Avoidance of Long Mononucleotide Repeats in Codon Pair Usage

Gu, Tingting; Tan, Shengjun; Gou, Xiaoxi; Araki, Hitoshi; Tian, Dacheng (2010). Avoidance of Long Mononucleotide Repeats in Codon Pair Usage. Genetics, 186(3), pp. 1077-1084. Bethesda, Md.: Genetics Society of America 10.1534/genetics.110.121137

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Protein is an essential component for life, and its synthesis is mediated by codons in any organisms on earth. While some codons encode the same amino acid, their usage is often highly biased. There are many factors that can cause the bias, but a potential effect of mononucleotide repeats, which are known to be highly mutable, on codon usage and codon pair preference is largely unknown. In this study we performed a genomic survey on the relationship between mononucleotide repeats and codon pair bias in 53 bacteria, 68 archaea, and 13 eukaryotes. By distinguishing the codon pair bias from the codon usage bias, four general patterns were revealed: strong avoidance of five or six mononucleotide repeats in codon pairs; lower observed/expected (o/e) ratio for codon pairs with C or G repeats (C/G pairs) than that with A or T repeats (A/T pairs); a negative correlation between genomic GC contents and the o/e ratios, particularly for C/G pairs; and avoidance of C/G pairs in highly conserved genes. These results support natural selection against long mononucleotide repeats, which could induce frameshift mutations in coding sequences. The fact that these patterns are found in all kingdoms of life suggests that this is a general phenomenon in living organisms. Thus, long mononucleotide repeats may play an important role in base composition and genetic stability of a gene and gene functions.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Biology > Institute of Ecology and Evolution (IEE)

UniBE Contributor:

Araki, Hitoshi






Genetics Society of America




Factscience Import

Date Deposited:

04 Oct 2013 14:17

Last Modified:

17 Mar 2015 19:22

Publisher DOI:


Web of Science ID:



https://boris.unibe.ch/id/eprint/5250 (FactScience: 209981)

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