柯萨奇病毒B组5型分离株VP1区序列基因组成和密码子使用模式分析

Analysis of gene composition and codon usage pattern of VP1 region of Coxsackievirus B5 isolated strains

目的探索柯萨奇病毒B组5型(Coxsackievirus group B5,CVB5)分离株VP1区序列基因组成和密码子使用模式。方法在GenBank核苷酸数据库检索CVB5毒株的VP1区全长序列,应用CodonW软件,计算CVB5分离株基因组成和密码子使用偏爱性参数,包括密码子和氨基酸含量、同义密码子各碱基含量、同义密码子第3位GC含量(GC_(3))、有效密码子数(ENC)和同义密码子相对使用度(Relative Synonymous Codon Usage,RSCU);通过ENC曲线、中性绘图、RSCU和奇偶规则(PR2)分析自然选择和突变对病毒的进化影响。结果共纳入413株CVB5分离株,其VP1区碱基含量由高到低依次为A(29.78%)、C(24.84%)、G(24.16%)、T(21.22%);密码子第3位密码子含量均值分别为A_(3)(25.90%)、T_(3)(23.31%)、C_(3)(26.31%)和G_(3)(24.49%);密码子含量前3位依次为GTG(4.67%)、ACA(3.73%)和CCA(3.70%),氨基酸含量前3位依次为Thr(11.25%)、Ser(8.11%)和Val(7.92%);共有59组密码子,其中29个同义密码子相对使用度(RSCU)均值>1,占49.15%。CVB5毒株VP1区有效密码子数(ENC)值为(55.96±2.40),中性绘图分析显示,GC_(3)和GC_(12)含量有统计学关联,但相关性较弱(b=0.046,r=0.316,P<0.001);PR2分析显示,自然选择对CVB5病毒密码子使用偏爱性作用为95.40%。结论 CVB5分离株总体密码子使用相似、偏爱性较弱,受到自然选择和突变双重影响,病毒进化相对保守。

Objective To explore the gene composition and codon usage pattern of VP1 region of Coxsackievirus B5(CVB5)isolated strains.Methods The full-length VP1 region sequences of CVB5 strains were obtained from GenBank nucleic acid database.CodonW software was used to analyze the gene composition and codon usage pattern parameters such as contents of codons and amino acids,the content of each base of synonymous codons,the content of GC at the third position of synonymous codons(GC_(3)),effective number of of codon(ENC)and relative synonymous codon usage(RSCU).The effects of natural selection and mutation on virus evolution were analyzed by ENC plot,neutral plot,RSCU and PR2 analysis.Results A total of413 CVB5 strains were included in the study,the contents of each base in VP1 coding regions were A(accounted for 29.78%),C(accounted for 24.84%),G(accounted for 24.16%)and T(accounted for 21.22%)in descending order.The top 3 codons used were GTG(accounted for 4.67%),ACA(accounted for 3.73%)and CCA(accounted for 3.70%);while the top 3 amino acids were Thr(accounted for 11.25%),Ser(accounted for 8.11%)and Val(accounted for 7.92%).Among 59 codons used in VP1 coding region,29 were with average RSCU value>1,accounted for 49.15%.The ENC value of CVB5 VP1 region was(55.96± 2.40);neutral plot analysis showed that GC_(3) and GC_(12) were weakly correlated(b=0.046,r=0.316,P<0.001);while PR2 analysis showed that 95.40%of CVB5 virus codon usage was favored by natural selection.Conclusion CVB5 isolated strains have similar codon usage patterns and weak preference,whch are affected by both natural selection and mutation.The virus evolution is relatively conservative.