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Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome
Burns, F., L. Cogburn, G. Ankley, Dan Villeneuve, E. Waits, Y. Chang, V. Llaca, S. Deschamps, R. Jackson, AND R. Hoke. Sequencing and De novo Draft Assemblies of the Fathead Minnow (Pimphales promelas)Reference Genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, 35(1):212-217, (2016).
The application of post-genomic tools and analyses has great potential to enhance systems-level assessments of risks to human health and the environment based on inference from toxicological model organisms. The fathead minnow (Pimephales promelas) is the most widely used small fish model for regulatory ecotoxicology in North America. However, the genome-scale resources and associated tools required to fully exploit this species for modern pathway-based toxicological research, functional genomics, and identification genetic factors that may influence toxicological outcomes were lacking. This research, supported in part through a US EPA Pathfinder Innovation Project Award, represents a major leap forward in developing genome-scales resources for this critical ecotoxicological model. It provided approximately 90% coverage of the fathead minnow genome sequence based on two de novo assemblies of cost effective short read Illumina sequence libraries. Given the widespread use of this model within the ecotoxicological research community, the availability of these genomic resources would be expected to have a broad, transformative impact on the field of aquatic toxicology both within and outside the agency. Following genome annotation and construction of a genetic map (underway), this research will place the fathead minnow on par with zebrafish as a versatile and powerful fish model for both ecological and human health research. Furthermore, the approach successfully employed in this research provides a road map for conducting similar, cost-effective, genome projects for other species important to EPA and the broader environmental research community.
This study was undertaken to develop genome-scale resources for the fathead minnow (Pimphales promelas) an important model organism widely used in both aquatic ecotoxicology research and in regulatory toxicity testing. We report on the first sequencing and two draft assemblies for the genome of this species. Approximately 100X sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrates they are of sufficient quality to be useful for genome-enabled studies. Among a set of 458 core eukaryotic genes, 418 could be mapped to at least one of the assemblies, suggesting 91% completeness of the genome sequence. In addition to its immediate utility, this work provides a strong foundation upon which to build further refinements of the fathead minnow genome.
Record Details:Record Type: DOCUMENT (JOURNAL/PEER REVIEWED JOURNAL)
Organization:U.S. ENVIRONMENTAL PROTECTION AGENCY
OFFICE OF RESEARCH AND DEVELOPMENT
NATIONAL HEALTH AND ENVIRONMENTAL EFFECTS RESEARCH LABORATORY
MID-CONTINENT ECOLOGY DIVISION