The de novo Draft Genome Assembly of Yellowtail, Seriola lalandi

Seriola species (S. dumerili, S. lalandi, S. rivoliana, S. quinqueradiata), collectively known as amberjacks, are fish of particular interest to the growing aquaculture industry due to their high value, forming a billion dollar plus component of the sashimi industry. Of these species, the native California Seriola lalandi, is considered a prime candidate for aquaculture development in southern California. We are developing genetic resources for S. lalandi to help improve aquaculture techniques. In a collaborative effort between the SWFSC and the Genome Informatics Facility at Iowa State University, we have created a de novo draft assembly of the genome for Seriola lalandi. Roughly, 1.2 billion raw reads was obtained from Illumina HiSeq 2500, resulting in an estimated 160X coverage of the 685Mb genome.  A comparison of the assemblies from ALLPATHS-LG (v1.1) and MaSuRCA revealed that MaSuRCA resulted in a better assembly. CEGMA analysis indicated that the MaSurCA assembly contained 425/458 (93%) of the Core Eukaryotic genes. Genes were annotated using Maker2. A web portal (Genome Browser) to directly view the genome, gene annotations, gene models, and markers was also created to provide a publically available resource.  Using these genomic resources, advances can be made in broodstock selection through identification of genes underlying complex and/or economically important traits, characterization of variation (both beneficial and detrimental), and marker-assisted selection for this and other Seriola species.