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. 2010 Sep 9;6(9):e1001104.
doi: 10.1371/journal.pgen.1001104.

Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?

Eduardo P C Rocha  1 , Edward J Feil
Affiliations

Mutational patterns cannot explain genome composition: Are there any neutral sites in the genomes of bacteria?

Eduardo P C Rocha et al. PLoS Genet. .
No abstract available

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. The GC composition of genomes is strongly correlated with second codon (GC2) and 4-fold degenerate positions (GC4) .
Second codon positions show low variability due to purifying selection on non-synonymous changes. 4-fold degenerate positions vary between 5% and 97% GC among published genomes. In the classical neutral scenario (red), 4-fold degenerate positions are nearly neutral and their composition results essentially from mutational patterns. These patterns are modified in bacteria that lose repair genes, such as mutators, which show additional AT pressure (grey area) . In the selectionist view (blue), the composition of 4-fold degenerate positions results from selection for GC content, the mutational patterns are AT-rich relative to genome composition, and there are no neutral positions. Naturally, this is an idealized view of genomes that code for many additional overlapping signals that are under selection, e.g., codon usage bias, regulatory signals, etc.
See this image and copyright information in PMC

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