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CLC number: Q939.46; S432.1

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Received: 2008-01-06

Revision Accepted: 2008-05-30

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Journal of Zhejiang University SCIENCE B 2008 Vol.9 No.9 P.667-674


Analysis of synonymous codon usage and evolution of begomoviruses

Author(s):  Xiao-zhong XU, Qing-po LIU, Long-jiang FAN, Xiao-feng CUI, Xue-ping ZHOU

Affiliation(s):  College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China; more

Corresponding email(s):   zzhou@zju.edu.cn

Key Words:  Begomovirus, Synonymous codon usage, Evolution, Bioinformatics

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Xiao-zhong XU, Qing-po LIU, Long-jiang FAN, Xiao-feng CUI, Xue-ping ZHOU. Analysis of synonymous codon usage and evolution of begomoviruses[J]. Journal of Zhejiang University Science B, 2008, 9(9): 667-674.

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%A Qing-po LIU
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%DOI 10.1631/jzus.B0820005

T1 - Analysis of synonymous codon usage and evolution of begomoviruses
A1 - Xiao-zhong XU
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A1 - Long-jiang FAN
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PB - Zhejiang University Press & Springer
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DOI - 10.1631/jzus.B0820005

begomoviruses are single-stranded DNA viruses and cause severe diseases in major crop plants worldwide. Based on current genome sequence analyses, we found that synonymous codon usage variations in the protein-coding genes of begomoviruses are mainly influenced by mutation bias. Base composition analysis suggested that the codon usage bias of AV1 and BV1 genes is significant and their expressions are high. Fourteen codons were determined as translational optimal ones according to the comparison of codon usage patterns between highly and lowly expressed genes. Interestingly the codon usages between begomoviruses from the Old and the New Worlds are apparently different, which supports the idea that the bipartite begomoviruses of the New World might originate from bipartite ones of the Old World, whereas the latter evolve from the Old World monopartite begomoviruses.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


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