Prediction of prophages and defense systems in MicroScope

Bacteriophages (phages) are the most abundant viruses on the planet. The majority of free-living prokaryotic species are thought to be infected by phages, as evidenced by the widespread presence of prophages in prokaryotic genomes. A prophage is a bacteriophage genome that is integrated into the genome of a prokaryote. Given the abundance and diversity of phages, prokaryotes have developed multiple antiviral mechanisms to fight against phages, and several of these antiviral systems can co-occur in the same strain.

The Comparative genomics menu of the MicroScope platform has been enhanced with a new page dedicated to Prophage & Defense System Prediction.

  • Prophage regions are identified with the tool Phigaro (Starikova et al, 2020). You can access to the list of prophage regions predicted for a given organism and explore the gene content of a prophage of interest. These genes may be associated to prokaryotic viral orthologous groups (pVOGs).
  • DefenseFinder (Tesson et al., 2022) is used to automatically detects known antiviral systems in prokaryotic genomes using 229 models. You can access to the list of defense systems predicted for a given organism and explore their gene content.

These prediction results can be queried in the Search by keyword functionality. They are also cross referenced in the pangenome-RGP page. Indeed for each region of genomic plasticity (RGP), we indicate if this region contains predicted prophages or defense systems.

Elizaveta V Starikova and others, Phigaro: high-throughput prophage sequence annotation, Bioinformatics, Volume 36, Issue 12, 15 June 2020, Pages 3882–3884,

Tesson, F., Hervé, A., Mordret, E. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat Commun 13, 2561 (2022).

Prediction of prophages and defense systems in MicroScope
Tagged on: