title: Compositional bias is a major determinant of the distribution pattern and abundance of palindromes in Drosophila melanogaster.
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.
authors.affiliation: The Institute of Bioengineering and Technology, Inner Mongolia University of Science and Technology, Baotou 014010, China. gqliu1010@163.com
authors.forename: Guoqing
authors.initials: G
authors.lastname: Liu
authors.forename: Jia
authors.initials: J
authors.lastname: Liu
authors.forename: Bingjie
authors.initials: B
authors.lastname: Zhang
mesh_terms: D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D004331:Drosophila melanogaster / Q000235:genetics*; D005091:Exons / Q000235:genetics; D049750:Genome, Insect; D023281:Genomics; D055029:Inverted Repeat Sequences; D008969:Molecular Sequence Data; D011995:Recombination, Genetic; D017422:Sequence Analysis, DNA; D018709:Statistics, Nonparametric