Table_1_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX

Understanding the structure of a bacterial population is essential in order to understand bacterial evolution. Estimating the core genome (those genes common to all, or nearly all, strains of a species) is a key component of such analyses. The size and composition of the core genome varies by datase...

Full description

Bibliographic Details
Main Authors: Andries J. van Tonder, James E. Bray, Keith A. Jolley, Melissa Jansen van Rensburg, Sigríður J. Quirk, Gunnsteinn Haraldsson, Martin C. J. Maiden, Stephen D. Bentley, Ásgeir Haraldsson, Helga Erlendsdóttir, Karl G. Kristinsson, Angela B. Brueggemann
Format: Dataset
Language:unknown
Published: 2019
Subjects:
Online Access:https://doi.org/10.3389/fmicb.2019.00317.s002
https://figshare.com/articles/Table_1_Genomic_Analyses_of_3_100_Nasopharyngeal_Pneumococci_Revealed_Significant_Differences_Between_Pneumococci_Recovered_in_Four_Different_Geographical_Regions_XLSX/7764824
id ftfrontimediafig:oai:figshare.com:article/7764824
record_format openpolar
spelling ftfrontimediafig:oai:figshare.com:article/7764824 2023-05-15T16:51:23+02:00 Table_1_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX Andries J. van Tonder James E. Bray Keith A. Jolley Melissa Jansen van Rensburg Sigríður J. Quirk Gunnsteinn Haraldsson Martin C. J. Maiden Stephen D. Bentley Ásgeir Haraldsson Helga Erlendsdóttir Karl G. Kristinsson Angela B. Brueggemann 2019-02-25T14:54:15Z https://doi.org/10.3389/fmicb.2019.00317.s002 https://figshare.com/articles/Table_1_Genomic_Analyses_of_3_100_Nasopharyngeal_Pneumococci_Revealed_Significant_Differences_Between_Pneumococci_Recovered_in_Four_Different_Geographical_Regions_XLSX/7764824 unknown doi:10.3389/fmicb.2019.00317.s002 https://figshare.com/articles/Table_1_Genomic_Analyses_of_3_100_Nasopharyngeal_Pneumococci_Revealed_Significant_Differences_Between_Pneumococci_Recovered_in_Four_Different_Geographical_Regions_XLSX/7764824 CC BY 4.0 CC-BY Microbiology Microbial Genetics Microbial Ecology Mycology next generation sequencing bacterial population structure core genome accessory genome pan-genome pneumococcus Dataset 2019 ftfrontimediafig https://doi.org/10.3389/fmicb.2019.00317.s002 2019-02-27T23:59:00Z Understanding the structure of a bacterial population is essential in order to understand bacterial evolution. Estimating the core genome (those genes common to all, or nearly all, strains of a species) is a key component of such analyses. The size and composition of the core genome varies by dataset, but we hypothesized that the variation between different collections of the same bacterial species would be minimal. To investigate this, we analyzed the genome sequences of 3,118 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (United States), and Maela (Thailand). The analyses revealed a “supercore” genome (genes shared by all 3,118 pneumococci) of 558 genes, although an additional 354 core genes were shared by pneumococci from Reykjavik, Southampton, and Boston. Overall, the size and composition of the core and pan-genomes among pneumococci recovered in Reykjavik, Southampton, and Boston were similar. Maela pneumococci were distinctly different in that they had a smaller core genome and larger pan-genome. The pan-genome of Maela pneumococci contained several >25 Kb sequence regions (flanked by pneumococcal genes) that were homologous to genomic regions found in other bacterial species. Overall, our work revealed that some subsets of the global pneumococcal population are highly heterogeneous, and our hypothesis was rejected. This is an important finding in terms of understanding genetic variation among pneumococci and is also an essential point of consideration before generalizing the findings from a single dataset to the wider pneumococcal population. Dataset Iceland Frontiers: Figshare
institution Open Polar
collection Frontiers: Figshare
op_collection_id ftfrontimediafig
language unknown
topic Microbiology
Microbial Genetics
Microbial Ecology
Mycology
next generation sequencing
bacterial population structure
