead minnow (Pimephales promelas) genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, USA, 36(12): 3436-3442, (2017).