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Volume 11, Issue 5

Gene conversion and duplication contribute to genetic variation in an outbreak of Open Access

Abstract

Repeats are the most diverse and dynamic but also the least well-understood component of microbial genomes. For all we know, repeat-associated mutations such as duplications, deletions, inversions and gene conversion might be as common as point mutations, but because of short-read myopia and methodological bias, they have received much less attention. Long-read DNA sequencing opens the perspective of resolving repeats and systematically investigating the mutations they induce. For this study, we assembled the genomes of 16 closely related strains of the bacterial pathogen from Pacific Biosciences HiFi reads, with the aim of characterizing the full spectrum of DNA polymorphisms. We found that complete and accurate genomes can be assembled from HiFi reads, with read size being the main limitation in the presence of duplications. By combining a reference-free pangenome graph with extensive repeat annotation, we identified 110 variants, 58 of which could be assigned to repeat-associated mutational mechanisms such as strand slippage and homologous recombination. Whilst recombination events were less frequent than point mutations, they affected large regions and introduced multiple variants at once, as shown by three gene conversion events and a duplication of 7.3 kb that involved and , two genes possibly involved in immune subversion. The vast majority of variants were present in single isolates, such that phylogenetic resolution was only marginally increased when estimating a tree from complete genomes. Our study shows that the contribution of repeat-associated mechanisms of mutation can be similar to that of point mutations at the microevolutionary scale of an outbreak. A large reservoir of unstudied genetic variation in this ‘monomorphic’ bacterial pathogen awaits investigation.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): long-read sequencing , pangenome graph , PE/PPE genes , phylogenetic resolution , recombination and repeats
Funding
This study was supported by the:
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Award CRSII5_213514)
    • Principle Award Recipient: SebastienGagneux
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Award 320030-227432)
    • Principle Award Recipient: SebastienGagneux
  • European Research Council (Award 883582)
    • Principle Award Recipient: SebastienGagneux
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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Gene conversion and duplication contribute to genetic variation in an outbreak of Mycobacterium tuberculosis
M Gen 11, 001396 (2025); https://doi.org/10.1099/mgen.0.001396
/content/journal/mgen/10.1099/mgen.0.001396
/content/journal/mgen/10.1099/mgen.0.001396
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