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Journal of Molecular Evolution

, Volume 75, Issue 3–4, pp 130–140 | Cite as

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

  • Guoqing LiuEmail author
  • Jia Liu
  • Bingjie Zhang
Article

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.

Keywords

Palindrome GC content Recombination Gene conversion 

Notes

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).

Supplementary material

239_2012_9527_MOESM1_ESM.doc (591 kb)
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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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  1. 1.The Institute of Bioengineering and TechnologyInner Mongolia University of Science and TechnologyBaotouChina
  2. 2.School of Mathematics, Physics and Biological EngineeringInner Mongolia University of Science and TechnologyBaotouChina
  3. 3.Inner Mongolia Key Laboratory of Biomass-Energy ConversionBaotouChina

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