The Role of Context-Dependent Mutations in Generating Compositional and Codon Usage Bias in Grass Chloroplast DNA |
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Authors: | Brian R Morton |
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Institution: | (1) Department of Biological Sciences, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA, |
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Abstract: | Abstract
The influence of local base composition on mutations in chloroplast DNA (cpDNA) is studied in detail and the resulting, empirically
derived, mutation dynamics are used to analyze both base composition and codon usage bias. A 4 × 4 substitution matrix is
generated for each of the 16 possible flanking base combinations (contexts) using 17,253 noncoding sites, 1309 of which are
variable, from an alignment of three complete grass chloroplast genome sequences. It is shown that substitution bias at these
sites is correlated with flanking base composition and that the A+T content of these flanking sites as well as the number
of flanking pyrimidines on the same strand appears to have general influences on substitution properties. The context-dependent
equilibrium base frequencies predicted from these matrices are then applied to two analyses. The first examines whether or
not context dependency of mutations is sufficient to generate average compositional differences between noncoding cpDNA and
silent sites of coding sequences. It is found that these two classes of sites exist, on average, in very different contexts
and that the observed mutation dynamics are expected to generate significant differences in overall composition bias that
are similar to the differences observed in cpDNA. Context dependency, however, cannot account for all of the observed differences:
although silent sites in coding regions appear to be at the equilibrium predicted, noncoding cpDNA has a significantly lower
A+T content than expected from its own substitution dynamics, possibly due to the influence of indels. The second study examines
the codon usage of low-expression chloroplast genes. When context is accounted for, codon usage is very similar to what is
predicted by the substitution dynamics of noncoding cpDNA. However, certain codon groups show significant deviation when followed
by a purine in a manner suggesting some form of weak selection other than translation efficiency. Overall, the findings indicate
that a full understanding of mutational dynamics is critical to understanding the role selection plays in generating composition
bias and sequence structure. |
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Keywords: | Transition Transversion Mutation bias Codon usage bias Chloroplast genome |
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