1. Introduction
Penaeid shrimps are marine crustaceans in the Penaeidae family, which comprises a number of economical important species, including the kuruma prawn (Marsupenaeus japonicus ) the giant tiger prawn (Penaeus monodon ), and the Pacific whiteleg shrimp (Litopenaeus vannamei ) (Koyama et al., 2010; Wilson et al., 2000; Yuan et al., 2018). These crustaceans are farmed commercially, making them valuable aquaculture species internationally (FAO, 2019). Penaeid shrimps have complex body patterns and specific structures, including appendages, segments, and antennae with lateral line-like sense organs (Thornber et al., 2019). Therefore, research using these species provides insights into the developmental biology of crustaceans. High quality crustacean genomes assembled at the chromosome level are currently available; however, the presence of high numbers or repeat sequences and the large genome size mean that most of these assemblies are incomplete.
Marsupenaeus japonicus is distributed widely, ranging from the Red Sea and East Africa to Japan and South‑East Asia (Tsoi et al., 2007). In 2016, the global annual production of M. japonicusreached 57, 351 tons, the yield of which represented over 5% of the world’s shrimp output, with an output value of more than 860 million US dollars (Figure 1) (FAO, 2019). Among shrimp, M. japonicus is one of the most cultured, and has several popular features, such as a good taste, high economic value, rapid growth rate, and low oxygen tolerance, making it suitable for live transportation (Zhao et al., 2021). However, kuruma shrimp have been greatly overexploited in recent years, causing a significant decrease in its natural abundance and prompting the initiation of artificial breeding (Zheng et al., 2020, Ren et al., 2020). Uniquely, M. japonicus are able to survive without water for long periods, permitting live transportation of these shrimp to distant markets (Francis et al., 2021). In China, M. japonicus is a good choice for species diversification because of its capability for live transportation, export demand, and high price (Wang et al., 2020).
Kuruma shrimp engage in sand diving; therefore, their growth is promoted by including sand substrates in shrimp ponds during aquaculture (Wang et al., 2018; Zhao et al., 2021). These sand substrates also contain mud, and provide an environment that promotes the growth of microorganisms and benthic organisms, which in turn provide nutrients to the shrimp and maintain the water quality (Almeida et al., 2012; Silva & Martinelli-Lemos, 2012). M. japonicus’ adaptive plasticity, i.e., its ability to cope with changing environmental conditions, could be revealed via transcriptome sequencing combined with a reference genome. In studies on prawns, the distinctions between the morphological and physiological characteristics have rarely been explored, and little is known about its genetic changes. There are two publicly available (short-read based) draft genome assemblies; however, because the kuruma shrimp genome contains a high proportion of repetitive sequences; therefore, these assemblies are highly fragmented, comprising N50 contig lengths of 912 bp (Yuan et al., 2018) and 234,949 bp (Kawato et al., 2021). These genome resources are helpful to understand the genetics of kuruma shrimp; however, they lack the required completeness and contiguity (Ren et al., 2020). Thus, we still lack high-quality genome information at the chromosome level.
In the present study, a chromosome-anchored reference genome of M. japonicus was constructed, which is an important addition to the high-quality genome assemblies of decapods, which are currently only available for the black tiger shrimp Penaeus monodon(Uengwetwanit et al., 2021), the Pacific white shrimp Litopenaeus vannamei (Zhang et al., 2019), the Chinese shrimp (Fenneropenaeus chinensis ) (Wang et al., 2021b), the marbled crayfish Procambarus virginalis (Gutekunst et al., 2018), and the swimming crabPortunus trituberculatus (Tang et al., 2020). Although two draftM. japonicas genomes are available, few efforts to relate the species’ biology to the genome assembly have been made. We constructed a chromosome-level genome assembly of M. japonicus by combining Pacific Bioscience oriented single-molecule real-time (SMRT) sequencing with Illumina paired-end sequencing and high‐throughput chromosome conformation capture (Hi-C) technology. By constructing this chromosome-based genome assembly, we not only aimed to promote research into the genetic changes underpinning the ecological traits of M. japonicus , but also to provide important resources for the protection and breeding management of M. japonicus .