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Volume 7, Issue 9

Gene-gene relationships in an accessory genome are linked to function and mobility Open Access

Abstract

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 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Escherichia coli , evolution , gene co-occurrence and pangenome
Funding
This study was supported by the:
  • h2020 marie skłodowska-curie actions (Award 793818)
    • Principle Award Recipient: FionaJ Whelan
  • wellcome trust (Award Wellcome Midas DTP)
    • Principle Award Recipient: ChristopherConnor
  • wellcome trust (Award Wellcome AAMR DTP)
    • Principle Award Recipient: ElizabethA Cummins
  • biotechnology and biological sciences research council (Award BB/N018044/2)
    • Principle Award Recipient: JamesO McInerney
© 2021 The Authors
  • 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.
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2021-09-09
2024-04-24
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Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility
M Gen 7, 000650 (2021); https://doi.org/10.1099/mgen.0.000650
/content/journal/mgen/10.1099/mgen.0.000650
/content/journal/mgen/10.1099/mgen.0.000650
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