新现HIV-1L亚型的密码子偏爱性研究  

Study on the codon usage preference of the newly emerging L subtype of HIV-1

作　　者：石哲芳 周国庆 刘奇 SHI Zhe-fang;ZHOU Guo-qing;LIU Qi(Integrated Lab of Pathogen Biology,College of Basic Medicine,Dali University,Dali,China 671000;The Eighth Hospital Affiliated with Dali University)

机构地区：[1]大理大学基础医学院病原生物学综合实验室,云南大理671000 [2]大理大学第八附属医院

出　　处：《中国病原生物学杂志》2021年第5期497-501,506,共6页Journal of Pathogen Biology

基　　金：国家自然科学基金项目(No.81703573,81660337);大理大学创新团队项目(No.ZKLX2019105)。

摘　　要：目的分析新现HIV-1L亚型密码子使用偏爱性及其影响因素,并基于密码子偏爱性分析L亚型与其他亚型之间的关系。方法依据HIV-1各亚型的基因编码序列,利用EMBOSS的子程序CUSP、CodonW和SPSS22.0软件对其密码子偏爱性进行统计分析,使用SigmaPlot进行绘图,并用MEGA10.0构建系统进化树,SPSS22.0进行聚类分析。结果HIV-1L亚型ENc为46.19,和其他型别(43.75~47.97)相当,其RSCU>1的密码子中A/U结尾的占约71.8%。中性绘图、ENc-plot及PR2-plot分析表明,包括L亚型在内的HIV-1密码子的偏爱性主要受自然选择的影响。系统发育分析显示新现L亚型与HIV-1M组C亚型的分离株形成一个分支。基于env和gag编码序列密码子偏爱性的聚类分析均显示L亚型与C亚型聚为一类。不论是系统发育分析还是聚类分析,其结果均表明L亚型与C亚型有着更密切的关系。结论新现L亚型HIV-1偏爱使用A/U结尾的密码子,其偏爱性主要受自然选择压力的影响。此外L亚型密码子偏爱性与流行较为广泛的HIV-1C亚型关系密切,需加强其流行病学监控。Objective To analyze the codon usage preference of the L subtype of HIV-1and factors influencing it and to analyze the relationship between the L subtype and other subtypes based on codon preference.Methods The EMBOSS program CUSP,the program CodonW,and the software SPSS 22.0were used to statistically analyze the codon preference of each subtype of HIV-1based on the gene coding sequence,SigmaPlot was used for related mapping,MEGA10.0was used to construct different phylogenetic trees,and SPSS 22.0was used for cluster analysis.Results The L subtype of HIV-1had an ENc of 46.19,which was equivalent to that of other types(43.75-47.97).Codons ending with A/U accounted for 71.8%of all codons with RSCU>1.Neutrality Plot,ENc-plot,and PR2-plot analysis all indicated that the codon preference of HIV-1,as well as its L subtype,was mainly affected by natural selection.Phylogenetic analysis indicated that the new L subtype is most closely related to the C subtype of the M group of HIV-1.Cluster analysis based on the codon preference of the env and gag coding sequences indicated that the L subtype and the C subtype were clustered together.Both phylogenetic analysis and cluster analysis indicated that the L subtype is closely related to the C subtype.Conclusion HIV-1prefers codons ending in A/U,and its preference is mainly affected by natural selection pressure.In addition,the codon preference of the L subtype is closely related to the more widespread C subtype of HIV-1,and its epidemiological monitoring needs to be enhanced.

关 键 词：HIV-1 L亚型 密码子偏爱性 新现 

分 类 号：R373.9[医药卫生—病原生物学]