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A fathead minnow genome browser provides simplified access to annotated genomic sequences
Citation:
Cavallin, J., T. Saari, A. Schroeder, G. Ankley, AND D. Villeneuve. A fathead minnow genome browser provides simplified access to annotated genomic sequences. SETAC North America, Toronto, ON, CANADA, November 03 - 07, 2019.
Impact/Purpose:
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. To address this, a first generation genome annotation for fathead minnow was developed and made available to the aquatic toxicology research community via 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.
Description:
The fathead minnow (Pimephales promelas) is a laboratory model organism widely used in regulatory toxicity testing and ecotoxicology research. To address this, a first generation genome annotation for fathead minnow was developed and made available to the aquatic toxicology research community via 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 presentation will provide an overview of the fathead minnow genome browser capabilities in order to facilitate broader use within by SETAC members.High-throughput technologies are being utilized with increased frequency in all aspects of biological research, including environmental toxicology. As these types of experiments produce large volumes of data, a new need arises for the creation of data portals which can allow researchers to easily access this information. One such data portal a genome browser containing gene annotation data related to the fathead minnow (Pimephales promelas) is hosted at genome.setac.org. This tool greatly simplifies exploration of the characterized regions of the fathead minnow draft genome and allows simple retrieval of sequence information. The genome browser contains fathead minnow experimental data as it relates to the draft genome, such as alignments of baseline RNAseq, Expressed Sequence Tags (ESTs), and proteins, to the genome assembly. In addition, it contains Ab initio gene predictions, as well as alignments of coding sequence from the closely related and well-characterized zebrafish (Danio rerio). Taken together, these data give valuable insight into the coding regions of the fathead minnow, which is useful in tasks varying from primer design for targeted gene expression analysis to whole-transcriptome analysis. Although each class of information may be useful on its own, collectively, the information assembled in the genome browser allows for a much more comprehensive characterization of the coding portion of the genome, highlighting the importance of a centralized resource and data portal for the fathead minnow genome. Over time, it is expected that a number of additional high-throughput sequencing experiments will provide greater coverage and more thorough characterization of the fathead minnow genome. We are hopeful that this genome browser will serve as a SETAC-driven, collaborative genome research and development project that will benefit the ecotoxicology and ecological risk assessment communities.