Telomere-to-telomere haplotype-resolved genome assembly of a female oyster pompano (Trachinotus anak)

Oyster pompano (Trachinotus anak) is currently the highest-yielding marine aquaculture fish species in China. However, previously available genome assemblies were fragmented and incomplete, hindering advances in genomic research and breeding applications. Here, we generated two haplotype-resolved, telomere-to-telomere (T2T) genome assemblies for a female T. anak using PacBio HiFi, ONT ultra-long, and Hi-C data. The resulting assemblies (haplotype A and B) span 663.78 Mb and 661.09 Mb with contig N50 of 28.62 Mb and 29.02 Mb, respectively. Both haplotypic assemblies were anchored into 24 gap-free chromosomes, each comprising a complete set of 48 telomeres. The quality value (QV) scores were 70.45 and 68.66, and Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness scores were 98.9% and 99.0% for haplotype A and B, respectively. Genome annotation identified 187.94 Mb and 178.63 Mb of repetitive sequences, and predicted 23,118 and 23,119 protein-coding genes in haplotypes A and B, respectively, with 99.79% and 99.78% functionally annotated. These two high-quality T2T assemblies provide invaluable resources for molecular breeding and advancing biological and evolutionary research in T. anak.