Keywords
Cephalopholis
sonnerati ,
chromosome-level
genome assembly,
genome
annotation,
comparative
genome analyse
Introduction
Groupers (subfamily Epinephelinae species, Serranidae, Percoidei,
Perciformes), the largest subfamily in the Serranidae family, consist of
more than 160 species in 16 genera (Zhang et al., 2013). These
commercially important fishes possess special characteristics of a long
lifespan, large size, slow growth, vulnerability and delayed
reproduction (Morris et al., 2000). Moreover, they usually inhabit coral
reefs of tropical and subtropical coasts. Of them, the genusCephalopholisis the most abundant serranid in the Gulf of Aqaba (Red Sea) (Shpigel &
Fishelson, 2010).
The tomato hindCephalopholis sonnerati(Valenciennes)
(Serranidae),
belonging to the genusCephalopholis , is a
bottom-dwelling coral reef of 12–120-m depth in the Indo-Pacific and
Red
Sea.C.sonnerati are protogynous hermaphrodites in life and feeding on
little fish and invertebrates (Shpigel, 1985; Shpigel & Fishelson,
1989a,b; Shpigel & Fishelson, 2010).
Furthermore, they are also
characterized
by complex social structures and behavioural mechanisms. They naturally
form social groups, with males and several females occupying individual
territories within the male’s larger territory (Meyer, 2008; Shpigel &
Fishelson, 1989b). However, due to overfishing, anthropogenic activities
and water pollution, the natural populations of C.sonnerati have directly declined (Hawkins & Roberts, 1994).
Previous studies of the genusCephalopholimainly focused on fishery management, species conservation
(Galal-Khallaf et al., 2018), behavior biology (Shpigel & Fishelson,
2010), nutrition biology, and phylogeographic biology (Gaither et al.,
2011). Nevertheless, owing to the lack of genomic resources,
molecular-genetic studies and genomic breeding remain unexplored in this
species.
PacBio (a single-molecule real-time [SMRT] sequencing), a newly
third-generation
sequencing technology, generates long reads with uniform coverage and
high consensus accuracy compared with the
second-generation
sequencing technology that generates short reads (Rhoads & Au, 2015).
Morever, third-generation sequencing technology is less expensive than
second-generation sequencing technology and does not depend on
amplification for library generation (Ze-Gang & Shao-Wu, 2018).
Additionally, Hi-C, a chromosome conformation capture-based method, can
convert chromatin interactions, reflecting topological chromatin
structures into digital information (Belaghzal et al., 2017). Presently,
it has become a mainstream technology in 3D genomics. Despite that more
than 270 aquatic organisms’ genome sequences have been published
(https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/fish), only
three genome sequences of grouper species (the giant grouperEpinephelus
lanceolatus [Zhou et al., 2019], the red-spotted grouperEpinephelus akaara [Ge et al., 2019] and the leopard coral
grouper, Plectropomus leopardus [Zhou et al., 2020] are
available. Therefore, it is significantly important to gain more genome
sequences of grouper species for the research on the classification,
evolutionary, genetics, and biological studies of groupers.
In the present study, we
reported
the first chromosome-level genome
assembly of C.sonnerati, which was obtained by using
PacBio long-read sequencing and
Hi-C sequencing technologies. Our reference genome will lay a
solid
foundation for studies on the genetics conservation, resistance breeding
and evolutionary of C. sonnerati .