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Microbial Genomics logo Microbial Genomics

Volume 11, Issue 5

Pangenomics to understand prophage dynamics in the genus and the radiating lineages of Open Access

Abstract

Bacterial pathogens of the genus are responsible for soft-rot and blackleg diseases in a wide range of crops and have a global impact on food production. The emergence of new lineages and their competitive succession is frequently observed in species, in particular in . With a focus on one such recently emerged lineage in the Netherlands that causes blackleg in potatoes, we studied genome evolution in this genus using a reference-free graph-based pangenome approach. We clustered 1,977,865 proteins from 454 spp genomes into 30,156 homology groups. The genus pangenome is open, and its growth is mainly contributed by the accessory genome. Bacteriophage genes were enriched in the accessory genome and contributed 16% of the pangenome. Blackleg-causing isolates had increased genome size with high levels of prophage integration. To study the diversity and dynamics of these prophages across the pangenome, we developed an approach to trace prophages across genomes using pangenome homology group signatures. We identified lineage-specific as well as generalist bacteriophages infecting species. Our results capture the ongoing dynamics of mobile genetic elements, even in the clonal lineages. The observed lineage-specific prophage dynamics provide mechanistic insights into pangenome growth and contribution to the radiating lineages of .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): pangenome , Pectobacterium and prophages
Funding
This study was supported by the:
  • Ministerie van Economische Zaken (Award LWV20.235)
    • Principle Award Recipient: TheoA. J. van der Lee
© 2025 Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB Wageningen
  • 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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2025-05-24
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Pangenomics to understand prophage dynamics in the Pectobacterium genus and the radiating lineages of Pectobacterium brasiliense
M Gen 11, 001392 (2025); https://doi.org/10.1099/mgen.0.001392
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