Analysing codon usage bias of cyprinid herpesvirus 3 and adaptation of this virus to the hosts
Analysing codon usage bias of cyprinid herpesvirus 3 and adaptation of this virus to the hosts
复制标题
鲤科疱疹病毒3型密码子使用偏差分析及该病毒对宿主的适应
DOI：
10.1111/jfd.12316
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发表时间：
2015-07-01
影响因子：
2.5
通讯作者：
Ke, H.
中科院分区：
文献类型：
--
作者：
Ma, Y. P.;Liu, Z. X.;Ke, H.
对鲤鱼疱疹病毒3型（CyHV-3）开放阅读框（ORF）的密码子使用模式进行了研究。GC（12）%和GC（3）%之间的高度相关性表明，突变压力而不是自然选择是决定CyHV-3中密码子使用和碱基组分的主要因素，而突变压力效应则是由于GC（3）%与主成分分析的第一主轴（Axis 1）在相对同义密码子使用（RSCU）上的高度相关性病毒功能基因的价值。然而，绝对密码子使用偏好和GC（3）%之间的相互作用表明，除了突变压力之外，其他选择也参与了密码子使用的形成。值得注意的是，CyHV-3与金鱼Carassius auratus（L.）比病毒与鲤鱼的毒力高，提示金鱼在CyHV-3的密码子使用模式中比鲤鱼起着更重要的作用。对CyHV-3密码子使用的研究可以为CyHV-3的分子进化提供一定的证据。通过分析CyHV-3与宿主的密码子使用模式，可以丰富我们对CyHV-3与宿主关系的认识。
The codon usage patterns of open reading frames (ORFs) in cyprinid herpesvirus 3 (CyHV-3) have been investigated in this study. The high correlation between GC(12)% and GC(3)% suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage and base component in the CyHV-3, while mutational pressure effect results from the high correlation between GC(3)% and the first principal axis of principle component analysis (Axis 1) on the relative synonymous codon usage (RSCU) value of the viral functional genes. However, the interaction between the absolute codon usage bias and GC(3)% suggests that other selections take part in the formation of codon usage, except for the mutational pressure. It is noted that the similarity degree of codon usage between the CyHV-3 and goldfish, Carassius auratus (L.), is higher than that between the virus and common carp, Cyprinus carpioL., suggesting that the goldfish plays a more important role than the common carp in codon usage pattern of the CyHV-3. The study of codon usage in CyHV-3 can provide some evidence about the molecular evolution of the virus. It can also enrich our understanding about the relationship between the CyHV-3 and its hosts by analysing their codon usage patterns.