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Appears in Collections:Biological and Environmental Sciences Journal Articles
Peer Review Status: Refereed
Title: The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages
Author(s): Nowell, Reuben W
Green, Sarah
Laue, Bridget E
Sharp, Paul M
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Keywords: bacterial genome fluctuation
horizontal gene transfer
Pseudomonas syringae
Issue Date: Jun-2014
Date Deposited: 17-Apr-2024
Citation: Nowell RW, Green S, Laue BE & Sharp PM (2014) The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages. <i>Genome Biology and Evolution</i>, 6 (6), pp. 1514-1529.
Abstract: Horizontal gene transfer (HGT) and gene loss are key processes in bacterial evolution. However, the role of gene gain and loss in the emergence and maintenance of ecologically differentiated bacterial populations remains an open question. Here, we use whole-genome sequence data to quantify gene gain and loss for 27 lineages of the plant-associated bacterium Pseudomonas syringae. We apply an extensive error-control procedure that accounts for errors in draft genome data and greatly improves the accuracy of patterns of gene occurrence among these genomes. We demonstrate a history of extensive genome fluctuation for this species and show that individual lineages could have acquired thousands of genes in the same period in which a 1% amino acid divergence accrues in the core genome. Elucidating the dynamics of genome fluctuation reveals the rapid turnover of gained genes, such that the majority of recently gained genes are quickly lost. Despite high observed rates of fluctuation, a phylogeny inferred from patterns of gene occurrence is similar to a phylogeny based on amino acid replacements within the core genome. Furthermore, the core genome phylogeny suggests that P. syringae should be considered a number of distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. Gained genes are transferred from a variety of sources, reflecting the depth and diversity of the potential gene pool available via HGT. Overall, our results provide further insights into the evolutionary dynamics of genome fluctuation and implicate HGT as a major factor contributing to the diversification of P. syringae lineages.
DOI Link: 10.1093/gbe/evu123
Rights: © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
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