Table_2_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...
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ftfrontimediafig:oai:figshare.com:article/7764827 2023-05-15T16:51:23+02:00 Table_2_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.s003 https://figshare.com/articles/Table_2_Genomic_Analyses_of_3_100_Nasopharyngeal_Pneumococci_Revealed_Significant_Differences_Between_Pneumococci_Recovered_in_Four_Different_Geographical_Regions_XLSX/7764827 unknown doi:10.3389/fmicb.2019.00317.s003 https://figshare.com/articles/Table_2_Genomic_Analyses_of_3_100_Nasopharyngeal_Pneumococci_Revealed_Significant_Differences_Between_Pneumococci_Recovered_in_Four_Different_Geographical_Regions_XLSX/7764827 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.s003 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 |
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Open Polar |
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Frontiers: Figshare |
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ftfrontimediafig |
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unknown |
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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_2_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_2_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX |
title_short |
Table_2_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX |
title_full |
Table_2_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX |
title_fullStr |
Table_2_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX |
title_full_unstemmed |
Table_2_Genomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.XLSX |
title_sort |
table_2_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.s003 https://figshare.com/articles/Table_2_Genomic_Analyses_of_3_100_Nasopharyngeal_Pneumococci_Revealed_Significant_Differences_Between_Pneumococci_Recovered_in_Four_Different_Geographical_Regions_XLSX/7764827 |
genre |
Iceland |
genre_facet |
Iceland |
op_relation |
doi:10.3389/fmicb.2019.00317.s003 https://figshare.com/articles/Table_2_Genomic_Analyses_of_3_100_Nasopharyngeal_Pneumococci_Revealed_Significant_Differences_Between_Pneumococci_Recovered_in_Four_Different_Geographical_Regions_XLSX/7764827 |
op_rights |
CC BY 4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmicb.2019.00317.s003 |
_version_ |
1766041502368137216 |