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Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
,
Steven Dunn,
Tristan Sreecharan,
Minna Vehkala,
Niko Välimäki,
Michael B. Prentice,
Amgad Ashour,
Oren Avram,
Tal Pupko,
Ulrich Dobrindt,
Ivan Literak,
Sebastian Guenther,
Katharina Schaufler,
Lothar H. Wieler,
Zong Zhiyong,
Samuel K. Sheppard,
James O. McInerney,
Jukka Corander
PLOS Genetics, Volume: 12, Issue: 9, Start page: e1006280
Swansea University Author:
Ben Pascoe
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© 2016 McNally et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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DOI (Published version): 10.1371/journal.pgen.1006280
Abstract
The use of whole-genome phylogenetic analysis has revolutionized our understandingof the evolution and spread of many important bacterial pathogens due to the highresolution view it provides. However, the majority of such analyses do not consider thepotential role of accessory genes when inferring e...
| Published in: | PLOS Genetics |
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| ISSN: | 1553-7404 |
| Published: |
Public Library of Science (PLoS)
2016
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| Online Access: |
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| URI: | https://cronfa.swan.ac.uk/Record/cronfa23502 |
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| Abstract: |
The use of whole-genome phylogenetic analysis has revolutionized our understandingof the evolution and spread of many important bacterial pathogens due to the highresolution view it provides. However, the majority of such analyses do not consider thepotential role of accessory genes when inferring evolutionary trajectories. Moreover,the recently discovered importance of the switching of gene regulatory elementssuggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide a super-resolution view into the evolutionof a bacterial population. Here we demonstrate this principle by applying it to aworldwide multi-host sample of the important pathogenic E. coli lineage ST131. Ourapproach reveals the existence of multiple circulating subtypes of the major drugresistantclade of ST131 and provides the first ever population level evidence of coregenome substitutions in gene regulatory regions associated with the acquisition andmaintenance of different accessory genome elements. |
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| College: |
Faculty of Medicine, Health and Life Sciences |
| Issue: |
9 |
| Start Page: |
e1006280 |