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Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types
The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E....
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9836092/ https://www.ncbi.nlm.nih.gov/pubmed/36748558 http://dx.doi.org/10.1099/mgen.0.000903 |
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author | Cummins, Elizabeth A. Hall, Rebecca J. Connor, Chris McInerney, James O. McNally, Alan |
author_facet | Cummins, Elizabeth A. Hall, Rebecca J. Connor, Chris McInerney, James O. McNally, Alan |
author_sort | Cummins, Elizabeth A. |
collection | PubMed |
description | The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification, depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that ongoing gene gain and loss in the E. coli pangenome is sequence type-specific, which may be a consequence of distinct sequence type-specific evolutionary drivers. |
format | Online Article Text |
id | pubmed-9836092 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-98360922023-01-13 Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types Cummins, Elizabeth A. Hall, Rebecca J. Connor, Chris McInerney, James O. McNally, Alan Microb Genom Research Articles The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification, depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that ongoing gene gain and loss in the E. coli pangenome is sequence type-specific, which may be a consequence of distinct sequence type-specific evolutionary drivers. Microbiology Society 2022-11-23 /pmc/articles/PMC9836092/ /pubmed/36748558 http://dx.doi.org/10.1099/mgen.0.000903 Text en © 2022 The Authors https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution. |
spellingShingle | Research Articles Cummins, Elizabeth A. Hall, Rebecca J. Connor, Chris McInerney, James O. McNally, Alan Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types |
title | Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types |
title_full | Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types |
title_fullStr | Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types |
title_full_unstemmed | Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types |
title_short | Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types |
title_sort | distinct evolutionary trajectories in the escherichia coli pangenome occur within sequence types |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9836092/ https://www.ncbi.nlm.nih.gov/pubmed/36748558 http://dx.doi.org/10.1099/mgen.0.000903 |
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