EPA Science Inventory

First generation annotations for the fathead minnow (Pimephales promelas) genome

Citation:

Saari, T., A. Schroeder, G. Ankley, AND Dan Villeneuve. First generation annotations for the fathead minnow (Pimephales promelas) genome. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY. Society of Environmental Toxicology and Chemistry, Pensacola, FL, 36(12):3436-3442, (2017).

Description:

Ab initio gene prediction and evidence alignment were used to produce the first annotations for the fathead minnow SOAPdenovo genome assembly. Additionally, a genome browser hosted at genome.setac.org provides simplified access to the annotation data in context with fathead minnow genomic sequence. This work is meant to extend the utility of fathead minnow genome as a resource and enable the continued development of this species as a model organism.

Purpose/Objective:

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. Products of this research have already been applied to support on-going research efforts within the Chemical Safety for Sustainability Program.

URLs/Downloads:

https://doi.org/10.1002/etc.3939   Exit

Record Details:

Record Type: DOCUMENT (JOURNAL/PEER REVIEWED JOURNAL)
Completion Date: 12/01/2017
Record Last Revised: 12/07/2017
Record Created: 12/07/2017
Record Released: 12/07/2017
OMB Category: Other
Record ID: 338610

Organization:

U.S. ENVIRONMENTAL PROTECTION AGENCY

OFFICE OF RESEARCH AND DEVELOPMENT

NATIONAL HEALTH AND ENVIRONMENTAL EFFECTS RESEARCH LABORATORY

MID-CONTINENT ECOLOGY DIVISION