Scaling up the phylogenetic detection of lateral gene transfer events

Chan, Cheong Xin, Beiko, Robert G. and Ragan, Mark A. (2017). Scaling up the phylogenetic detection of lateral gene transfer events. In Bioinformatics (pp. 421-432) New York, United States: Humana Press. doi:10.1007/978-1-4939-6622-6_16


Author Chan, Cheong Xin
Beiko, Robert G.
Ragan, Mark A.
Title of chapter Scaling up the phylogenetic detection of lateral gene transfer events
Title of book Bioinformatics
Place of Publication New York, United States
Publisher Humana Press
Publication Year 2017
Sub-type Research book chapter (original research)
DOI 10.1007/978-1-4939-6622-6_16
Open Access Status Not yet assessed
ISBN 9781493966202
9781493966226
ISSN 1064-3745
Volume number 1525
Chapter number 16
Start page 421
End page 432
Total pages 12
Total chapters 18
Subjects 1312 Molecular Biology
1311 Genetics
Abstract/Summary Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from sequenced genomes typically involves a series of steps in which homologous sequences are identified and aligned, phylogenetic trees are inferred, and their topologies are compared to identify unexpected or conflicting relationships. These types of approach have been used to elucidate the nature and extent of LGT and its physiological and ecological consequences throughout the Tree of Life. Advances in DNA sequencing technology have led to enormous increases in the number of sequenced genomes, including ultra-deep sampling of specific taxonomic groups and single cell-based sequencing of unculturable “microbial dark matter.” Environmental shotgun sequencing enables the study of LGT among organisms that share the same habitat. This abundance of genomic data offers new opportunities for scientific discovery, but poses two key problems. As ever more genomes are generated, the assembly and annotation of each individual genome receives less scrutiny; and with so many genomes available it is tempting to include them all in a single analysis, but thousands of genomes and millions of genes can overwhelm key algorithms in the analysis pipeline. Identifying LGT events of interest therefore depends on choosing the right dataset, and on algorithms that appropriately balance speed and accuracy given the size and composition of the chosen set of genomes.
Keyword Horizontal genetic transfer
Lateral genetic transfer
Multiple sequence alignment
Orthology
Phylogenetic analysis
Phylogenomics
Q-Index Code B1
Q-Index Status Provisional Code
Institutional Status UQ

 
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