安徽农业大学学报2026，Vol.53Issue(2)：249-260,12.DOI:10.13610/j.cnki.1672-352x.20260514.002
李属坏死环斑病毒CP基因的密码子偏好性与谱系动力学研究
Study on codon usage bias and phylogenetic dynamics of CP gene in prunus necrotic ringspot virus
摘要
Abstract
[Objective]This study aimed to analyze the codon usage bias of the coat protein encoded gene(CP)of prunus necrotic ringspot virus(PNRSV),explore its molecular evolutionary patterns and adaptability to hosts,research its phylogenetic dynamics,and provide a scientific basis for control strategies.[Method]Total 273 PNRSV CP gene sequences were collected from the GenBank database and analyzed using bioinformatics softwares MEGA and CodonW for codon usage and composition analysis.Systematic phylogenetic analysis and Bayesian phylogenet-ic methods were combined to infer the virus's origin,evolution,and dispersal patterns.[Result]Phylogenetic analysis revealed that 273 PNRSV CP gene isolates were classified into four lineages:CH30,PE5,PV96,and PV32,with the CH30 and PE5 lineages predominantly found in peach hosts.Analysis of the effective number of codons indicated weak codon usage bias in the PNRSV CP genes from different hosts,while a general preference for synonymous codons ending with G or U was observed.ENC-plot and parity rule 2 analysis demonstrated that the codon usage bias of PNRSV CP genes was influenced by both natural selection and mutational pressure,with natural selection playing a more significant role.Bayesian maximum clade credibility analysis suggested that Chinese isolates of PNRSV CP primarily belonged to the PV32 group and that the most recent common ancestor of PNRSV likely originated in the United States.Bayesian skyline plot analysis showed fluctuations in the PNRSV population size between 2010 and 2020.[Conclusion]The PNRSV CP gene exhibits weak codon usage bias,which is signifi-cantly influenced by natural selection and may be associated with the viral replication efficiency and pathogenicity within hosts.The recent active evolutionary process of PNRSV is likely closely linked to the global expansion of Rosaceae plant cultivation(including cherry,plum,apricot,peach,Japanese apricot,crabapple,etc.)and the in-creased frequency of seedling trade,suggesting a potential role of international trade in virus dissemination.These findings not only enhance the understanding of PNRSV epidemiology,but also provide a scientific basis for de-veloping targeted prevention and control measures.关键词
李属坏死环斑病毒/CP 基因/密码子偏好性/系统进化分析/谱系动力学Key words
prunus necrotic ringspot virus/CP gene/codon usage bias/phylogenetic analysis/phylogenetic dynamics分类
农业科技引用本文复制引用
曹烨,丁诗文,孟悦,孙文豪,赵海婷,江彤,贺振,李帅..李属坏死环斑病毒CP基因的密码子偏好性与谱系动力学研究[J].安徽农业大学学报,2026,53(2):249-260,12.基金项目
国家自然科学基金项目(32302320) （32302320）
国家重点研发计划重点专项(2024YFD1400700) （2024YFD1400700）
泰州市"凤城英才计划"双创引进专项 （）
