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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

Alan McNally, Yaara Oren, Darren Kelly, Ben Pascoe Orcid Logo, 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 Orcid Logo

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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...

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Published in: PLOS Genetics
ISSN: 1553-7404
Published: Public Library of Science (PLoS) 2016
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URI: https://cronfa.swan.ac.uk/Record/cronfa23502
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spelling 2020-10-22T18:59:43.2412503 v2 23502 2015-09-27 Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations 4660c0eb7e6bfd796cd749ae713ea558 0000-0001-6376-5121 Ben Pascoe Ben Pascoe true false 2015-09-27 PMSC 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. Journal Article PLOS Genetics 12 9 e1006280 Public Library of Science (PLoS) 1553-7404 31 8 2016 2016-08-31 10.1371/journal.pgen.1006280 COLLEGE NANME Medicine COLLEGE CODE PMSC Swansea University 2020-10-22T18:59:43.2412503 2015-09-27T23:55:15.2752913 Faculty of Medicine, Health and Life Sciences Swansea University Medical School - Medicine Alan McNally 1 Yaara Oren 2 Darren Kelly 3 Ben Pascoe 0000-0001-6376-5121 4 Steven Dunn 5 Tristan Sreecharan 6 Minna Vehkala 7 Niko Välimäki 8 Michael B. Prentice 9 Amgad Ashour 10 Oren Avram 11 Tal Pupko 12 Ulrich Dobrindt 13 Ivan Literak 14 Sebastian Guenther 15 Katharina Schaufler 16 Lothar H. Wieler 17 Zong Zhiyong 18 Samuel K. Sheppard 19 James O. McInerney 20 Jukka Corander 21 0023502-19012017102812.PDF journalpgen1006280.PDF 2017-01-19T10:28:12.7100000 Output 6757827 application/pdf Version of Record true 2017-01-19T00:00:00.0000000 © 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. true eng https://creativecommons.org/licenses/by/4.0/
title Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
spellingShingle Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
Ben Pascoe
title_short Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
title_full Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
title_fullStr Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
title_full_unstemmed Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
title_sort Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
author_id_str_mv 4660c0eb7e6bfd796cd749ae713ea558
author_id_fullname_str_mv 4660c0eb7e6bfd796cd749ae713ea558_***_Ben Pascoe
author Ben Pascoe
author2 Alan McNally
Yaara Oren
Darren Kelly
Ben Pascoe
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
format Journal article
container_title PLOS Genetics
container_volume 12
container_issue 9
container_start_page e1006280
publishDate 2016
institution Swansea University
issn 1553-7404
doi_str_mv 10.1371/journal.pgen.1006280
publisher Public Library of Science (PLoS)
college_str Faculty of Medicine, Health and Life Sciences
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hierarchy_top_id facultyofmedicinehealthandlifesciences
hierarchy_top_title Faculty of Medicine, Health and Life Sciences
hierarchy_parent_id facultyofmedicinehealthandlifesciences
hierarchy_parent_title Faculty of Medicine, Health and Life Sciences
department_str Swansea University Medical School - Medicine{{{_:::_}}}Faculty of Medicine, Health and Life Sciences{{{_:::_}}}Swansea University Medical School - Medicine
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description 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.
published_date 2016-08-31T03:27:43Z
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