Assembly and Annotation of the Etheostoma tallapoosae Genome

The family Percidae contains over 200 species, most of which are within the subfamily Etheostomatinae. This subfamily (the darters) represents a species rich radiation of freshwater fishes in North America. Evolutionary relationships between the various darter species have been deduced from morphological, mitochondrial DNA sequence and limited nuclear DNA sequence comparisons. However, a thorough understanding of the evolution of the darter species will require comparisons at the whole genome level. As a first step, the genome of the Tallapoosa darter (Etheostoma tallapoosae) has been sequenced utilizing two Illumina MiSeq 250-PE runs generating 52 million reads. This provided an average 12 fold coverage of the estimated 1 billion nucleotide genome. The sequences were assembled with Minia into contigs and these were assembled into scaffolds with SSPACE. A BLAST server has been set up to allow for the identification of Tallapoosa darter scaffolds homologous to sequences of interest. The scaffolds were also imported into an instance of WebApollo along with gene evidence tracks generated by fgenesh. A set of scripts were developed to facilitate the formatting and import of these tracks and scaffold sequences into WebApollo that will make it simple for labs to set up WebApollo instances for their own genome data without extensive computer system experience. A web site has been developed that gives access to both the BLAST and WebApollo servers to the public to spur interest in darter genomics and to enable annotation of the Tallapoosa darter genome by a community of darter researchers.