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Computational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content

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Pseudogenes

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1167))

Abstract

Spectral entropy and GC content analyses reveal comprehensive structural features of DNA sequences. To illustrate the significance of these features, we analyze the β-esterase gene cluster, including the Est-6 gene and the ψEst-6 putative pseudogene, in seven species of the Drosophila melanogaster subgroup. The spectral entropies show distinctly lower structural ordering for ψEst-6 than for Est-6 in all species studied. However, entropy accumulation is not a completely random process for either gene and it shows to be nucleotide dependent. Furthermore, GC content in synonymous positions is uniformly higher in Est-6 than in ψEst-6, in agreement 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 ψEst-6 and Est-6 after the duplication event. The data obtained show the relevance and significance of entropy and GC content analyses for pseudogene identification and for the comparative study of gene–pseudogene evolution.

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Acknowledgment

We are grateful to Elena Balakireva for encouragement and help.

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Authors and Affiliations

  1. Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA

    Evgeniy S. Balakirev Ph.D. & Francisco J. Ayala

  2. A. V. Zhirmunsky Institute of Marine Biology, Russian Academy of Science, Far Eastern Branch, ul. Palchevskogo 17, 690041, Vladivostok, Russia

    Evgeniy S. Balakirev Ph.D.

  3. Theoretical Department of Division for Perspective Investigations, Troitsk Institute of Innovation and Thermonuclear Investigations (TRINITI), Troitsk, Moscow, Russia

    Vladimir R. Chechetkin

  4. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia

    Vladimir R. Chechetkin

  5. School of Physics, University of Sydney, Sydney, Australia

    Vasily V. Lobzin

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  1. Evgeniy S. Balakirev Ph.D.
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  2. Vladimir R. Chechetkin
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  3. Vasily V. Lobzin
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  4. Francisco J. Ayala
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Correspondence to Evgeniy S. Balakirev Ph.D. .

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  1. Istituto Toscano Tumori, Pisa, Italy

    Laura Poliseno

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Balakirev, E.S., Chechetkin, V.R., Lobzin, V.V., Ayala, F.J. (2014). Computational Methods of Identification of Pseudogenes Based on Functionality: Entropy and GC Content. In: Poliseno, L. (eds) Pseudogenes. Methods in Molecular Biology, vol 1167. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0835-6_4

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  • DOI: https://doi.org/10.1007/978-1-4939-0835-6_4

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