Gene-sharing networks and evolutionary modules define the genetic landscape of Shigella bacteriophages

Shigella phages are the major sources of genetic variability for Shigella sp. populations, but the evolutionary relationships among these phages remain unclear. To bridge the gap, we analyzed 371 complete phage genomes using a multi-scale framework integrating ANI clustering, protein-family diversity, gene-sharing networks, reticulate membership patterns, evolutionary modules, and proteomic phylogeny. ANI revealed a highly structured genomic landscape with 104 clusters, including several large lifestyle-pure groups. Virulent phages dominated by Straboviridae and Andersonviridae formed tight islands, whereas temperate phages assembled into broader, taxonomically mixed units enriched for Peduoviridae , Casjensviridae , and related lineages. The gene-sharing network exposed a strong lifestyle asymmetry: the largest connected component was dominated by temperate phages. In contrast, the highest-degree hubs were dominated by virulent Straboviridae phages, reflecting conserved structural/replication blocks in virulent lineages. In the case of betweenness, temperate genomes were predominant, indicating their role as evolutionary bridges. Membership analysis showed that most genomes exhibited strongly concentrated cluster signatures, demonstrating the dominance of consistent lineage backbones, and that very few temperate phages displayed broadened memberships consistent with concept of mosaicism. Module profiling revealed a two-tier module architecture, consistent head-tail replication modules conserved across major families, and a fluid accessory layer enriched for regulatory, host-interaction, lysis, and hypothetical proteins. These accessory modules were cluster-restricted or scattered across a few lineages, consistent with episodic gene flow, niche-specific adaptation, and mobile genomic islands. The proteomic tree demonstrated that all detected ICTV families formed monophyletic clades, with a strong phylogenetic signal for lifestyle and lifestyle transitions representing rare, evolutionarily costly events. Together, these results show that Shigella phages evolve through the interplay of deep lineage structure, lifestyle-specific evolutionary constraints, and modular gene exchange, producing a structured genomic relationship among Shigella bacteriophages.