Journal of Zhejiang University SCIENCE B

, Volume 9, Issue 9, pp 667–674 | Cite as

Analysis of synonymous codon usage and evolution of begomoviruses

  • Xiao-zhong Xu
  • Qing-po Liu
  • Long-jiang Fan
  • Xiao-feng Cui
  • Xue-ping Zhou


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.

Key words

Begomovirus Synonymous codon usage Evolution Bioinformatics 

CLC number

Q939.46 S432.1 


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Copyright information

© Zhejiang University and Springer-Verlag GmbH 2008

Authors and Affiliations

  • Xiao-zhong Xu
    • 1
  • Qing-po Liu
    • 2
  • Long-jiang Fan
    • 1
  • Xiao-feng Cui
    • 1
  • Xue-ping Zhou
    • 1
  1. 1.College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
  2. 2.School of Agriculture and Food ScienceZhejiang Forestry UniversityLin’anChina

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