title: Sequencing and de novo draft assemblies of a fathead minnow (Pimephales promelas) reference genome.
abstract: The present study was undertaken to provide the foundation for development of genome-scale resources for the fathead minnow (Pimephales promelas), an important model organism widely used in both aquatic toxicology research and regulatory testing. The authors report on the first sequencing and 2 draft assemblies for the reference genome of this species. Approximately 120× sequence coverage was achieved via Illumina sequencing of a combination of paired-end, mate-pair, and fosmid libraries. Evaluation and comparison of these assemblies demonstrate that they are of sufficient quality to be useful for genome-enabled studies, with 418 of 458 (91%) conserved eukaryotic genes mapping to at least 1 of the assemblies. In addition to its immediate utility, the present work provides a strong foundation on which to build further refinements of a reference genome for the fathead minnow.
authors.affiliation: Haskell Global Centers for Health and Environmental Sciences, E.I. du Pont de Nemours, Newark, Delaware, USA.
authors.forename: Frank R
authors.initials: FR
authors.lastname: Burns
authors.affiliation: Haskell Global Centers for Health and Environmental Sciences, E.I. du Pont de Nemours, Newark, Delaware, USA.
authors.forename: Amarin L
authors.initials: AL
authors.lastname: Cogburn
authors.affiliation: Mid-Continent Ecology Division, US Environmental Protection Agency, Duluth, Minnesota, USA.
authors.forename: Gerald T
authors.initials: GT
authors.lastname: Ankley
authors.affiliation: Mid-Continent Ecology Division, US Environmental Protection Agency, Duluth, Minnesota, USA.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Villeneuve
authors.affiliation: US Environmental Protection Agency, Cincinnati, Ohio, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Waits
authors.affiliation: High-Performance Biological Computing, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Yun-Juan
authors.initials: YJ
authors.lastname: Chang
authors.affiliation: Agricultural Biotechnology, E.I. du Pont de Nemours, Wilmington, Delaware, USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Llaca
authors.affiliation: Agricultural Biotechnology, E.I. du Pont de Nemours, Wilmington, Delaware, USA.
authors.forename: Stephane D
authors.initials: SD
authors.lastname: Deschamps
authors.affiliation: Central Research and Development Biotechnology, E.I. du Pont de Nemours, Wilmington, Delaware, USA.
authors.forename: Raymond E
authors.initials: RE
authors.lastname: Jackson
authors.affiliation: Haskell Global Centers for Health and Environmental Sciences, E.I. du Pont de Nemours, Newark, Delaware, USA.
authors.forename: Robert Alan
authors.initials: RA
authors.lastname: Hoke
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D003530:Cyprinidae / Q000235:genetics*; D004247:DNA / Q000235:genetics; D005796:Genes; D016678:Genome / Q000235:genetics*; D015698:Genomic Library; D005810:Multigene Family / Q000235:genetics; D012016:Reference Values; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: Ecotoxicogenomics; Fathead minnow; Genetics; Genome