Journal of Genetics

, Volume 84, Issue 1, pp 55–62 | Cite as

Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species

  • Qingpo Liu
  • Qingzhong Xue
Research Article


A detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm speciesOryza sativa, Zea mays, Triticum aestivum andArabidopsis thaliana. The average GC content of the entire genes, and at the three codon positions individually, was higher in nuclear than in chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots suggested that nucleotide compositional constraint had a large contribution to codon usage bias of nuclear genes inO. sativa, Z. mays, andT. aestivum, whereas natural selection was likely to be playing a large role in codon usage bias in chloroplast genomes. Correspondence analysis and chi-test showed that regardless of the genomic environment (species) of the host, the codon usage pattern of chloroplast genes differed from nuclear genes of their host species by their AU-richness. All the chloroplast genomes have predominantly A- and/or U-ending codons, whereas nuclear genomes have G-, C- or U-ending codons as their optimal codons. These findings suggest that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome. However, one feature common to both chloroplast and nuclear genomes in this study was that pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.


codon usage bioinformatics chloroplast plant genome 


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Copyright information

© Indian Academy of Sciences 2005

Authors and Affiliations

  • Qingpo Liu
    • 1
  • Qingzhong Xue
    • 1
  1. 1.Department of AgronomyCollege of Agriculture and Biotechnology, Zhejiang UniversityHangzhouChina

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