Zhang Jihu, Zhang Cheng-Long, Chen Hong Ju, Ji Xiang Shan, Zhao Yan
Key Laboratory of Efficient Utilization of Non-grain Feed Resources (Co-construction by Ministry and Province) of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, Taian, Shandong, China.
Shandong Provincial Key laboratory for Livestock Germplasm Innovation & Utilization, Shandong Agricultural University, Taian, Shandong, China.
Mar Biotechnol (NY). 2025 Jan 14;27(1):30. doi: 10.1007/s10126-024-10408-7.
In China, the red swamp crayfish (Procambarus clarkii), a notorious invasive species, has become an important economic freshwater species. In order to compare the genetic diversity and population structure of crayfish from northern and southern China, we collected 60 crayfish individuals from 4 crayfish populations in northern China and 2 populations in southern China for sequencing using the 2b-RAD technique. Additionally, the whole genome sequence information obtained by 2b-RAD of 90 individuals from 2 populations in northern China and 7 populations in southern China were downloaded from NCBI. After quality control, a total of 25,371 SNPs were detected from approximately 54.22 billion raw reads. Based on these SNPs, high genetic diversity was observed in the 15 crayfish populations in China. The pairwise F values indicated that there was a large genetic differentiation of crayfish populations in northern and southern China. Despite common genetic backgrounds, due to geographical barriers, genetic divergence has been observed in northern and southern China crayfishes. The principal component analysis in combination with Admixture and Neighbor-Joining tree analysis showed that the crayfish fell into two clusters corresponding to geographical regions. The integrated analysis of whole genome and transcriptome data showed that two genes (CETN4 and CPEB2) might play important roles during crayfish resistance to a cold environment. This study reveals the genetic differentiation of crayfish populations in northern and southern China and provides clues to the genetic mechanism related to cold adaptation.
在中国，克氏原螯虾（Procambarus clarkii），一种臭名昭著的入侵物种，已成为重要的经济淡水物种。为了比较中国北方和南方小龙虾的遗传多样性和种群结构，我们使用2b-RAD技术从中国北方的4个小龙虾种群和南方的2个小龙虾种群中收集了60只小龙虾个体进行测序。此外，从NCBI下载了通过2b-RAD技术获得的来自中国北方2个种群和南方7个种群的90个个体的全基因组序列信息。经过质量控制，从约542.2亿条原始读数中总共检测到25371个单核苷酸多态性（SNP）。基于这些SNP，在中国的15个小龙虾种群中观察到了高遗传多样性。成对F值表明中国北方和南方的小龙虾种群存在较大的遗传分化。尽管有共同的遗传背景，但由于地理障碍，在中国北方和南方的小龙虾中都观察到了遗传分歧。主成分分析结合Admixture和邻接树分析表明，小龙虾分为两个与地理区域相对应的聚类。全基因组和转录组数据的综合分析表明，两个基因（CETN4和CPEB2）可能在小龙虾对寒冷环境的抗性中发挥重要作用。本研究揭示了中国北方和南方小龙虾种群的遗传分化，并为与冷适应相关的遗传机制提供了线索。
