<b>Comparative Genomics of </b><b><i>Vibrio splendidus</i></b><b>: Unraveling key features of diversity, Virulence and Adaptive Strategies</b>

<i>Vibrio splendidus</i>, a member of the Splendidus clade, is an opportunistic pathogen with significant ecological and economic impacts in aquaculture. Despite its importance, <i>V. splendidus</i> genetic diversity and pathogenic mechanisms remain unclear, mainly due to its close genetic similarity to other species within the Splendidus clade. Through a comprehensive analysis of 130 <i>V. splendidus</i> genomes, including 12 newly sequenced isolates, we explored its genomic diversity, phylogeographic patterns, virulence potential, and other key features. Phylogenetic analysis revealed six distinct clusters, with varying degrees of genomic homogeneity and geographic distribution. Pangenome analysis indicated an open pangenome, driven by horizontal gene transfer, with cluster-specific adaptations in virulence and antimicrobial resistance genes. Prophage diversity was widespread, with 46.9% of genomes harboring prophages, primarily from the Caudoviricetes and Faserviricetes classes, suggesting a predominant role in genomic plasticity and ecological adaptation. Additionally, we identified diverse antiviral defense systems, including CRISPR-Cas and Restriction-Modification systems, highlighting the complex interplay between <i>V. splendidus</i> and its viral predators. Virulence factors such as the RTX toxin and type III secretion systems were unevenly distributed across clusters, reflecting niche-specific adaptations. This study provides a broad genomic analysis <i>V. splendidus</i>, revealing key elements associated with its genomic plasticity and adaptation.