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doi:10.1534/genetics.105.049916
A more recent version of this article appeared on January 1, 2006.
REGULAR RESEARCH PAPERS |
Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition
Brian R Morton 1*, Irie V Bi 2, Michael D McMullen 2 and Brandon S Gaut 3
1 Barnard College, Columbia University
2 University of Missouri, Columbia
3 University of California, Irvine
* To whom correspondence should be addressed. E-mail: bmorton{at}barnard.columbia.edu.
Submitted on August 22, 2005
Revised on September 24, 2005
Accepted on 4 October 2005
We examine variation in mutation dynamics across a single genome (Zea mays) in relation to regional and flanking base composition using a dataset of 10,472 SNPs generated by resequencing 1,776 transcribed regions. We report several relationships between flanking base composition and mutation pattern. The A+T content of the two sites immediately flanking the mutation site is correlated with rate, transition bias and GC -> AT pressure. We also observe a significant CpG effect, or increase in transition rate at CpG sites. At the regional level we find that the strength of the CpG effect is correlated with regional A+T content, ranging from a 1.7-fold increase in transition rate in relatively G+C-rich regions to a 2.6-fold increase in A+T-rich regions. We also observe a relationship between locus A+T content and GC -> AT pressure. This regional effect is in opposition to the influence of the two immediate neighbors, in that GC -> AT pressure increases with increasing locus A+T content but decreases with increasing flanking base A+T content, and may represent a relationship between genome location and mutation bias. The data indicate multiple context effects on mutations resulting in significant variation in mutation dynamics across the genome.
Key Words: Context dependency, Molecular evolution, Mutation dynamics, Single Nucleotide Polymorphism
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