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Viral DNA polymerases (DNAPs) are frequently swapped between different phage families, suggesting adaptation to avoid host defenses or replicon incompatibility. This study identifies multiple instances of DNAP gene exchange in tailed phages.

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Area of Science:

  • Virology
  • Molecular Biology
  • Genomics

Background:

  • Double-stranded DNA viruses (Duplodnaviria) exhibit diverse DNA replication protein repertoires.
  • DNA polymerases (DNAPs) are crucial for DNA replication and are classified into four families (A-D).
  • Previous work identified DNAP family swaps in the order Crassvirales.

Purpose of the Study:

  • To investigate the occurrence and patterns of DNA polymerase (DNAP) gene swapping in tailed phages (Caudoviricetes).
  • To explore the evolutionary implications of DNAP gene exchange within viral genomes.

Main Methods:

  • Comparative genomic analysis of tailed phage genomes.
  • Identification and classification of DNA polymerase families within viral genomes.
  • Phylogenetic analysis to trace the evolutionary history of DNAP genes.

Main Results:

  • Four new groups of tailed phages exhibiting evidence of DNAP gene swapping were identified.
  • Swaps occurred between DNAP families A, B, and C, as well as within family A subfamilies.
  • DNAP gene swaps occurred "in situ" without altering the organization of surrounding genes.
  • Two novel, divergent groups of family A DNAPs were discovered in some phage genomes.

Conclusions:

  • DNAP swapping is a recurrent evolutionary event in tailed phages, driven by selection pressures.
  • Potential drivers include evading host antiviral mechanisms and overcoming replicon incompatibility.
  • The identified novel DNAPs may play roles in viral replication or adaptation.