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 (<i>Eriocheir japonica sinensis</i>) 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 <i>E. j.sinensis</i> 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 <i>Penaeus vannamei</i> ~373.6 million years ago, with a faster evolution rate than shrimp. We anticipate that the annotated high-quality genome of <i>E. j. sinensis</i> will promote research on its basic development and evolution and make substantial contributions to comparative genomic analyses of crustaceans.