First Generation Annotations for the Fathead Minnow (Pimephales promelas) Genome

Metadata Updated: February 13, 2019

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).

Access & Use Information

Public: This dataset is intended for public access and use. License: See this page for license information.

Downloads & Resources

References

https://dx.doi.org/10.1002/etc.3929

Dates

Metadata Created Date July 31, 2017
Metadata Updated Date February 13, 2019

Metadata Source

Harvested from EPA ScienceHub

Additional Metadata

Resource Type Dataset
Metadata Created Date July 31, 2017
Metadata Updated Date February 13, 2019
Publisher U.S. EPA Office of Research and Development (ORD)
Unique Identifier https://doi.org/10.23719/1369565
Maintainer
Daniel Villeneuve
Maintainer Email
Public Access Level public
Bureau Code 020:00
Schema Version https://project-open-data.cio.gov/v1.1/schema
Harvest Object Id b3ad8f9d-e4bd-4b15-950e-40688c5e14f3
Harvest Source Id cf9b0004-f9fd-420e-bade-a86839e82acf
Harvest Source Title EPA ScienceHub
License https://pasteur.epa.gov/license/sciencehub-license.html
Data Last Modified 2017-07-13
Program Code 020:095
Publisher Hierarchy U.S. Government > U.S. Environmental Protection Agency > U.S. EPA Office of Research and Development (ORD)
Related Documents https://dx.doi.org/10.1002/etc.3929
Source Datajson Identifier True
Source Hash 2d02175133d85ce719fb461cc5a9b08faf06628f
Source Schema Version 1.1

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