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.