Heterogeneity of the transition/transversion ratio in drosophila and hominidae genomes

Vladimir B. Seplyarskiy, Peter Kharchenko, Alexey S. Kondrashov, Georgii A. Bazykin

Research output: Contribution to journalArticlepeer-review

23 Citations (Scopus)

Abstract

Mutation rate varies between sites in the genome. Part of this variation can be explained by well-recognized short nucleotide contexts, but a large component of this variation remains cryptic. We used data on interspecies divergence and intraspecies polymorphism in Drosophila and Hominidae to analyze variation of the average rate of the 12 possible kinds of single-nucleotide mutations and in the transition/transversion ratio κ at single-nucleotide resolution. Both the average mutation rate and κ vary by a factor of ∼3 between nucleotide sites. The characteristic scale of variation in κ is up to at least ∼30 nucleotides in Drosophila and ∼5 nucleotides in Hominidae. Genome segments with locally elevated mutation rates possess lower values of κ; however, a substantial fraction of variation in κ cannot be directly explained by the local mutation rates.

Original languageEnglish
Pages (from-to)1943-1955
Number of pages13
JournalMolecular Biology and Evolution
Volume29
Issue number8
DOIs
Publication statusPublished - Aug 2012
Externally publishedYes

Keywords

  • D. melanogaster
  • H. sapiens
  • mutagenesis
  • SNP
  • transition/transversion ratio

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