气候变化领域集成服务门户(CCPortal): Population structure and adaptability analysis of Schizothorax o'connori based on whole-genome resequencing

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DOI	10.1186/s12864-024-09975-9
	Population structure and adaptability analysis of Schizothorax o'connori based on whole-genome resequencing
	Gao, Kuo; He, Zhi; Xiong, Jinxin; Chen, Qiqi; Lai, Bolin; Liu, Fei; Chen, Ping; Chen, Mingqiang; Luo, Wenjie; Huang, Junjie; Ding, Wenxiang; Wang, Haochen; Pu, Yong; Zheng, Li; Jiao, Yuanyuan; Zhang, Mingwang; Tang, Ziting; Yue, Qingsong; Yang, Deying; Yan, Taiming
发表日期	2024
ISSN	1471-2164
起始页码	25
结束页码	1
卷号	25 期号:1
英文摘要	Background Schizothorax o'connori is an endemic fish distributed in the upper and lower reaches of the Yarlung Zangbo River in China. It has experienced a fourth round of whole gene replication events and is a good model for exploring the genetic differentiation and environmental adaptability of fish in the Qinghai-Tibet Plateau. The uplift of the Qinghai-Tibet Plateau has led to changes in the river system, thereby affecting gene exchange and population differentiation between fish populations. With the release of fish whole genome data, whole genome resequencing has been widely used in genetic evolutionary analysis and screening of selected genes in fish, which can better elucidate the genetic basis and molecular environmental adaptation mechanisms of fish. Therefore, our purpose of this study was to understand the population structure and adaptive characteristics of S. o'connori using the whole-genome resequencing method. Results The results showed that 23,602,746 SNPs were identified from seven populations, mostly distributed on chromosomes 2 and 23. There was no significant genetic differentiation between the populations, and the genetic diversity was relatively low. However, the Zangga population could be separated from the Bomi, Linzhi, and Milin populations in the cluster analysis. Based on historical dynamics analysis of the population, the size of the ancestral population of S. o'connori was affected by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Glacial Age. The selected sites were mostly enriched in pathways related to DNA repair and energy metabolism. Conclusion Overall, the whole-genome resequencing analysis provides valuable insights into the population structure and adaptive characteristics of S. o'connori. There was no obvious genetic differentiation at the genome level between the S. o'connori populations upstream and downstream of the Yarlung Zangbo River. The current distribution pattern and genetic diversity are influenced by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Ice Age. The selected sites of S. o'connori are enriched in the energy metabolism and DNA repair pathways to adapt to the low temperature and strong ultraviolet radiation environment at high altitude.
英文关键词	Schizothorax o'connori; Genetic diversity; Environmental adaptation; Whole genome resequencing; Yarlung Zangbo River
语种	英语
WOS研究方向	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS类目	Biotechnology & Applied Microbiology ; Genetics & Heredity
WOS记录号	WOS:001158394500002
来源期刊	BMC GENOMICS
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/310026
作者单位	Sichuan Agricultural University
推荐引用方式 GB/T 7714	Gao, Kuo,He, Zhi,Xiong, Jinxin,et al. Population structure and adaptability analysis of Schizothorax o'connori based on whole-genome resequencing[J],2024,25(1).
APA	Gao, Kuo.,He, Zhi.,Xiong, Jinxin.,Chen, Qiqi.,Lai, Bolin.,...&Yan, Taiming.(2024).Population structure and adaptability analysis of Schizothorax o'connori based on whole-genome resequencing.BMC GENOMICS,25(1).
MLA	Gao, Kuo,et al."Population structure and adaptability analysis of Schizothorax o'connori based on whole-genome resequencing".BMC GENOMICS 25.1(2024).