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Updated: Mar 31, 2026

Novel Sequence Discovery by Subtractive Genomics
Published on: January 25, 2019
Sequencing and de novo draft assemblies of a fathead minnow (Pimephales promelas) reference genome
Frank R Burns1, Amarin L Cogburn1, Gerald T Ankley2
1Haskell Global Centers for Health and Environmental Sciences, E.I. du Pont de Nemours, Newark, Delaware, USA.
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.
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