诺如病毒GⅡ.4型密码子偏爱性及聚类分析

Codon preference and cluster analysis of Norovirus G Ⅱ.4

[目的]分析诺如病毒GⅡ.4基因型密码子的偏爱性变化,探索其聚类情况。[方法]从NCBI上下载GⅡ.4型所有完整毒株,使用CodonW、EMBOSS、SigmaPlot14.0软件对诺如病毒GⅡ.4型密码子偏爱性进行分析,使用SPSS软件对GⅡ.4型聚类分析。[结果]诺如病毒GⅡ.4型三种编码框的ENC值均>50;RSCU>1的密码子以U/C结尾的居多;ENC-Plot显示GⅡ.4型三种编码框绝大多数位于标准曲线之下;PR2分析中,GⅡ.4型三种编码框四个象限分布不均匀;GⅡ.4型按照年份的聚类分析显示不同年份之间存在着一定程度的聚类。[结论]诺如病毒GⅡ.4型三种编码框的偏爱性较弱,密码子使用以U/C结尾为主,其使用偏倚受到突变和自然选择,但以自然选择为主,近年来存在着聚类情况。

[Objective]Analyzed the preference changes in the codon of Norovirus GⅡ.4 genotype and explored its clustering situation.[Method]Downloaded all complete strains of GⅡ.4 from NCBI,analyzed the codon preference of Norovirus GⅡ.4 using CodonW,EMBOSS and SigmaPlot14.O,and performed cluster analysis on G Ⅱ.4 using SPSS software.[Result]The ENC values of the three coding boxes of Norovirus GⅡ.4 were all greater than 50;Most codons with RSCU>1 end with U/C;ENC-Plot showed that the vast majority of the three coding boxes of G II.4 type were located below the standard curve;In PR2 analysis,the distribution of the four quadrants of the three coding boxes of G Ⅱ.4 type is uneven;The clustering analysis of G Ⅱ.4 type by year showed that there was a certain degree of clustering between different years.[Conclusion]The preference of the three encoding boxes in G Ⅱ.4 was weak,and the codon usage was mainly U/C terminated.Its usage bias was mainly influenced by natural selection.In recent years,there had been new clustering situations that need to be taken seriously.