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

dc.contributor.authorMcNally, Alan
dc.contributor.authorOren, Yaara
dc.contributor.authorKelly, Darren
dc.contributor.authorPascoe, Ben
dc.contributor.authorDunn, Steven
dc.contributor.authorSreecharan, Tristan
dc.contributor.authorVehkala, Minna
dc.contributor.authorVälimäki, Niko
dc.contributor.authorPrentice, Michael B.
dc.contributor.authorAshour, Amgad
dc.contributor.authorAvram, Oren
dc.contributor.authorPupko, Tal
dc.contributor.authorDobrindt, Ulrich
dc.contributor.authorLiterak, Ivan
dc.contributor.authorGuenther, Sebastian
dc.contributor.authorSchaufler, Katharina
dc.contributor.authorWieler, Lothar H.
dc.contributor.authorZhiyong, Zong
dc.contributor.authorSheppard, Samuel K.
dc.contributor.authorMcInerney, James O.
dc.contributor.authorCorander, Jukka
dc.contributor.funderRoyal Society, United Kingdom
dc.contributor.funderEuropean Research Council
dc.contributor.funderAcademy of Finland
dc.contributor.funderGerman Research Foundation
dc.date.accessioned2016-10-10T09:32:42Z
dc.date.available2016-10-10T09:32:42Z
dc.date.issued2016-09-12
dc.description.abstractThe 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.sponsorshipRoyal 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.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleide1006280
dc.identifier.citationMcNally, 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.1006280en
dc.identifier.doi10.1371/journal.pgen.1006280
dc.identifier.endpage16en
dc.identifier.issn1553-7390
dc.identifier.issued9en
dc.identifier.journaltitlePLOS Geneticsen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/3169
dc.identifier.volume12en
dc.language.isoenen
dc.publisherPublic Library of Scienceen
dc.rightsCopyright: © 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.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectPhylogenetic analysisen
dc.subjectPathogenen
dc.subjectAccessory genesen
dc.subjectEvolutionen
dc.titleCombined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populationsen
dc.typeArticle (peer-reviewed)en
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