Large-scale network analysis captures biological features of bacterial plasmids.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
15 05 2020
15 05 2020
Historique:
received:
03
10
2019
accepted:
23
04
2020
entrez:
17
5
2020
pubmed:
18
5
2020
medline:
13
8
2020
Statut:
epublish
Résumé
Many bacteria can exchange genetic material through horizontal gene transfer (HGT) mediated by plasmids and plasmid-borne transposable elements. Here, we study the population structure and dynamics of over 10,000 bacterial plasmids, by quantifying their genetic similarities and reconstructing a network based on their shared k-mer content. We use a community detection algorithm to assign plasmids into cliques, which correlate with plasmid gene content, bacterial host range, GC content, and existing classifications based on replicon and mobility (MOB) types. Further analysis of plasmid population structure allows us to uncover candidates for yet undescribed replicon genes, and to identify transposable elements as the main drivers of HGT at broad phylogenetic scales. Our work illustrates the potential of network-based analyses of the bacterial 'mobilome' and opens up the prospect of a natural, exhaustive classification framework for bacterial plasmids.
Identifiants
pubmed: 32415210
doi: 10.1038/s41467-020-16282-w
pii: 10.1038/s41467-020-16282-w
pmc: PMC7229196
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2452Subventions
Organisme : Medical Research Council
ID : MR/P007597/1
Pays : United Kingdom
Organisme : Wellcome Trust
ID : 19RX03
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R01356X/1
Pays : United Kingdom
Organisme : Department of Health
Pays : United Kingdom
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