Synonymous codon usage analysis of thirty two mycobacteriophage genomes

Abstract

Synonymous codon usage of protein coding genes of thirty two completely sequenced mycobacteriophage genomes was studied using multivariate statistical analysis. One of the major factors influencing codon usage is identified to be compositional bias. Codons ending with either C or G are preferred in highly expressed genes among which C ending codons are highly preferred over G ending codons. A strong negative correlation between effective number of codons (Nc) and GC3s content was also observed, showing that the codon usage was effected by gene nucleotide composition. Translational selection is also identified to play a role in shaping the codon usage operative at the level of translational accuracy. High level of heterogeneity is seen among and between the genomes. Length of genes is also identified to influence the codon usage in 11 out of 32 phage genomes. Mycobacteriophage Cooper is identified to be the highly biased genome with better translation efficiency comparing well with the host specific tRNA genes.

Figure 1

Nc plot of thirty two mycobacteriophages. The genes for individual phages are represented by different colors.

Figure 2

Plot of Nc versus Gene length for all mycobacteriophage genomes.

Figure 3

Correspondence analysis of Relative Synonymous Codon Usage values of mycobacteriophages (32 genomes).

Figure 4

Scatter plot of mycobacteriophages and Nc values.

Figure 5

Scatter plot of mycobacteriophages and GC3s values.