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Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments

Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments
Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments
Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). While genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, i.e. host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of non-functional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a predictive marker of pathogenicity in bacteria.,For each genus containing at least one pathogen and one non-pathogen, we downloaded all available complete genomes (see Table S2). (Draft genomes were excluded because we observed that they varied substantially in length for a few species.) We then used Phylosift (Darling et al. 2014) to align 37 single copy orthologs identified as universal to all bacteria. Concatenated alignments of these loci were checked and corrected by eye.,
DRYAD
Charlesworth, Jane
733c16f1-61ea-433f-9016-b9739188a9b7
Murray, Gemma
86231714-9345-4c7c-895a-b354b6324d41
Miller, Eric
cd6b1fe7-7e37-44a9-99ed-792390489df1
Casey, Michael
3f316614-e401-4955-b400-0815e03af431
Lloyd, Catrin
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Gottschalk, Marcello
dcdba408-0e80-48d5-bdd3-57e74368745d
Tucker, Dan
2e88e67b-5056-4cee-937c-1dbc3522e4dc
Welch, John
49904884-0a6f-4734-9637-3c3d96fa96fa
Weinert, Lucy
f8661adb-f8b3-4cef-a269-4f9ca8b27c3f
Charlesworth, Jane
733c16f1-61ea-433f-9016-b9739188a9b7
Murray, Gemma
86231714-9345-4c7c-895a-b354b6324d41
Miller, Eric
cd6b1fe7-7e37-44a9-99ed-792390489df1
Casey, Michael
3f316614-e401-4955-b400-0815e03af431
Lloyd, Catrin
60f67b52-00a9-466b-9d75-1b487ea7c8f9
Gottschalk, Marcello
dcdba408-0e80-48d5-bdd3-57e74368745d
Tucker, Dan
2e88e67b-5056-4cee-937c-1dbc3522e4dc
Welch, John
49904884-0a6f-4734-9637-3c3d96fa96fa
Weinert, Lucy
f8661adb-f8b3-4cef-a269-4f9ca8b27c3f

Charlesworth, Jane and Miller, Eric (2020) Genome reduction is associated with bacterial pathogenicity across different scales of temporal and ecological divergence - between species core gene alignments. DRYAD doi:10.5061/dryad.nzs7h44qc [Dataset]

Record type: Dataset

Abstract

Emerging bacterial pathogens threaten global health and food security, and so it is important to ask whether these transitions to pathogenicity have any common features. We present a systematic study of the claim that pathogenicity is associated with genome reduction and gene loss. We compare broad-scale patterns across all bacteria, with detailed analyses of Streptococcus suis, an emerging zoonotic pathogen of pigs, which has undergone multiple transitions between disease and carriage forms. We find that pathogenicity is consistently associated with reduced genome size across three scales of divergence (between species within genera, and between and within genetic clusters of S. suis). While genome reduction is also found in mutualist and commensal bacterial endosymbionts, genome reduction in pathogens cannot be solely attributed to the features of their ecology that they share with these species, i.e. host restriction or intracellularity. Moreover, other typical correlates of genome reduction in endosymbionts (reduced metabolic capacity, reduced GC content, and the transient expansion of non-functional elements) are not consistently observed in pathogens. Together, our results indicate that genome reduction is a predictive marker of pathogenicity in bacteria.,For each genus containing at least one pathogen and one non-pathogen, we downloaded all available complete genomes (see Table S2). (Draft genomes were excluded because we observed that they varied substantially in length for a few species.) We then used Phylosift (Darling et al. 2014) to align 37 single copy orthologs identified as universal to all bacteria. Concatenated alignments of these loci were checked and corrected by eye.,

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More information

Published date: 1 January 2020

Identifiers

Local EPrints ID: 449319
URI: http://eprints.soton.ac.uk/id/eprint/449319
PURE UUID: 533d79ed-281c-42d0-bff6-03ba737efd69

Catalogue record

Date deposited: 24 May 2021 16:32
Last modified: 24 May 2021 16:33

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Contributors

Creator: Jane Charlesworth
Contributor: Gemma Murray
Creator: Eric Miller
Contributor: Michael Casey
Contributor: Catrin Lloyd
Contributor: Marcello Gottschalk
Contributor: Dan Tucker
Contributor: John Welch
Contributor: Lucy Weinert

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