Charybdis japonica genome provides insights into desiccation adaptation and sex-determining region

Charybdis japonica (shore swimming crab) predominantly inhabits the intertidal zones and has high desiccation tolerance. We present the first chromosome-level C. japonica genome, which contains 51 pseudochromosomes, and the revised genome is 1431.02 Mb in length and has a contig N50 size of 29.67 Mb. Additionally, 824.02 Mb repeat elements, 30,900 coding genes, 474 miRNAs, 15,570 tRNAs, 309 rRNAs, and 157 miRNAs were identified in the C. japonica genome. The whole-genome resequencing data can contribute to the identification of sex-related single-nucleotide polymorphisms and insertion–deletion mutations. The 0-10,120,000 bp of chromosome 37 is the sex-determining region of C. japonica. Comparative genome analysis identified 832 C. japonica-specific gene families. Phylogenetic analysis showed that C. japonica has a close relationship with Portunus trituberculatus, which also belongs to family Portunidae. Compared with other species, metabolism rate, oxygen supply, oxidative stress, and various transporter-related genes were expanded or underwent positive selection in C. japonica, which might contribute to C. japonica’s ability to overcome diverse stresses in drought environment. Decoding the present genome provides valuable information for revealing the desiccation-adaptive and sex-determining mechanisms of C. japonica and also enriches the genetic information to explore the evolutionary history and environmental adaptation strategies of other Portunidae crabs.