Analysis of synonymous codon usage patterns in duck hepatitis A virus: a comparison on the roles of mutual pressure and natural selection

被引：18

作者：

Chen Y. ^{[1
]}

Chen Y.-F. ^{[2
]}

机构：

[1] Department of Renewable Resources, University of Alberta, Edmonton, T6G 2H1, AB

[2] College of Software, Harbin Normal University, Harbin, Heilongjiang

来源：

VirusDisease | 2014年 / 25卷 / 3期

关键词：

Compositional constraint; Multivariate statistics; Mutational pressure; Natural selection; Optimal codons; Synonymous substitution;

D O I：

10.1007/s13337-014-0191-2

中图分类号：

学科分类号：

摘要：

Codon usage patterns of duck hepatitis A virus (HAV) were studied in the present study. The major trends of codon usage patterns were analyzed using principal component analysis on the basis of the relative synonymous codon usage values. Correlation analysis was utilized to reveal the associations of the first two major axes of PCA and nucleotide- or amino acid-relevant indices. Our results showed that compositional constraint and/or mutational pressure are major factors influencing codon usage bias patterns of HAV. However, the influence of natural selection is also prevalent, as indicated by strongly significant correlations between the hydrophobicity, aromaticity, aliphaticity and ionization and the first axis of PCA. Also, ionization could characterize the second axis of PCA. At last, maximum likelihood phylogenetic analysis shows that there are no remarkable geographic clustering patterns of HAV strains in the phylogenetic tree. However, through MANOVA test, there are significant differences on the codon usage patterns among HAV strains from different countries. In conclusion, both mutational pressure and natural selection are of equally great importance to codon usage patterns of duck HAV genomes. © 2014, Indian Virological Society.

引用

页码：285 / 293

页数：8

共 24 条

[1]

Bashal A., Mukherjee R., Chakraborty C., Synonymous codon usage pattern analysis of hepatitis D virus, Virus Res, 173, 2, pp. 350-353, (2013)

[2]

Botzman M., Margalit H., Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles, Genome Biol, 12, (2011)

[3]

Bouquet J., Cherel P., Pavio N., Genetic characterization and codon usage bias of full-length hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution, Infect Genet Evol, 12, pp. 1842-1853, (2012)

[4]

Chen Y., A comparison of synonymous codon usage bias patterns in DNA and RNA virus genomes: quantifying the relative importance of mutational pressure and natural selection, Biomed Res Int, 2013, (2013)

[5]

Das S., Paul S., Dutta C., Synonymous codon usage in adenoviruses: influence of mutation, selection and protein hydropathy, Virus Res, 117, pp. 227-236, (2006)

[6]

Gong X., Fan S., Cui Z., Li X., The CpG suppression of polymerase segments and its impact on codon usage bias in H1N1 influenza virus, Acta Biophys Sin, 27, pp. 537-544, (2011)

[7]

Hu J., Wang Q., Zhang J., Et al., The characteristic of codon usage pattern and its evolution of hepatitis C virus, Infect Genet Evol, 11, pp. 2098-2102, (2011)

[8]

Karlin S., Burge C., Dinucleotide relative abundance extremes: a genomic signature, Trends Genet, 11, pp. 283-290, (1995)

[9]

Liu X., Wu C., Chen A., Codon usage bias and recombination events for neuraminidase and hemagglutinin genes in Chinese isolates of influenza A virus subtype H9N2, Arch Virol, 155, pp. 685-693, (2010)

[10]

Ma M., Ha X., Ling H., Et al., The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern, Virol J, 8, (2011)

← 1 2 3 →