1 Introduction
The Chinese shrimp Fenneropenaeus chinensis is one of the most
commercially important cultured shrimp species in China (Figure 1a). It
is mainly distributed in the Yellow Sea and Bohai Sea of China, and west
and south coast of the Korean Peninsula (Wang et al., 2017).Fenneropenaeus chinensis is an annual species; they migrate to
warmer sea areas to overwinter after mating and swim back to the
original coast for oviposition. With the development of aquaculture
techniques, F. chinensis became the most important cultured
shrimp species in China in the 1990s. However, in 1993, the production
of F. chinensis decreased sharply owing to an outbreak of the
white spot syndrome virus (WSSV)
disease. Since 1997, breeding
efforts have been made to increase the production and disease resistance
of F. chinensis . After continuous artificial selection, several
cultured varieties possessing excellent characteristics, such as high
yield, disease resistance, and stress resistance, have been developed
and cultured during the past two decades in China.
Because of their structural complexity and high heterozygosity (Yu et
al., 2015), only a few crustacean genomes have been completely
characterized. Recently, third-generation sequencing, characterized as
long reads, has helped to ameliorate the difficulties engendered by
heterozygosity and repetitive sequences in genome assembly (van Dijk,
Jaszczyszyn, Naquin, & Thermes, 2018). An assembled genome of F.
chinensis was published recently using Illumina short reads, PacBio
long reads and Hi-C technology; the assembled genome covered 1.58 Gb in
8768 scaffolds, with N50 length of 28.92 Mb (Yuan et al., 2021).
Furthermore, the reference genome of Litopenaeus vannamei ,
which—similar to F. chinensis— previously belonged to the
genus Penaeus , has been reported also using both Illumina short
reads and PacBio long reads (X. Zhang et al., 2019), covering 1.66 Gb in
4,683 scaffolds, with N50 length of 605.56 Kb, and was improved to 31.30
Mb by using Hi-C technology (Yuan et al., 2021). Two genomic resources
for another Penaeus species, Penaeus monodon , was released
lately (Uengwetwanit et al., 2021; Van Quyen et al., 2020); the improved
genome was generated using long-read PacBio and long-range Chicago,
producing a final genome assembly of 2.39 Gb, with contig N50 length of
79 Kb (Uengwetwanit et al., 2021).
A high-quality reference genome is essential for resolving the molecular
mechanism of important biological processes (You, Shan, & Shi, 2020).
In this research, an improved chromosome-level genome of F.
chinensis was assembled using the PacBio sequencing platform and Hi-C
technology, in an attempt to explain the genetic changes during
evolution and domestication. Quality of the genome assembly could affect
the accuracy of following studies (You et al., 2020). Therefore, the new
version assembled genome provides a high-quality reference, and will be
a valuable resource for the further investigations of biological process
and mechanism in F. chinensis .