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Compositional Bias is a Major Determinant of the Distribution Pattern and Abundance of Palindromes in Drosophila melanogaster

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Abstract

Palindromic sequences are important DNA motifs related to gene regulation, DNA replication and recombination, and thus, investigating the evolutionary forces shaping the distribution pattern and abundance of palindromes in the genome is substantially important. In this article, we analyzed the abundance of palindromes in the genome, and then explored the possible effects of several genomic factors on the palindrome distribution and abundance in Drosophila melanogaster. Our results show that the palindrome abundance in D. melanogaster deviates from random expectation and the uneven distribution of palindromes across the genome is associated with local GC content, recombination rate, and coding exon density. Our data suggest that base composition is the major determinant of the distribution pattern and abundance of palindromes and the correlation between palindrome density and recombination is a side-product of the effect of compositional bias on the palindrome abundance.

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Acknowledgments

We thank Xiu-Juan Zhao for her helpful discussions. This work was supported by grants from the National Natural Science Foundation (61102162), the Research Program of Higher Education of Inner Mongolia Autonomous Region (NJ10098) and the Innovation Fund of Inner Mongolia University of Science and Technology (2009NC005).

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Authors and Affiliations

  1. The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou, 014010, China

    Guoqing Liu

  2. School of Mathematics, Physics and Biological Engineering, Inner Mongolia University of Science and Technology, Baotou, 014010, China

    Guoqing Liu, Jia Liu & Bingjie Zhang

  3. Inner Mongolia Key Laboratory of Biomass-Energy Conversion, Baotou, 014010, China

    Guoqing Liu

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  1. Guoqing Liu
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  2. Jia Liu
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  3. Bingjie Zhang
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Correspondence to Guoqing Liu.

Electronic supplementary material

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239_2012_9527_MOESM1_ESM.doc

Supplementary Fig. 1 Comparison of palindrome abundance in the repeat-masked genome of D. melanogaster and random sequences. The size of palindromes is illustrated in the parentheses behind the title of ordinate. The ordinate represents the average of palindrome densities for both the non-overlapping 100-kb fragments of the repeat-masked D. melanogaster genome and the corresponding composition-constrained random sequences (see Methods for detail). Analysis of variance shows that the palindrome densities for natural sequences and random sequences are significantly different (1 × 10−31 < P < 0.008). (DOC 591 kb)

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Liu, G., Liu, J. & Zhang, B. Compositional Bias is a Major Determinant of the Distribution Pattern and Abundance of Palindromes in Drosophila melanogaster . J Mol Evol 75, 130–140 (2012). https://doi.org/10.1007/s00239-012-9527-y

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  • DOI: https://doi.org/10.1007/s00239-012-9527-y

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