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. 2011 Oct;106(1):45-50.
doi: 10.1016/j.biosystems.2011.06.005. Epub 2011 Jun 17.

Analysis of codon usage in type 1 and the new genotypes of duck hepatitis virus

Meng Wang  1 , Jie Zhang, Jian-Hua Zhou, Hao-Tai Chen, Li-Na Ma, Yao-Zhong Ding, Wen-Qian Liu, Yuan-Xing Gu, Feng Zhao, Yong-Sheng Liu
Affiliations

Analysis of codon usage in type 1 and the new genotypes of duck hepatitis virus

Meng Wang et al. Biosystems. 2011 Oct.

Abstract

In this study, an abundant (A+U)% and low codon bias were revealed in duck hepatitis virus type 1 (DHV-1) and the new serotype strains isolated from Taiwan, South Korea and Mainland China (DHV-N). The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in these samples. By comparative analysis of the codon usage patterns of 40 ORFs of DHV, we found that all of DHV-1 strains grouped in genotype C; the DHV-N strains isolated in South Korea and China clustered into genotypes B; and the DHV-N strains isolated from Taiwan clustered into genotypes A. The findings revealed that more than one subtype of DHV-1 circulated in East Asia. Furthermore, the results of phylogenetic analyses based on RSCU values and Clustal W method indicated obvious phylogenetic congruities. This suggested that better genome consistency of DHV may exist in nature and phylogenetic analyses based on RSCU values maybe a good method in classifying genotypes of the virus. Our work might give some clues to the features and some evolutionary information of DHV.

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Figures

Fig. 1
Fig. 1
Graphs showing the relationship between ENC and the (G + C)3%. The curve indicates the expected codon usage if GC compositional constraints alone account for codon usage bias.
Fig. 2
Fig. 2
A plot of the values of the Axis 1a (34.555%) and the Axis 2a (12.701%) of 40 ORFs of DHV-1 genomes in principle component analysis. China is stand for Mainland China. SK is stand for South Korea. TaiB is stand for China Taipei. The A, B and C indicate lineage A, B and C, respectively.
Fig. 3
Fig. 3
Phylogenetic trees, based on the ORF, showing the relationship among these available DHV sequences. The same classification of lineage A, lineage B or lineage C after the GenBank accession number was obtained with that of principle component analysis.
Fig. 4
Fig. 4
Qualitative evaluation of codon usage bias in three lineages of DHV.
See this image and copyright information in PMC

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