De novo sequencing and chromosomal-scale genome assembly of leopard coral grouper, Plectropomus leopardus.

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 resource 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 a combination of 10× Genomics, high-throughput chromosome conformation capture (Hi-C) and PacBio long read sequencing technologies. The genome assembly has a total length of 881.55 Mb with a scaffold N50 of 34.15 Mb, consisting of 24 pseudo-chromosomes scaffolds. BUSCO analysis showed that 97.2% of the conserved single-copy genes were retrieved, indicating a good entirety of the assembly. We predicted 25,248 protein-coding genes, among which 96.5% were functionally annotated. Comparative genomic analyses revealed that gene family expansions in P. leopardus were associated with immune related pathways. In addition, we identified 5,178,453 SNPs based on genome resequencing of 54 individuals. The P. leopardus genome and variation data provide valuable genomic resource for genetics, evolutionary and biological studies of the grouper species. Particularly, it is expected to benefit the development of genomic breeding programs in the farming industry.