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.

日本𫊻（shore swimming crab）主要栖息于潮间带，且具有极强的耐旱耐受能力。本研究首次报道日本𫊻的染色体级基因组组装结果：该基因组包含51条假染色体，组装总长度为1431.02 Mb，contig N50值为29.67 Mb。此外，本研究在该基因组中共注释得到824.02 Mb的重复序列元件、30900个编码基因、474个microRNA（miRNAs）、15570个转运RNA（tRNAs）、309个核糖体RNA（rRNAs）以及157个miRNAs。全基因组重测序数据可助力鉴定与性别相关的单核苷酸多态性（single-nucleotide polymorphisms, SNPs）及插入缺失突变（insertion–deletion mutations, InDels）。日本𫊻的37号染色体上0~10120000 bp区间为其性别决定区域。比较基因组分析共鉴定出832个日本𫊻特异性基因家族。系统发育分析结果显示，日本𫊻与同隶属于梭子蟹科的三疣梭子蟹（Portunus trituberculatus）亲缘关系密切。相较于其他物种，日本𫊻体内的代谢调控、供氧、氧化应激及各类转运蛋白相关基因家族发生了扩张或正选择，这可能是其能够耐受干旱环境下多种胁迫的分子基础。本研究解析的日本𫊻基因组，不仅为揭示其耐旱适应性与性别决定机制提供了宝贵的遗传资源，同时也为探究梭子蟹科其他蟹类的演化历史与环境适应策略丰富了数据储备。