Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes

Molecular Biology and Evolution
Vladimir B SeplyarskiyGeorgii A Bazykin

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.

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Citations

Mar 1, 2013·Molecular Biology and Evolution·Nadezhda V TerekhanovaVladimir B Seplyarskiy
Apr 1, 2014·Nucleic Acids Research·Hervé RouaultVincent Hakim
Sep 18, 2015·Molecular Biology and Evolution·Vladimir B SeplyarskiyRuslan A Soldatov
Jul 15, 2015·Molecular Biology and Evolution·Maria A BaranovaAlexey S Kondrashov
Apr 19, 2015·BMC Bioinformatics·Maochun QinJianmin Wang
Jan 22, 2015·Meta Gene·Christelle Melodelima, Stéphane Lobréaux
Feb 7, 2017·Genome Biology and Evolution·Julie M CridlandSantiago R Ramírez
Mar 8, 2017·PLoS Genetics·Thomas M ConnorPatrick H Maxwell
Dec 13, 2016·Genome Research·Vladimir B SeplyarskiyGeorgii A Bazykin
Jul 13, 2020·Genome Biology and Evolution·Valentina BurskaiaGeorgii A Bazykin
Jul 1, 2017·Molecular Genetics and Genomics : MGG·Sujata Mohanty, Radhika Khanna
Jun 25, 2021·Nature Reviews. Genetics·Vladimir B Seplyarskiy, Shamil Sunyaev
Jun 4, 2021·Genetics·Juraj Bergman, Mikkel Heide Schierup
Aug 1, 2014·Genome Research·Kelley Harris, Rasmus Nielsen

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