Decades of technological advancements in DNA sequencing platforms and reference sequence databases (e.g., NCBI GenBank) have enabled fish geneticists to derive powerful breeding tools from aquatic genetic resources. Genomic selection (GS) is applied in commercial aquaculture to accelerate domestication, optimize selective breeding, and maximize performance and production. GS can increase genetic gain and mitigate inbreeding depression by capturing the additive genetic variance of single-nucleotide polymorphisms (SNPs) on whole-genome segments (e.g., contigs, scaffolds, or chromosomes), which is important for traits with low heritability. Key phenotypic traits for seedstock including disease resistance, faster growth rates, and efficient sexual maturity, are typically polygenically regulated. However, resolving such complex genome-to-phenome interactions within different aquaculture environments depends on the availability of reference-quality genomes for economically valuable species.
This study is part of a large-scale, multi-year project with the USDA-ARS (Agreement 6034-22000-047-001-A) focused on developing GS tools to support the U.S. warmwater marine finfish aquaculture industry. Our model species for genetic improvement is Florida pompano (Trachinotus carolinus) due to its market value, consumer popularity, and captive-spawning fitness. Here, we report the first high-quality de novo genome assembly for T. carolinus (GenBank Accession: JBEWCC000000000). With near-chromosome-level contiguity (Table 1), our 26-scaffold reference genome constitutes a major update to our 8,107-contig draft assembly (GCA_040938265.1). We took a hybrid assembly approach to rebuild the T. carolinus contigs from our original raw PacBio Sequel 20 kb reads and Illumina HiSeq paired-end 150 bp reads. The contigs were scaffolded using the golden pompano (T. ovatus) genome as a sequence map for ordering and orientation. Scaffolds were then polished using both the long and short reads to correct base errors, misassemblies, and gaps. Our polished assembly was evaluated with QUAST and BUSCO for completeness based on k-mer statistics, sequence variation and coverage statistics, and conserved gene predictions. SNP analysis was also conducted on a mix of wild-caught and captive-bred Florida pompano using our assembly as the reference genome for genotyping. Ultimately, our T. carolinus genome represents the foundation for a GS breeding program that will facilitate producers in enhancing the genetic quality of seedstock and maintaining the introgression of superior performance traits.