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Volume 9, Issue 5

Challenges in prokaryote pangenomics Open Access

Abstract

Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche. Predicting the presence or absence of genes can be a highly error-prone process that can confound efforts to understand the dynamics of horizontal gene transfer. This review discusses both the challenges in accurately constructing a pangenome and the potential consequences errors can have on downstream analyses. We hope that by summarizing these issues researchers will be able to avoid potential pitfalls, leading to improved bacterial pangenome analyses.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bacteria , gene annotation , horizontal gene transfer and pangenome
Funding
This study was supported by the:
  • European Research Council (Award 742158)
    • Principle Award Recipient: JukkaCorander
  • Norges Forskningsråd (Award 2999131)
    • Principle Award Recipient: GerryTonkin-Hill
© 2023 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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2023-05-25
2024-04-29
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Challenges in prokaryote pangenomics
M Gen 9, 001021 (2023); https://doi.org/10.1099/mgen.0.001021
/content/journal/mgen/10.1099/mgen.0.001021
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