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Microbial Genomics logo Microbial Genomics

Volume 10, Issue 7

: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events Open Access

Abstract

The use of -mers to capture genetic variation in bacterial genome-wide association studies (bGWAS) has demonstrated its effectiveness in overcoming the plasticity of bacterial genomes by providing a comprehensive array of genetic variants in a genome set that is not confined to a single reference genome. However, little attempt has been made to interpret -mers in the context of genome rearrangements, partly due to challenges in the exhaustive and high-throughput identification of genome structure and individual rearrangement events. Here, we present , a pre- and post-bGWAS processing methodology that leverages the unique properties of -mers to facilitate bGWAS for genome rearrangements. Repeat sequences are common instigators of genome rearrangements through intragenomic homologous recombination, and they are commonly found at rearrangement boundaries. Using whole-genome sequences, repeat sequences are replaced by short placeholder sequences, allowing the regions flanking repeats to be incorporated into relatively short -mers. Then, locations of flanking regions in significant -mers are mapped back to complete genome sequences to visualise genome rearrangements. Four case studies based on two bacterial species ( and ) and a simulated genome set are presented to demonstrate the ability to identify phenotype-associated rearrangements. is available at https://github.com/DorothyTamYiLing/GWarrange.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bacterial genome-wide association studies , Bordetella pertussis , Enterococcus faecium , genome rearrangement , k-mers and repeat sequences
Funding
This study was supported by the:
  • Leverhulme Trust (Award RPG-2019-373)
    • Principle Award Recipient: AndrewPreston
© 2024 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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2024-07-09
2025-05-19
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GWarrange: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events
M Gen 10, 001268 (2024); https://doi.org/10.1099/mgen.0.001268
/content/journal/mgen/10.1099/mgen.0.001268
/content/journal/mgen/10.1099/mgen.0.001268
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