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Genome Landscapes and Bacteriophage Codon Usage

Figure 2

Snapshots of simulated synonymous mutation in the lambda phage genome.

(A) Shows GC3 and (B) shows CAI landscapes. In between successive snapshots (labeled by integers), N synonymous mutations are introduced into the genome and the resulting landscape is shown, where N is the number of codons in the lambda phage genome (see the Genome Landscapes section). These snapshots show that the simulated genome landscapes approach the random null model, indicated by the purple band (see Figure 1). The final CAI landscape (3) lies almost completely within the purple band. Using the lambda phage mutation rate of 7.7×10−8 mutations/bp/replication [57], we can estimate that approximately 107 genome replications would be required to relax within the purple bars.

Figure 2

doi: https://doi.org/10.1371/journal.pcbi.1000001.g002