Codon bias is a major factor explaining phage evolution in translationally biased hosts.

Area of Science:

• Microbiology
• Genomics
• Evolutionary Biology

Background:

• Studying bacteriophage diversity requires quantitative methods to analyze phage differences.
• Challenges include small genome sizes and complex comparative genomics due to lateral gene transfer.

Purpose of the Study:

• To analyze codon bias in bacteriophage genomes to understand host-imposed selective pressures.
• To propose a new phage classification system based on adaptation patterns.
• To investigate host adaptation in phage capsid and other functional genes.

Main Methods:

• Large-scale codon bias analysis of 116 DNA phages from 11 translationally biased bacterial hosts.
• Development of a computational method for comparing phages based on homologous proteins.
• Detailed analysis of the Microviridae phage family.

Main Results:

• Phage genomes consistently exhibit codon selective pressure from their hosts.
• Capsid genes are most impacted by host translational bias across all phages.
• Coliphages show adaptation in virion morphogenesis, host interaction, and ssDNA binding genes.
• Adaptation significantly affects both large and small phages.

Conclusions:

• Phage classification based on adaptation patterns offers a novel approach.
• Host translational bias plays a crucial role in shaping phage genome evolution.
• Phage adaptation patterns do not necessarily align with bacterial phylogeny, as seen in Microviridae.