Compositional Bias is a Major Determinant of the Distribution Pattern and Abundance of Palindromes in Drosophila melanogaster
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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.
KeywordsPalindrome GC content Recombination Gene conversion
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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