Characterization of Codon usage bias in the newly identified DEV UL18 gene

Xiwen Chen; Anchun Cheng; Mingshu Wang; Jun Xiang

doi:10.1117/12.913536

1 October 2011 Characterization of Codon usage bias in the newly identified DEV UL18 gene

Xiwen Chen, Anchun Cheng, Mingshu Wang, Jun Xiang

Proceedings Volume 8285, International Conference on Graphic and Image Processing (ICGIP 2011); 82857Q (2011) https://doi.org/10.1117/12.913536
Event: 2011 International Conference on Graphic and Image Processing, 2011, Cairo, Egypt

Abstract

In this study, Codon usage bias (CUB) of DEV UL18 gene was analyzed, the results showed that codon usage bias in the DEV UL18 gene was strong bias towards the synonymous codons with A and T at the third codon position. Phylogenetic tree based on the amino acid sequences of the DEV UL18 gene and the 27 other herpesviruses revealed that UL18 gene of the DEV CHv strain and some fowl herpesviruses such as MeHV-1, GaHV-2 and GaHV-3 were clustered within a monophyletic clade and grouped within alphaherpesvirinae. The ENC-GC3S plot indicated that codon usage bias has strong species-specificity between DEV and 27 reference herpesviruses, and suggests that factors other than gene composition, such as translational selection leading to the codon usage variation among genes in different organisms, contribute to the codon usage among the different herpesviruses. Comparison of codon preferences of DEV UL18 gene with those of E. coli , yeast and humans showed that there were 20 codons showing distinct usage differences between DEV UL18 and yeast, 22 between DEV UL18 and humans, 23 between DEV UL18 and E.coli, which indicated the codon usage bias pattern in the DEV UL18 gene was similar to that of yeast. It is infered that the yeast expression system may be more suitable for the DEV UL18 expression.

Citation Download Citation

Xiwen Chen, Anchun Cheng, Mingshu Wang, and Jun Xiang "Characterization of Codon usage bias in the newly identified DEV UL18 gene", Proc. SPIE 8285, International Conference on Graphic and Image Processing (ICGIP 2011), 82857Q (1 October 2011); https://doi.org/10.1117/12.913536

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