Abstract
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 novosequencing 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 functional annotated. Comparative genomic analyses revealed that gene family expansions inP. 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.
Keywords : leopard coral grouper, Plectropomus leopardus , genome sequencing, chromosomal assembly, genome annotation
Introduction
Groupers (Perciformes, Epinephelinae), acting as the main carnivorous predators, are important biological members in the coral reef ecosystem. The abundance and variety of the groupers have great impact on this fairly complex ecosystem. The family Epinephelidae is comprised of approximately 165 species in 16 genus, classified based on 12S, 16S and histone H3 gene sequences (Craig & Hastings, 2007). However, the taxonomy of these species is still in discussion with a previous classification of family Serranidae (Saad, 2019). Therefore, more genomic evidence are needed to clarify the taxonomy of groupers. However, to date, only two genome sequences of grouper species, the giant grouper (Epinephelus lanceolatus ) (Zhou et al., 2019) and the red-spotted grouper (Epinephelus akaara ) (Ge et al., 2019), are available, which significantly hinders the taxonomical, evolutionary and biological studies of the groupers.
The leopard coral grouper, Plectropomus leopardus , also namely coral trout or spotted coral grouper, is a representative fish in genus Plectropomus. It naturally inhabits in tropical or subtropical waters of the Indo-Pacific Oceans from southern Japan to Australia and eastwards to the Caroline Islands, Fiji and Tonga (Froese & Pauly, 2019). Like most other groupers, P. leopardus is protogynous hermaphroditism, starting out of females and sex-reverse to male later in life (Ferreira, 1995). They are also characterized by complex social structures and a variety of body colour, such as bright red and brown.
Due to low-fat and high-protein flesh, impressive taste and beautiful skin colour, P. leopardus has recently become an important commercial species worldwide with a high trading price (Fabinyi, 2012). The increasing demands trigger a rapid development of the aquaculture ofP. leopardus in many Asian countries and regions, which requires advanced aquaculture technology, such as genomic breeding and metabolic control.
Previous studies in P. leopardus mainly focused on species classification (Harrison et al., 2014; Herwerden et al., 2006), reproductive biology (Zeller, 1998), physiological stress responses (Frisch & Anderson, 2005) and behaviour biology (Leis & Carsonewart, 1999; Light & Jones, 1997). Genomic and genetic studies of this species were reported in the development of microsatellite markers (Zhang et al., 2010), the transcriptomic comparison in two colour morphs (Wang et al., 2015), and the muscle metabolic mechanism revealed by gene expression and metabolome analyses (Mekuchi et al., 2017). The insufficient exploitation of genomic resource largely limits the genetic study, conservation and genomic breeding of this species.
Here we report a chromosomal-scale genome assembly and annotation ofP. leopardus , which was generated using 10× Genomic and Hi-C sequencing technology. The well-annotated genome and the massive sequencing data of leopard coral grouper will provide a crucial resource for genomic, biological and ecological studies of this species, and will efficiently promote its genomic breeding program in aquaculture. In addition, this genome will facilitate future evolutionary, phylogenetic and comparative studies, as well as resource conservation within family Epinephelinae.