Comparative Genome Metrics for 90 Staphylococcus Aureus Bacteriophages

Ana Gamkrelidze's comparative analysis of 90 Staphylococcus aureus bacteriophages, published in 2026, examines genome heterogeneity and codon usage bias across virulent, temperate, and prophage lineages. The dataset likely contains metrics for 30 virulent phages, 30 temperate phages, and 30 intact prophages, including genome size distributions, GC content, Codon Adaptation Index (CAI), and effective number of codons (Nc).

Use Cases

• Compare genome heterogeneity metrics between virulent and temperate phage lineages based on pairwise divergence and bimodal size distributions.
• Analyze codon usage bias across functional gene categories based on GC3, CAI, and Nc values.
• Investigate evolutionary trajectories of phage lineages based on recombinational connectivity and translational selection signals.

Strengths

• Includes 90 bacteriophage genomes categorized into three distinct lifestyle groups (30 virulent, 30 temperate, 30 prophages).
• Provides specific statistical metrics: median genome sizes (virulent ≈130 kb, temperate ≈43 kb), pairwise divergence percentages (59.1%), and significant Cliff's δ effects for codon usage.

Limitations

• Column-level documentation is absent; field semantics must be inferred after download.
• Row count is unknown, which may limit suitability assessment.
• Data is presented in a PDF format (462.1 KB), which may require extraction for computational analysis.

Provenance

Source

figshare

Collection Method

Comparative analysis of publicly available phage genome sequences.

Freshness

Last updated 2026-05-20 05:50:15; freshness should be verified.