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Detecting Lateral Genetic Transfer

A Phylogenetic Approach

  • Protocol
Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 452))

Abstract

Nucleotide sequences of microbial genomes provide evidence that genes have been shared among organisms, a phenomenon known as lateral genetic transfer (LGT). Hypotheses about the importance of LGT in the evolution and diversification of microbes can be tested by analyzing the extensive quantities of sequence data now available. Some analysis methods identify genes with sequence features that differ from those of the surrounding genome, whereas other methods are based on inference and comparison of phylogenetic trees. A large-scale search for LGT in 144 genomes using phylogenetic methods has revealed that although parent-to-offspring (“vertical”) inheritance has been the dominant mode of gene transmission, LGT has nonetheless been frequent, especially among organisms that are closely related or share the same habitat. This chapter outlines how bioinformatic and phylogenetic analyses can be built into a workflow to identify LGT among microbial genomes.

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Acknowledgments

Cheong Xin Chan, Nicholas Hamilton, Tim Harlow, and Jonathan Keith provided vital assistance in developing and executing the phylogenetic pipeline described in this chapter. We acknowledge the Australian Research Council (CE0348221) and the Australian Partnership for Advanced Computing for support.

Author information

Authors and Affiliations

  1. Dalhousie University, Halifax, Nova Scotia, Canada

    Robert G. Beiko (Faculty of Computer Science)

  2. ARC Centre of Excellence in Bioinformatics, and Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia

    Mark A. Ragan

Authors
  1. Robert G. Beiko
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  2. Mark A. Ragan
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Editor information

Editors and Affiliations

  1. School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia

    Jonathan M. Keith PhD

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© 2008 Humana Press, a part of Springer Science+Business Media, LLC

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Beiko, R.G., Ragan, M.A. (2008). Detecting Lateral Genetic Transfer. In: Keith, J.M. (eds) Bioinformatics. Methods in Molecular Biology™, vol 452. Humana Press. https://doi.org/10.1007/978-1-60327-159-2_21

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  • DOI: https://doi.org/10.1007/978-1-60327-159-2_21

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-707-5

  • Online ISBN: 978-1-60327-159-2

  • eBook Packages: Springer Protocols

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