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 University of Helsinki, Department of Mathematics and Statistics en
dc.contributor University of Helsinki, Genome-Scale Biology (GSB) Research Program en
dc.contributor University of Helsinki, Department of Mathematics and Statistics en
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 Zong Zhiyong,
dc.contributor.author Sheppard, Samuel K.
dc.contributor.author McInerney, James O.
dc.contributor.author Corander, Jukka
dc.date.accessioned 2016-11-21T09:51:05Z
dc.date.available 2016-11-21T09:51:05Z
dc.date.issued 2016-09
dc.identifier.citation McNally , A , Oren , Y , Kelly , D , Pascoe , B , Dunn , S , Sreecharan , T , Vehkala , M , Välimäki , N , Prentice , M B , Ashour , A , Avram , O , Pupko , T , Dobrindt , U , Literak , I , Guenther , S , Schaufler , K , Wieler , L H , Zong Zhiyong , Sheppard , S K , McInerney , J O & Corander , J 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 , vol. 12 , no. 9 , 1006280 . DOI: 10.1371/journal.pgen.1006280 en
dc.identifier.issn 1553-7404
dc.identifier.other PURE: 71906514
dc.identifier.other PURE UUID: 1a5e05ee-ec65-4eed-99d1-3f2745109625
dc.identifier.other WOS: 000386069000016
dc.identifier.other Scopus: 84990240770
dc.identifier.uri http://hdl.handle.net/10138/169214
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.format.extent 16
dc.language.iso eng
dc.relation.ispartof PLoS Genetics
dc.rights en
dc.subject RESISTANT ESCHERICHIA-COLI en
dc.subject PHYLOGENETIC TREES en
dc.subject ST131 CLONE en
dc.subject OUTBREAK en
dc.subject ANNOTATION en
dc.subject DIVERSITY en
dc.subject EMERGENCE en
dc.subject PLASMIDS en
dc.subject 1184 Genetics, developmental biology, physiology 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
dc.description.version Peer reviewed
dc.identifier.doi https://doi.org/10.1371/journal.pgen.1006280
dc.type.uri info:eu-repo/semantics/other
dc.type.uri info:eu-repo/semantics/publishedVersion
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