Analysis of codon usage in Newcastle disease virus.
In this study, the relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents, and dinucleotide were used to investigate codon usage pattern of each protein-coding gene and genome among 31 Newcastle disease virus (NDV) isolates. The result shows that the overall extent of codon usage bias in NDV is low (mean ENC = 56.15 > 40). The good correlation between the (C + G)(12)% and (G + C)(3)% suggests that the mutational pressure, rather than natural selection, is the main factor that determines the codon usage bias and base component in NDV. It is observed that synonymous codon usage pattern in NDV genes is gene function and geography specific, but not host specific. By contrasting synonymous codon usage patterns of different NDV isolates, we suggest that more than one genotype of NDV circulates in waterfowl in USA; and gene length has no significant effect on the variations of synonymous codon usage in these virus genes. CpG under-represented is a characteristic for NDV to fit in its host. These results not only provide an insight into the variation of codon usage pattern among the genomes of NDV, but also may help in understanding the processes governing the evolution of NDV.
Key Laboratory of Animal Virology of Ministry of Agriculture, State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 Gansu, People's Republic of China.
Meng
M
Wang
Yong-Sheng
YS
Liu
Jian-Hua
JH
Zhou
Hao-Tai
HT
Chen
Li-Na
LN
Ma
Yao-Zhong
YZ
Ding
Wen-Qian
WQ
Liu
Yuan-Xing
YX
Gu
Jie
J
Zhang
D001482:Base Composition; D003062:Codon / Q000032:analysis / Q000235:genetics*; D019143:Evolution, Molecular; D016679:Genome, Viral; D016014:Linear Models; D009154:Mutation; D009522:Newcastle disease virus / Q000235:genetics*; D025341:Principal Component Analysis; D012367:RNA, Viral / Q000235:genetics
D003062:Codon; D012367:RNA, Viral
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