Spotted scat (Scatophagus argus) is an economically important marine cultured fish species in Asia, especially in Southeast China. As an XY sex-determining type fish species, spotted scat can be used as a model for understanding the mechanism of novel sex determination system evolution in vertebrates. However, genomic resources of spotted scat are lacking, and no highly contiguous reference genome has been released. In this study, the first chromosome-level genome of spotted scat was constructed using PacBio’s single-molecule real-time (SMRT) sequencing and high-throughput chromosome conformation capture (Hi-C) sequencing technologies. The genome comprised 572.42 Mb, with the contig N50 of 19.60 Mb. A total of 24,256 protein-coding genes were predicted in the genome, and 96.30% of the predicted genes were functionally annotated. Evolutionary analysis showed that spotted scat diverged from the common ancestor of Japanese puffer (Takifugu rubripes) approximately 114.8 million years ago. In addition, doublesex and mab-3 related transcription factor 1 (dmrt1), a gene associated with sex determination process, was not found in the high-quality female genome, while it existed in the re-sequencing data of three XY genotype male fish. The conserved dmrt1 locus of vertebrates was substituted by its truncated homologue (dmrt1b), which derives from dmrt1 via allelic diversification and munitions. The genomic resources offer a strong foundation for further research on the sex determination of spotted scat and facilitate the understanding of the evolution of sex chromosomes in teleost species.

Silver sillago, Sillago sihama is a member of the family Sillaginidae and found in all Chinese inshore waters. It is an emerging commercial marine aquaculture species in China. In this study, high-quality chromosome-level reference genome of S. sihama was first constructed using PacBio Sequel sequencing and high-throughput chromosome conformation capture (Hi-C) technique. A total of 66.16 Gb clean reads were generated by PacBio sequencing platforms. The genome-scale was 521.63 Mb with 556 contigs, and 13.54 Mb of contig N50 length. Additionally, Hi-C scaffolding of the genome resulted in 24 chromosomes containing 96.93 % of the total assembled sequences. A total of 23,959 protein-coding genes were predicted in the genome, and 96.51 % of the genes were functionally annotated in public databases. A total of 71.86 Mb repetitive elements were detected, accounting for 13.78% of the genome. The phylogenetic relationships of silver sillago with other teleosts showed that silver sillago was separated from the common ancestor of S. sinica about 7.92 million years ago. Comparative genomic analysis of silver sillago with other teleosts showed that 45 unique and 100 expansion gene families were identified in silver sillago. Expansion gene families were involved in immune and olfactory receptors. In this study, the genomic resources provide valuable reference genomes for functional genomics research of silver sillago.

The leopard coral grouper, Plectropomus leopardus, belonging to genus Plectropomus, family Epinephelinae, is a carnivorous coral reef fish widely distributing in the tropical and subtropical water of Indo-Pacific Oceans. Due to its appealing body appearance and delicious taste, P. leopardus has become a popular commercial fish for aquaculture in many countries. However, the lack of genomic and molecular resources for P. leopardus hinders its biological studies and genomic breeding programs. Here we report the de novo sequencing and assembly of P. leopardus genome using 10× Genomics and high-throughput chromosome conformation capture (Hi-C) technologies. Using 127.36 Gb 10× Genomics we generated a 902.90 Mb genome assembly with a contig and scaffold N50 of 31.8 Kb and 33.47 Mb, respectively. The scaffolds were clustered and oriented into 24 pseudo-chromosomes with 13.39 Gb valid Hi-C data. BUSCO analysis showed that 95.3% of the conserved single-copy genes were retrieved, indicating a good entirety of the assembly. We predicted 23,234 protein-coding genes, among which 96.5% were functional annotated. The P. leopardus genome provides a valuable genomic resource for genetics, evolutionary and biological studies of this species. Particularly, it is expected to benefit the development of genomic breeding programs in the farming industry.