Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems

Christopher M Bellas*, Declan C Schroeder, Arwyn Edwards, Gary Barker, Alexandre M Anesio

*Corresponding author for this work

Research output: Contribution to journalArticle (Academic Journal)peer-review

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Bacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large geographical distances and several years apart, conversely suggesting many are stably maintained. Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. By repeatedly reconstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants co-exist for each module in each location, however, the dominant variant shuffles independently in each module. These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage.
Original languageEnglish
Article number4403 (2020)
Number of pages10
JournalNature Communications
Publication statusPublished - 2 Sep 2020


  • metagenomics
  • phage biology
  • viral evolution
  • virus-host interactions


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