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 .