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MBE Advance Access published online on June 22, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi197
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted June 14, 2005

Research Article

Entropy and GC Content in the {beta}-Esterase Gene Cluster of the Drosophila melanogaster Subgroup

Evgeniy S. Balakirev 1, Vladimir R. Chechetkin 2, Vasily V. Lobzin 2, and Francisco J. Ayala 3*

1 Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA; Academy of Ecology, Marine Biology, and Biotechnology, Far Eastern State University, Vladivostok, Russia and Institute of Marine Biology, Vladivostok, Russia
2 Troitsk Institute of Innovation and Thermonuclear Investigations (TRINITI), Theoretical Department of Division for Perspective Investigations, Moscow Region, Russia
3 Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA

* To whom correspondence should be addressed.
Francisco J. Ayala, E-mail: fjayala{at}uci.edu


  Abstract

We perform spectral entropy and GC-content analyses in the {beta}-esterase gene cluster, including the Est-6 gene and the {psi}Est-6 putative pseudogene, in seven species of the Drosophila melanogaster species subgroup. {psi}Est-6 combines features of functional and nonfunctional genes. The spectral entropies show distinctly lower structural ordering for {psi}Est-6 than for Est-6 in all species studied. Our observations agree with previous results for D. melanogaster, and provide additional support to our hypothesis that after the duplication event Est-6 retained the esterase coding function and its role during copulation, while {psi}Est-6 lost that function but now operates in conjunction with Est-6 as an intergene. Entropy accumulation is not a completely random process for either gene. Structural entropy is nucleotide-dependent. The relative normalized deviations for structural entropy are higher for G than for C nucleotides. The entropy values are similar for Est-6 and {psi}Est-6 in the case of A and T, but are lower for Est-6 in the case of G and C. The GC content in synonymous positions is uniformly higher in Est-6 than in {psi}Est-6, which agrees with the reduced GC content generally observed in pseudogenes and nonfunctional sequences. The observed differences in entropy and GC content reflect an evolutionary shift associated with the process of pseudogenization and subsequent functional divergence of {psi}Est-6 and Est-6 after the duplication event.

Keywords: Drosophila melanogaster subgroup; {beta}-esterase gene cluster; Est-6; {psi}Est-6; entropy; GC content.
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