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OA

[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.