Supporting data of golden pompano genome assembly version 2

Golden pompano (Trachinotus ovatus) is a valuable and promising marine species in deep-sea fish farming. Efforts are needed to decode the genome and perform selection breeding. In this study, a chromosome-level genome assembly was constructed with PacBio long reads, Illumina short reads and Hi-C sequences. The N50 length of the preliminary contigs was 23.14 Mb. The chromosome-level assembly included 24 chromosome-level scaffolds and 52 debrises. The assembly was of high quality, with 97.8% of complete BUSCO genes detected, 0.98 of average Pearson correlation coefficient for each chromosome between positions on the assembly and genetic linkage map, and 98.24% of bases assigned a score above 30. The 24 largest scaffolds were 662.70 Mb, accounting for 103.67% of the estimated genome size. A total of 25,720 protein-coding genes and 3,502 ncRNAs were predicted, with 94.0% of the genes being functionally annotated. The completeness and length of transcripts, exons and introns were comparable to those for the annotations of other fishes. Furthermore, the phylogenetic position of this species was determined for the first time, and the divergence time between golden pompano and Asian seabass was estimated to be 82.24 million years ago. Enriched GO terms with transport functions for expanded genes were detected, which may be related to the restless habit of this species. The sex determination mechanism was different from that in Seriola fishes, which belong to the same family. This assembly will be a valuable genomic resource for genome evolution and selection breeding.