Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition.
We examine variation in mutation dynamics across a single genome (Zea mays ssp. mays) in relation to regional and flanking base composition using a data set of 10,472 SNPs generated by resequencing 1776 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.
Morton
Brian R
BR
Department of Biological Sciences, Barnard College, Columbia University, New York, New York 10027, USA. bmorton@barnard.edu
Bi
Irie V
IV
McMullen
Michael D
MD
Gaut
Brandon S
BS
D020856:AT Rich Sequence; D001482:Base Composition; D018899:CpG Islands; D019143:Evolution, Molecular; D020862:GC Rich Sequence; D014644:Genetic Variation; D018745:Genome, Plant; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics*; D003313:Zea mays / Q000235:genetics*