MBE Advance Access published online on March 27, 2009
Molecular Biology and Evolution, doi:10.1093/molbev/msp063
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Research Article |
Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria
1 State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
2 Department of Ecology & Evolution, University of Chicago, Chicago, IL 60637, USA
To whom correspondence should be addressed. E-mail: dtian{at}nju.edu.cn or mkre{at}midway.uchicago.edu
Received for publication September 12, 2008. Revision received March 1, 2009. Accepted for publication March 24, 2009.
Rates of nucleotide substitution and insertion/deletion (indel) are known to vary across the functional components of a genome. Little attention has been paid, however, to the quantitative relationship between the two. Here we investigate the ratio of nucleotide substitutions to indels (S/I) in different regions of four primate, 70 bacteria and eight other genomes. We find that the ratio differs at 5.4-times between coding and noncoding, 3.3-times between conserved and less-conserved-coding sequences, and 1.46-times between non-repeat and repeat regions. The S/I ratio is also positively correlated with the level of divergence between the genomes compared. Our results suggest that the S/I ratio may reflect differences in the efficacy of selection against indels. Due to the sensitivity of indel density in different regions, this ratio varies over a much larger range. With the recent discovery suggesting that indels act as local enhancers of mutation in surrounding sequences, nucleotide substitution rates are expected to be accelerated in regions of low constraint, where indels tend to accumulate, but will otherwise be modulated in proportion to the level of a sequence's functional constraint. Indels, therefore, may play a nontrivial role in controlling differences in genetic variation and divergence across functional regions of a genome.
Key Words: SNP • Insertion/deletion • Evolutionary rate • Divergence
* These authors contributed equally to this work.
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