1. Introduction
The Portunidae family, which comprises approximately 300 identified
species, has successfully settled in a variety of habitats from ocean
trenches to hydrothermal vents, intertidal mud flats, and terrenes (Cui
et al., 2021). Portunidae crabs have high ecological and economic value.
Although genomic information is believed to reveal the regulatory
mechanism of the biological characteristics of Portunidae members, only
a handful of Portunidae genomes have been published, such as those ofScylla paramamosain (Zhao et al., 2021) and Portunus
trituberculatus (Tang et al., 2020). Hence, completing the genome
database of Portunidae crabs is urgently
needed.
Charybdis japonica (H. Milne Edwards, 1861; Figure 1) belongs to
genus Charybdis of family Portunidae (Decapoda, Crustacea). This
species is a eurythermic and euryhaline marine crab (Yu et al., 2005)
and predominantly inhabits the intertidal zones of China, Japan, the
Korean Peninsula, and Southeast Asia countries. C. japonica is a
delicious aquatic food with high amino acid and unsaturated fatty acid
contents; thus, it has high economic and medicinal values (Yu et al.,
2004). This fishery resource was further developed after the 1990s and
gradually became an important fishery resource in China’s coastal areas
(Zheng, 2015). Meanwhile, artificial C. japonica farming is
active in China. The economic traits of C. japonica is gender
specific during the farming process. Specifically, male C.
japonica has a faster growth rate, but females show a higher economic
value (Kolpakov and Kolpakov, 2011). Additionally, C. japonicahas a higher desiccation tolerance than other crabs (Yu et al., 2004; Yu
et al., 2005; Zheng et al., 2013), which seems to help improve survival
rates for intertidal living and during farming and transportation
processes.
Dry
transportation is one of the important segments of artificial crustacean
culture, which is beneficial to improve crustacean welfare and reduce
economic loss. However, dry transportation can still more easily break
the balance between crustacean and water environment and lead to the
decrease of crustacean physique, vitality, and survival rate (Lorenzon
et al., 2008; Paital, 2013). The tissues of crustaceans under
desiccation are always subjected to water deficit stress and hypoxia
stress (Ridgway et al., 2006; Paital, 2013). The gills are the first
tissue to suffer from desiccation because it is the main respiratory
organ of many crustaceans. The gill prefers to use oxygen in water
rather than that in air. The absence of water media leads to the
aggregation of gill lamellae, which reduces the gas exchange area of the
gill and ultimately leads to gill dysfunction syndrome (Greenaway et
al., 1996; Taylor and Wheatley, 1989; Levin, 2003). Insufficient oxygen
supply will further hinder oxidative metabolism, reduce ATP production,
cause imbalance in cell homeostasis, and even cause body death (Li et
al., 2010).
Therefore,
desiccation tolerance is an important factor that influences the
biological processes and survival of many marine crustaceans, whether
living in the natural intertidal zone or in the dry transport process of
artificial farming.
Many aquatic organisms have evolved and obtained some adaptive
strategies to establish higher tolerance to desiccation. For example,
some organisms in drought conditions can increase oxygen supply by
beating their hearts faster (Morris et al., 1999). Reducing oxygen
consumption rate is also an effective strategy to deal with the hypoxia
stress caused by desiccation (Urbina et al., 2013). Aquatic organisms
exposed to desiccation can increase the synthesis of respiratory
proteins (such hemoglobin and hemocyanin) to enhance the oxygen-carrying
rate of proteins and oxygen transport (Pascual, 2003; Urbina et al.,
2013). Crustaceans living in intertidal zones may be exposed to air and
suffer from drought stress for several hours during low tide. These
crustaceans have evolved the hard chitin shell to keep their gills moist
for long periods of time to adapt to the periodic dryness of the
intertidal zone. Meanwhile, adjustments in metabolic mechanisms are also
valuable for crustaceans living in the intertidal zone (Taylor and
Greenaway, 1984; Lu et al., 2016). However, the molecular mechanism of
desiccation tolerance in crustaceans has not yet been satisfactorily
elucidated.
Considering the stronger desiccation tolerance of C. japonica (Yu
et al., 2004; Yu et al., 2005; Zheng et al., 2013), this species can be
used as a model crustacean to understand the regulation mechanism of
desiccation tolerance. Whole-genome genetic information can provide a
microperspective for revealing the desiccation-adaptive plasticity ofC. japonica , that is, its flexibility in terms of the capability
to cope with water deficit stress and hypoxia stress. Meanwhile, the sex
differentiation of C. japonica may be similar to that of many
crustaceans and controlled by androgenic or estrogen gland; thus, it is
susceptible to the influence of the external environment (Cui et al.,
2021). Therefore, decoding the whole-genome genetic information can also
enhance our understanding of the molecular mechanisms of the sex
differentiation of C. japonica . In fact, the publication of the
whole-genome information of C. japonica will help enrich the
genetic resources of family Portunidae and provide many insights into
their evolutionary history and environmental adaptation strategies.
Therefore, the whole-genome sequencing of C. japonica is
necessary to carry out.
Here,
we characterized a high-quality chromosome-anchored reference genome ofC. japonica for the first time by combining short Illumina reads,
long PacBio reads, and Hi-C reads. We tried to correlate the reported
genomic data with the biology, evolutionary history, and desiccation
tolerance mechanisms of this species. Additionally, the genome regions
associated with underlying sex determination in C. japonica were
predicted based on whole-genome resequencing data. In-depth study of
this extensive data will provide groundbreaking mechanical insights into
the genetic mechanisms associated with sex differentiation and
desiccation tolerance in C. japonica and other crustaceans.