You are here:
Bringing the fathead minnow (Pimephales promelas) into the genomic era
Citation:
Saari, T., Dan Villeneuve, G. Ankley, F. Burns, A. Cogburn, S. Deschamps, R. Jackson, R. Hoke, AND A. Schroeder. Bringing the fathead minnow (Pimephales promelas) into the genomic era. setac north america, Orlando, FL, November 06 - 10, 2016.
Impact/Purpose:
not applicable
Description:
The fathead minnow (Pimephales promelas) is a well-established ecotoxicological model organism that has been widely used for regulatory ecotoxicity testing and research for over a half century. Throughout this time, a lot of knowledge has been gained about the fathead minnow’s biological responses to various xenobiotics. However, despite its importance as a model organism, the fathead minnow still has few publicly available gene sequences. Recently, Burns et al. (2015; Environ. Toxicol. Chem. 35:212) described the sequencing and de-novo assembly of the fathead minnow genome. Two draft genome assemblies are now publicly available on the GenBank database. However, on their own the draft assemblies remain of limited use to researchers who are primarily interested in the functional units of the genome, i.e. the genes. In the present study, an annotation pipeline, consisting of gene prediction, evidence alignment, and data synthesis, was applied to the fathead minnow SOAPdenovo assembly. Ab initio gene prediction was performed using AUGUSTUS, which provided a starting point of 43,345 gene predictions. Fathead minnow Expressed Sequence Tags (ESTs) and zebrafish protein-coding sequences (CDSs) were then aligned to the assembly using the corresponding spliced alignment methods of the program Exonerate. Of the over 240,000 EST alignments, 73% were successfully aligned with 90% or greater sequence identity and query coverage. Similarly, 39% of nearly 45,000 zebrafish coding sequences were successfully aligned with 70% or greater sequence identity and 50% or greater query coverage. The alignments and gene predictions were then passed into the program MAKER, which combined the weighted evidence from various sources into individual gene structures. Together, these data will provide a valuable annotated genome resource to the community and lay a foundation for future studies which make use of and build upon fathead minnow molecular sequence information.