Red swamp crayfish Procambarus clarkii is an ecologically and economically important crustacean species. Here, based on a de novo assembly strategy combining PacBio with Hi-C sequencing, we presented a high quality chromosome-level P. clarkii genome. The assembled genome is 2.75 Gb in size with a contig N50 of 216.75 kb. Transposable elements (TEs) make up the largest fraction of the genome (~79.61%), and LINEs comprise the majority of the TEs. Frequent molting and rapid growth of the red swamp crayfish may be explained by the expansion of multiple gene families regarding growth or development. Phylogenetic analysis revealed that P. clarkii diverged from Portunus trituberculatus at 278–407 million years ago (Mya). PSMC analysis identified multiple bottleneck events of the P. clarkii population between 2 kaBP to 14 kaBP. The obtained P. clarkii genome should not only facilitate us understanding the development and evolution of the crayfish species, but also contribute to the genetic improvement in future breeding selections.

红沼泽小龙虾Procambarus clarkii是一种具有重要生态和经济意义的甲壳类动物。在这里，基于将 PacBio 与 Hi-C 测序相结合的从头组装策略，我们展示了高质量的染色体水平的克拉氏疟原虫基因组。组装的基因组大小为 2.75 Gb，contig N50 为 216.75 kb。转座因子(TE) 占基因组的最大部分 (~79.61%)，而 LINE 占 TE 的大部分。红沼泽小龙虾的频繁蜕皮和快速生长可能是由于多个基因家族在生长或发育方面的扩展。系统发育分析表明， P. clarkii从278-4.07亿年前的三结核梭子蟹（Mya）。PSMC 分析确定了2 kaBP 至 14 kaBP 之间的P. clarkii种群的多个瓶颈事件。获得的P. clarkii基因组不仅有助于我们了解小龙虾物种的发展和进化，而且有助于未来育种选择的遗传改良。