core genome
accessory genome
pan-genome
pneumococcus
spellingShingle Microbiology
Microbial Genetics
Microbial Ecology
Mycology
next generation sequencing
bacterial population structure
core genome
accessory genome
pan-genome
pneumococcus
Andries J. van Tonder
James E. Bray
Keith A. Jolley
Melissa Jansen van Rensburg
Sigríður J. Quirk
Gunnsteinn Haraldsson
Martin C. J. Maiden
Stephen D. Bentley
Ásgeir Haraldsson
Helga Erlendsdóttir
Karl G. Kristinsson
Angela B. Brueggemann
Table_1_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX
topic_facet Microbiology
Microbial Genetics
Microbial Ecology
Mycology
next generation sequencing
bacterial population structure
core genome
accessory genome
pan-genome
pneumococcus
description Understanding the structure of a bacterial population is essential in order to understand bacterial evolution. Estimating the core genome (those genes common to all, or nearly all, strains of a species) is a key component of such analyses. The size and composition of the core genome varies by dataset, but we hypothesized that the variation between different collections of the same bacterial species would be minimal. To investigate this, we analyzed the genome sequences of 3,118 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (United States), and Maela (Thailand). The analyses revealed a “supercore” genome (genes shared by all 3,118 pneumococci) of 558 genes, although an additional 354 core genes were shared by pneumococci from Reykjavik, Southampton, and Boston. Overall, the size and composition of the core and pan-genomes among pneumococci recovered in Reykjavik, Southampton, and Boston were similar. Maela pneumococci were distinctly different in that they had a smaller core genome and larger pan-genome. The pan-genome of Maela pneumococci contained several >25 Kb sequence regions (flanked by pneumococcal genes) that were homologous to genomic regions found in other bacterial species. Overall, our work revealed that some subsets of the global pneumococcal population are highly heterogeneous, and our hypothesis was rejected. This is an important finding in terms of understanding genetic variation among pneumococci and is also an essential point of consideration before generalizing the findings from a single dataset to the wider pneumococcal population.
format Dataset
author Andries J. van Tonder
James E. Bray
Keith A. Jolley
Melissa Jansen van Rensburg
Sigríður J. Quirk
Gunnsteinn Haraldsson
Martin C. J. Maiden
Stephen D. Bentley
Ásgeir Haraldsson
Helga Erlendsdóttir
Karl G. Kristinsson
Angela B. Brueggemann
author_facet Andries J. van Tonder
James E. Bray
Keith A. Jolley
Melissa Jansen van Rensburg
Sigríður J. Quirk
Gunnsteinn Haraldsson
Martin C. J. Maiden
Stephen D. Bentley
Ásgeir Haraldsson
Helga Erlendsdóttir
Karl G. Kristinsson
Angela B. Brueggemann
author_sort Andries J. van Tonder
title Table_1_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX
title_short Table_1_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX
title_full Table_1_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX
title_fullStr Table_1_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX
title_full_unstemmed Table_1_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX
title_sort table_1_genomic analyses of >3,100 nasopharyngeal pneumococci revealed significant differences between pneumococci recovered in four different geographical regions.xlsx
publishDate 2019
url https://doi.org/10.3389/fmicb.2019.00317.s002
https://figshare.com/articles/Table_1_Genomic_Analyses_of_3_100_Nasopharyngeal_Pneumococci_Revealed_Significant_Differences_Between_Pneumococci_Recovered_in_Four_Different_Geographical_Regions_XLSX/7764824
genre Iceland
genre_facet Iceland
op_relation doi:10.3389/fmicb.2019.00317.s002
https://figshare.com/articles/Table_1_Genomic_Analyses_of_3_100_Nasopharyngeal_Pneumococci_Revealed_Significant_Differences_Between_Pneumococci_Recovered_in_Four_Different_Geographical_Regions_XLSX/7764824
op_rights CC BY 4.0
op_rightsnorm CC-BY
op_doi https://doi.org/10.3389/fmicb.2019.00317.s002
_version_ 1766041502876696576