Sequencing and de novo draft assemblies of a fathead minnow (Pimephales promelas) reference genome

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 draf...

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Published in:Environmental toxicology and chemistry 2016-01, Vol.35 (1), p.212-217
Main Authors: Burns, Frank R., Cogburn, Amarin L., Ankley, Gerald T., Villeneuve, Daniel L., Waits, Eric, Chang, Yun-Juan, Llaca, Victor, Deschamps, Stephane D., Jackson, Raymond E., Hoke, Robert Alan
Format: Article
Language:English
Subjects:
Animals
Chromosome Mapping
Comparative analysis
Cyprinidae - genetics
DNA - genetics
Ecotoxicogenomics
Eukaryotes
Fathead minnow
Fish
Genes
Genetics
Genome
Genome - genetics
Genomes
Genomic Library
Genomics
Multigene Family - genetics
Pimephales promelas
Reference Values
Sequence Analysis, DNA
Toxicology
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Summary: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. Environ Toxicol Chem 2016;35:212–217. © 2015 SETAC
ISSN:0730-7268
1552-8618
DOI:10.1002/etc.3186