SPP 2330

GROUP KUPCZOK / Associated Project

Phage evolutionary rates estimated from genomes and metagenomes

Phages are highly abundant and important contributors to bacterial ecology and evolution and to biogeochemical cycles. The genomes of bacteriophages are highly diverse, with a high degree of variation even among closely related phages. Different evolutionary processes generate and maintain phage genome diversity: de novo mutation, recombination between related genomes, selection, and gene flow between subpopulations. Since this diversity crucially affects the outcome of phage-host interaction, it is highly interesting to understand the interplay of these evolutionary processes, how they contribute to the diversity of closely related phages, and how this diversity is distributed across space and time.

The recent increase in metagenomic sampling efforts made numerous viromes, i.e., viral metagenomes, from different environments publicly available, including time-series data. In this project, we will develop novel computational approaches to inventory the diversity within phage populations and to estimate evolutionary processes based on this diversity.

Principal Investigator(s)

Dr. Anne Kupczok
Bioinformatics Group
Wageningen University & Research

E-Mail: anne.kupczok@wur.nl
Homepage: https://annecmg.github.io/


PhD student(s)



  • Kupczok A, Bailey ZM, Refardt D, Wendling CC. Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages. Microb Genom. 2022 Nov;8(11):mgen000915. doi: 10.1099/mgen.0.000915.
  • Weidenbach K, Wolf S, Kupczok A, Kern T, Fischer MA, Reetz J, Urbańska N, Künzel S, Schmitz RA, Rother M. Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales. Viruses. 2021 Sep 26;13(10):1934. doi: 10.3390/v13101934.
  • Kupczok A, Dagan T. 2019. Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage. Viruses 11:720.
  • Kupczok A, Neve H, Huang KD, Hoeppner MP, Heller KJ, Franz CMAP, Dagan T. 2018. Rates of mutation and recombination in Siphoviridae phage genome evolution over three decades. Mol Biol Evol 35:1147–1159.