Utilization of Genomic Tools to Enhance the Commercial Aquaculture of the Florida Pompano Trachinotus carolinus

The goal of this project is to gain access to valuable genetic information that will be utilized to create a genetics-based selective breeding program. This selective breeding program will be implemented to produce and maintain a healthy and diverse breeding stock of the Florida Pompano Trachinotus carolinus. The Florida Pompano is a popular food fish found in abundance off Florida's east and west coasts. There has been interest in the aquaculture of this species for decades with minimal success. With recent improvements in aquaculture systems and nutrition, now is the time to bring this fish to commercialization. The main research objectives of this study are to create a bioinformatics workflow to generate a draft whole-genome of the Florida Pompano, identify variation sites within this genome, and run a comparative analysis with two closely related Trachinotus species, Permit T. falcatus and Palometa T. goodei. These two species were chosen because they are found in the same environment as the Florida Pompano but grow to substantially different sizes. To sequence and assemble the whole genome of the Florida Pompano, a hybrid method was applied using long and short-read sequencing technologies. The draft genome was found to be 733.5 Mb in length with a total of 26,891 protein-coding genes. Sites of variation within this assembled genome were identified using a 2b-RAD sequencing method on 62 individuals collected off Florida’s east and gulf coasts.