Comparative analysis of codon usage patterns in chloroplast genomes of the Asteraceae family
Codon usage bias (CUB) is an important evolutionary feature in a genome and has been widely documented from prokaryotes to eukaryotes. However, the significance of CUB in the Asteraceae family has not been well understood, with no Asteraceae species having been analyzed for this characteristic. Here, we use bioinformatics approaches to comparatively analyze the general patterns and influencing factors of CUB in five Asteraceae chloroplast (cp) genomes. The results indicated that the five genomes had similar codon usage patterns, showing a strong bias towards a high representation of NNA and NNT codons. Neutrality analysis showed that these cp genomes had a narrow GC distribution and no significant correlation was observed between GC12 and GC3. Parity Rule 2 (PR2) plot analysis revealed that purines were used more frequently than pyrimidines. Effective number of codons (ENc)-plot analysis showed that most genes followed the parabolic line of trajectory, but several genes with low ENc values lying below the expected curve were also observed. Furthermore, correspondence analysis of relative synonymous codon usage (RSCU) yielded a first axis that explained only a partial amount of variation of codon usage. These findings suggested that both natural selection and mutational bias contributed to codon bias, while selection was the major force to shape the codon usage in these Asteraceae cp genomes. Our study, which is the first to investigate codon usage patterns in Asteraceae plastomes, will provide helpful information about codon distribution and variation in these species, and also shed light on the genetic and evolutionary mechanisms of codon biology within this family.
KeywordChloroplast genome Codon usage bias Correspondence analysis Asteraceae
The authors are grateful to the anonymous reviewers for their valuable comments and suggestions, and also thank Yuerong Zhang and Licao Cui for their help with statistical analysis. This research was funded mainly by the National Basic Research and Development Program of China (Grant No. 2009CB119200) and 948 Program (2010-S1), Chinese Ministry of Agriculture.
- Bremer K (1994) Asteraceae: cladistics and classification. Timber, OregonGoogle Scholar
- Greenacre MJ (1984) Theory and applications of correspondence analysis. Academic, LondonGoogle Scholar
- Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH et al (1988) Codon usage in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within-species diversity. Nucleic Acids Res 16:8207–8711PubMedCentralPubMedCrossRefGoogle Scholar