Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations

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dc.contributor.author McNally, Alan
dc.contributor.author Oren, Yaara
dc.contributor.author Kelly, Darren
dc.contributor.author Pascoe, Ben
dc.contributor.author Dunn, Steven
dc.contributor.author Sreecharan, Tristan
dc.contributor.author Vehkala, Minna
dc.contributor.author Välimäki, Niko
dc.contributor.author Prentice, Michael B.
dc.contributor.author Ashour, Amgad
dc.contributor.author Avram, Oren
dc.contributor.author Pupko, Tal
dc.contributor.author Dobrindt, Ulrich
dc.contributor.author Literak, Ivan
dc.contributor.author Guenther, Sebastian
dc.contributor.author Schaufler, Katharina
dc.contributor.author Wieler, Lothar H.
dc.contributor.author Zhiyong, Zong
dc.contributor.author Sheppard, Samuel K.
dc.contributor.author McInerney, James O.
dc.contributor.author Corander, Jukka
dc.date.accessioned 2016-10-10T09:32:42Z
dc.date.available 2016-10-10T09:32:42Z
dc.date.issued 2016-09-12
dc.identifier.citation McNally, A., Oren, Y., Kelly, D., Pascoe, B., Dunn, S., Sreecharan, T., Vehkala, M., Välimäki, N., Prentice, M.B., Ashour, A. and Avram, O.(2016) 'Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations, PLoS Genetics, 12(9), e1006280 (16pp). doi: 10.1371/journal.pgen.1006280 en
dc.identifier.volume 12 en
dc.identifier.issued 9 en
dc.identifier.startpage 1 en
dc.identifier.endpage 16 en
dc.identifier.issn 1553-7390
dc.identifier.uri http://hdl.handle.net/10468/3169
dc.identifier.doi 10.1371/journal.pgen.1006280
dc.description.abstract The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug–resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements. en
dc.description.sponsorship Royal Society, United Kingdom (Project IE121459); European Research Council (Grant No. 239784); Academy of Finland (Grant No. 251170); German Research Foundation (Grant No. GU 1283/3) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Public Library of Science en
dc.rights Copyright: © 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. en
dc.rights.uri https://creativecommons.org/licenses/by/4.0/ en
dc.subject Phylogenetic analysis en
dc.subject Pathogen en
dc.subject Accessory genes en
dc.subject Evolution en
dc.title Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Michael Prentice, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: m.prentice@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Royal Society, United Kingdom
dc.contributor.funder European Research Council
dc.contributor.funder Academy of Finland
dc.contributor.funder German Research Foundation
dc.description.status Peer reviewed en
dc.identifier.journaltitle PLOS Genetics en
dc.internal.IRISemailaddress m.prentice@ucc.ie
dc.internal.IRISemailaddress m.prentice@ucc.ie en
dc.identifier.articleid e1006280


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Copyright: © 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. Except where otherwise noted, this item's license is described as Copyright: © 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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