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.