Sparus aurata isolate:wild Genome sequencing
Sparus aurata is an economically important marine aquaculture fish and a valuable model organism. To date, numerous omics and genetic studies have been conducted on this species. Researchers have identified abundant species-specific gene duplications, transposable elements and expanded gene families in its genome, and also found remarkable genetic differentiation of the vgll3 gene between wild and cultured populations. Nevertheless, all these studies were based on draft genomes assembled using second-generation sequencing. These draft assemblies suffer from poor quality and incomplete annotation of key chromosomal structures, which greatly limits further fundamental research and industrial application. Here, the first near telomere-to-telomere chromosome-scale genome assembly of S. aurata was constructed by using PacBio HiFi, Nanopore ONT ultra-long, and Hi-C sequencing. To enhance assembly quality, three independent assemblies were generated using NextDenovo, Hifiasm, and Verkko. Through comprehensive comparison, the NextDenovo assembly, which exhibited superior contiguity and completeness with all chromosomes completely gap-free and fully structured with telomeres and centromeres, was selected as the optimal one for subsequent analyses. This complete genome assembly is about 860.0 Mb with a high contig N50 level of 36.2 Mb. We anchored this assembly into 24 chromosomes with entire 48 telomeres and 24 centromeres. About 305.6 Mb of repetitive sequences and 32,541 protein-coding genes were estimated in this genome. The BUSCO analysis showed the completeness ratio of genome and protein sequences are 99.9% and 99.8%. The near T2T assembly of S. aurata supports functional gene and economic trait studies, improves breeding efficiency and germplasm quality, and promotes basic research on fish evolution and environmental adaptation.