High-Quality Genome Assembly of Eriocheir japonica sinensis Reveals Its Unique Genome Evolution

Abstract

As an important freshwater aquaculture species in China, the Chinese mitten crab (Eriocheir japonica sinensis) has high economic and nutritional value. However, limited genomic information is currently available for studying its basic development and genetic diversity. Here, we performed whole-genome sequencing on Oxford Nanopore Technologies Limited's platform using promethION. The assembled size of E. j.sinensis genome was approximately 1.27 Gb, which is close to the estimated size (1.19 Gb). Furthermore, based on assessment using Benchmarking Universal Single-Copy Orthologs (BUSCO) (Simao et al., 2015), 94.00% of the expected eukaryotic genes were completely present in the genome assembly. In addition, repetitive sequences accounted for ~61.42% of the assembled genome, and 22,619 protein-coding genes were annotated. Comparative genomics analysis demonstrated that the Chinese mitten crab diverged from Penaeus vannamei ~373.6 million years ago, with a faster evolution rate than shrimp. We anticipate that the annotated high-quality genome of E. j. sinensis will promote research on its basic development and evolution and make substantial contributions to comparative genomic analyses of crustaceans.

Keywords: Eriocheir japonica sinensis; crab; evolution; genome assembly and annotation; nanopore.

Figure 1

Chinese mitten crab, Eriocheir japonica sinensis.

Figure 2

Guanine–cytosine (GC) content of Chinese mitten crab and other genomes. The GC content values were calculated using a sliding window method and the window size is 2 Kb. The whole-genome sequences including the coding region and non-coding region were used for analysis.

Figure 3

Quality comparison of protein-coding genes. The distribution of mRNA, CDS, exon, and intron among these species were shown. The species include Eriocheir japonica sinensis, Aedes aegypti, Stegodyphus mimosarum, Drosophila melanogaster, and Penaeus vannamei.

Figure 4

Gene family analysis of Chinese mitten crab. (A) Orthologous genes among species. (B) Unique and shared gene families in species.

Figure 5

Phylogenetic relationships, divergence time, and evolution rate. (A) Phylogenetic relationship and divergence time of species. Red dot represents fossil record used here. (B) Relative evolution rate of species.