# Contrasting genome composition and codon usage in Listeria monocytogenes temperate versus virulent phages

## TL;DR

The study finds that temperate and virulent phages infecting Listeria monocytogenes differ in genome size, gene length, and codon usage, which may affect their host adaptation and potential biotechnological applications.

## Contribution

The study reveals distinct codon usage patterns and genome characteristics between temperate and virulent Listeria monocytogenes phages, linking these differences to host adaptation strategies.

## Key findings

- Temperate phages have smaller genomes and shorter genes compared to virulent phages.
- Codon adaptation is higher in temperate phages, while virulent phages show stronger codon usage bias and higher GC content.
- Codon adaptation index and GC content at the third codon position are strongly correlated across phage genomes.

## Abstract

Phage lifestyles impose distinct selective pressures on genome architecture and codon usage. This study compares gene length and codon usage patterns in Listeria monocytogenes phages, analysing 686 temperate and 1516 virulent phages coding sequences. Most temperate phages had significantly smaller genomes (41 022.5 ± 3225.2 kb) and shorter genes (555 ± 647.1 nt) than virulent phages (101 089.3 ± 44 030.4 kb; 629 ± 583.5 nt). Codon adaptation was higher in the temperate phages [codon adaptation index (CAI) = 0.711 ± 0.045 vs. 0.679 ± 0.047; P < 1.4 × 10−51], while codon usage bias was stronger in the virulent phages (effective number of codons = 44.80 ± 5.863 vs. 46.00 ± 6.647; P < 1.0 × 10−7), which also had higher guanine and cytosine (GC) content (35.84 ± 2.985% vs. 35.21 ± 3.791%). CAI and %GC3 correlated strongly (r = −0.77 to −0.97) genome-wide. These results demonstrate that L. monocytogenes phage lifestyle shapes codon usage through distinct strategies of host adaptation and translational optimization. Also importantly, these findings can advance the development of biotechnological and synthetic biology tools for improving rapid determination of lifestyle of phages and their use in therapeutic and biocontrol applications.