Analysis of synonymous codon usage in chloroplast genome of Populus alba

The pattern of codon usage in the chloroplast genome of Populus alba was investigated. Correspondence analysis (a commonly used multivariate statistical approach) and method of effective number of codons (ENc)-plot were conducted to analyze synonymous codon usage. The results of correspondence analysis showed that the distribution of genes on the major axis was significantly correlated with the frequency of use of G+C in synonymously variable third position of sense codon (GC3S), (r=0.349), and the positions of genes on the axis 2 and axis 3 were significantly correlated with CAI (r=-0.348, p<0.01 and r=0.602, p<0.01). The ENc for most genes was similar to that for the expected ENc based on the GC3S, but several genes with low ENC values were lying below the expected curve. All of these data indicated that codon usage was dominated by a mutational bias in chloroplast genome of P. alba. The selection in nature for translational efficiency only played a minor role in shaping codon usage in the chloroplast genome of P. alba. © 2008 Northeast Forestry University and Springer-Verlag GmbH.