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

Abstract

The leopard coral grouper, Plectropomus leopardus, belonging to the family Epinephelinae, is a carnivorous coral reef fish widely distributed in tropical and subtropical waters of the Indo-Pacific. 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 has hindered study of its biology and genomic breeding programmes. Here we report the de novo sequencing and assembly of the 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 881.55Mb with a scaffold N50 of 34.15Mb, consisting of 24 pseudochromosome scaffolds. busco analysis showed that 97.2% of the conserved single-copy genes were retrieved, indicating the assembly was almost entire. 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 single nucleotide polymorphisms based on genome resequencing of 54 individuals. The P.leopardus genome and genomic variation data provide valuable genomic resources for studies of its genetics, evolution and biology. In particular, it is expected to benefit the development of genomic breeding programmes in the farming industry.