The Florida Pompano (Trachinotus carolinus) is a warm water, marine teleost fish species belonging to the family Carangidae. It can be found in the Atlantic Ocean off the coast of Massachusetts, U.S. down to Brazil, but is most commonly found off the east and west coasts of Florida, U.S. In Florida, it is regarded as a prized catch to sport and commercial fishers alike due to its great taste and texture. Demand exceeds supply resulting in a high value at market. Interest in the commercial aquaculture of this species began in the 1960s, but there were difficulties in preventing high juvenile mortality. With recent advances in nutrition and recirculating systems, there is renewed interest in bringing this species into commercial aquaculture. Research has shown the Florida Pompano to be a good candidate for large-scale aquaculture due to its ability to be sustained on a pelleted diet, be reared at low salinities, and breed in captivity. However, an economical and technological challenge in expanding domestic production is the supply of high quality seedstock (juveniles for grow-out) optimized for the production environment. It is possible to identify traits of interest to select for in a genetics-based selective breeding program to create a high quality seedstock with molecular and computational tools.
Using a representative draft genome that we have previously assembled and annotated, we are conducting a comparative genetic analysis of the Florida Pompano genome to two closely related Trachinotus species, Permit (T. falcatus) and Palometa (T. goodei). These two species were chosen as they inhabit a similar geographic range to the Florida Pompano yet drastically differ in size compared to the Florida Pompano. When fully grown, the average Florida Pompano reaches 60 cm and 3.6 kg. However, Permit grow twice in length (122cm) and ten times in weight (36 kg), while Palometa only grow to 51 cm and 0.5 kg. By gaining access to genetic information within the Permit and Palometa genomes, we will be able to determine genes and variable DNA regions that are potentially associated with the different rates of growth.
The Permit and Palometa genomes were sequenced on the Illumina HiSeq 2500 System. These two genomes were assembled using our Florida Pompano draft genome as a reference. A bioinformatics workflow was developed to annotate and compare the three genomes. Reads per gene were analyzed focusing on known genes linked to growth in finfish. The overall research goal of this study is to identify growth-related genes that can ultimately inform a genetics-based selective breeding program for enhanced seedstock, and thereby increase production and profits for farmers.