Ma Y P, Liu Z X, Hao L, Ma J Y, Liang Z L, Li Y G, Ke H
Guangdong Public Laboratory of Veterinary Public Health, Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
South China Agricultural University, Guangzhou, China.
J Fish Dis. 2015 Jul;38(7):665-73. doi: 10.1111/jfd.12316. Epub 2014 Dec 9.
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 GC12 % and GC3 % 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 GC3 % 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 GC3 % 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 carpio L., 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.
本研究对鲤疱疹病毒3型（CyHV-3）开放阅读框（ORF）的密码子使用模式进行了调查。GC12%与GC3%之间的高度相关性表明，突变压力而非自然选择是决定CyHV-3密码子使用和碱基组成的主要因素，而突变压力效应源于GC3%与病毒功能基因相对同义密码子使用（RSCU）值的主成分分析第一主轴（轴1）之间的高度相关性。然而，绝对密码子使用偏好与GC3%之间的相互作用表明，除了突变压力外，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.)）之间的密码子使用相似程度高于该病毒与鲤鱼（Cyprinus carpio L.）之间的相似程度，这表明在CyHV-3的密码子使用模式中，金鱼比鲤鱼发挥着更重要的作用。对CyHV-3密码子使用的研究可为该病毒的分子进化提供一些证据。通过分析它们的密码子使用模式，还可以丰富我们对CyHV-3与其宿主之间关系的理解。
