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 .