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More single-nucleotide mutations surround small insertions than small deletions in primates

Authors

  • Shengfeng Huang,

    1. Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
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    • Both authors contributed equally to this work.

  • Ting Yu,

    1. Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
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    • Both authors contributed equally to this work.

  • Zelin Chen,

    1. Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
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  • Shaochun Yuan,

    1. Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
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  • Shangwu Chen,

    1. Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
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  • Anlong Xu

    Corresponding author
    1. Guangdong Key Laboratory of Pharmaceutical Functional Genes, College of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, People's Republic of China
    • Department of Molecular Biology and Immunology, State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen University, 135 XinGangXi Road, Guangzhou, People's Republic of China.
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  • Communicated by David N. Cooper

Abstract

Early studies have shown that single-nucleotide mutation rates increase close to insertions and deletions, but it is not fully understood how natural selection shapes genome-wide patterns of indels and their nearby single-nucleotide mutations. In this study, we find that, in primates, more single-nucleotide mutations surround small insertions than small deletions. This pattern affects <150 base pair (bp) sequences close to indels and persists under different genomic properties, such as exon/intron/intergenic contexts, repeated/nonrepeated sequences, replication timing, recombination rates, indel density, and guanine–cytosine (GC) content. We propose two different, but not mutually exclusive, hypothetical mechanisms to explain the pattern. One mechanism is that the sequence context preferring insertion formation may also favor nucleotide substitutions. Another mechanism is related to a hypothesis in which indel heterozygosity tends to increase nearby nucleotide substitution rates. It means that if insertions spend more time in heterozygotes, insertions may accumulate more surrounding single-nucleotide changes. In conclusion, we characterize a special genome-wide evolutionary pattern for indels and nearby single-nucleotide changes. This pattern may be driven by natural selection and bias primates' genome evolution and phenotypic variations. Hum Mutat 33:1099–1106, 2012. © 2012 Wiley Periodicals, Inc.

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