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

Content Provider	Springer Nature Link
Author	Chen, Youhua Chen, You Fang
Copyright Year	2014
Abstract	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.
Starting Page	285
Ending Page	293
Page Count	9
File Format	PDF
ISSN	23473584
Journal	VirusDisease
Volume Number	25
Issue Number	3
e-ISSN	23473517
Language	English
Publisher	Springer India
Publisher Date	2014-01-25
Publisher Place	India
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Synonymous substitution Multivariate statistics Optimal codons Compositional constraint Mutational pressure Natural selection Microbiology Life Sciences Biochemistry Protein Structure Cell Biology
Content Type	Text
Resource Type	Article
Subject	Infectious Diseases Virology

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

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