Detecting lateral genetic transfer: A phylogenetic approach

Beiko, Robert G. and Ragan, Mark A. (2008). Detecting lateral genetic transfer: A phylogenetic approach. In Jonathan M. Keith (Ed.), Bioinformatics: Data, Sequence Analysis and Evolution (pp. 457-469) Totow, NJ, U.S.A.: Humana Press. doi:10.1007/978-1-60327-159-2-21


Author Beiko, Robert G.
Ragan, Mark A.
Title of chapter Detecting lateral genetic transfer: A phylogenetic approach
Title of book Bioinformatics: Data, Sequence Analysis and Evolution
Place of Publication Totow, NJ, U.S.A.
Publisher Humana Press
Publication Year 2008
Sub-type Research book chapter (original research)
DOI 10.1007/978-1-60327-159-2-21
Year available 2008
Series Methods in Molecular Biology
ISBN 978-1-58829-707-5
ISSN 1064-3745
Editor Jonathan M. Keith
Volume number 452
Chapter number 21
Start page 457
End page 469
Total pages 13
Total chapters 24
Collection year 2009
Language eng
Subjects B1
970106 Expanding Knowledge in the Biological Sciences
069999 Biological Sciences not elsewhere classified
Abstract/Summary 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.
Keyword Lateral genetic transfer
phylogenetic analysis
multiple sequence alignment
orthology
edit paths
Q-Index Code B1
Q-Index Status Provisional Code

 
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Created: Thu, 11 Jun 2009, 14:54:21 EST by Jennifer Greder on behalf of Institute for Molecular Bioscience