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Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility
The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8715431/ https://www.ncbi.nlm.nih.gov/pubmed/34499026 http://dx.doi.org/10.1099/mgen.0.000650 |
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author | Hall, Rebecca J. Whelan, Fiona J. Cummins, Elizabeth A. Connor, Christopher McNally, Alan McInerney, James O. |
author_facet | Hall, Rebecca J. Whelan, Fiona J. Cummins, Elizabeth A. Connor, Christopher McNally, Alan McInerney, James O. |
author_sort | Hall, Rebecca J. |
collection | PubMed |
description | The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships. |
format | Online Article Text |
id | pubmed-8715431 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-87154312021-12-29 Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility Hall, Rebecca J. Whelan, Fiona J. Cummins, Elizabeth A. Connor, Christopher McNally, Alan McInerney, James O. Microb Genom Research Articles The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships. Microbiology Society 2021-09-09 /pmc/articles/PMC8715431/ /pubmed/34499026 http://dx.doi.org/10.1099/mgen.0.000650 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial 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 Hall, Rebecca J. Whelan, Fiona J. Cummins, Elizabeth A. Connor, Christopher McNally, Alan McInerney, James O. Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility |
title | Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility |
title_full | Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility |
title_fullStr | Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility |
title_full_unstemmed | Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility |
title_short | Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility |
title_sort | gene-gene relationships in an escherichia coli accessory genome are linked to function and mobility |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8715431/ https://www.ncbi.nlm.nih.gov/pubmed/34499026 http://dx.doi.org/10.1099/mgen.0.000650 |
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