The characteristic of the synonymous codon usage and phylogenetic analysis of hepatitis B virus.,Genes & Genomics

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The characteristic of the synonymous codon usage and phylogenetic analysis of hepatitis B virus.
Genes & Genomics ( IF 2.1 ) Pub Date : 2020-05-27 , DOI: 10.1007/s13258-020-00932-w
Xiaoming Qi _{1,

2,

3} , Chaojun Wei _{1,

2,

3} , Yonghong Li _{1,

2,

3} , Yu Wu _{1,

2,

3} , Hui Xu _{1,

2,

3} , Rui Guo _{1,

2,

3} , Yanjuan Jia _{1,

2,

3} , Zhenhao Li _{1,

2,

3} , Zhenhong Wei _{1,

2,

3} , Wanxia Wang _{1,

2,

3} , Jing Jia _{1,

2,

3} , Yuanting Li _{1,

2,

3} , Anqi Wang _{1,

2,

3} , Xiaoling Gao _{1,

2,

3}

Affiliation

Background

Hepatitis B virus (HBV) infection is a crucial medical issue worldwide. The dependence of HBV replication on host cell machineries and their co-evolutionary interactions prompt the codon usage pattern of viral genes to translation selection and mutation pressure.

Objective

The evolutionary characteristics of HBV and the natural selection effects of the human genome on the codon usage characteristics were analyzed to provide a basis for medication development for HBV infection.

Methods

The codon usage pattern of sequences from different HBV genotypes of our isolates and reference HBV genome sequences downloaded from the National Center for Biotechnology Information (NCBI) database were analyzed by computing the relative synonymous codon usage (RSCU), nucleotide content, codon adaptation index (CAI) and the effective number of codons (ENC).

Results

The highest ENC values were observed in the C genotypes, followed by the B genotypes. The ENC values indicated a weak codon usage bias (CUB) in HBV genome. The number of codons differentially used between the three genotypes was markedly higher than that of similarly used codons. High CAI values indicated a good adaptability of HBV to its host. The ENC plot indicated the occurrence of mutational pressure in the three genotypes. The mean Ka/Ks ratios in the three genotypes were lower than 1, which indicated a negative selection pressure. The CAI and GC3% plot indicated the existence of CUB in the HBV genome.

Conclusions

Nucleotide composition, mutation bias, negative selection and mutational pressure are key factors influencing the CUB and phylogenetic diversity in HBV genotypes. The data provided here could be useful for developing drugs for HBV infection.

中文翻译：

乙型肝炎病毒的同义密码子使用和系统发育分析的特征。

背景

乙型肝炎病毒（HBV）感染是世界范围内的关键医学问题。HBV复制对宿主细胞机器的依赖性及其共同进化的相互作用促使病毒基因的密码子使用模式对翻译选择和突变压力产生影响。

目的

分析了乙肝病毒的进化特征以及人类基因组对密码子使用特征的自然选择作用，为乙肝病毒感染药物的开发提供了基础。

方法

通过计算相对同义密码子使用量（RSCU），核苷酸含量，密码子适应指数（ CAI）和有效密码子数（ENC）。

结果

在C基因型中观察到最高的ENC值，其次是B基因型。ENC值表明HBV基因组中的密码子使用偏倚（CUB）较弱。三种基因型之间差异使用的密码子数量明显高于相似使用的密码子。高CAI值表明HBV对宿主具有良好的适应性。ENC图显示了三种基因型中突变压力的发生。三种基因型的平均Ka / Ks比均低于1，表明选择压力为负。CAI和GC3％图表明HBV基因组中存在CUB。