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

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.