Chemosensory landscape of order Vibrionales: Genome-scale phylogenomics uncovers four chemosensory architectures driven by bipartite genome organization

Abstract Chemosensory systems (CSSs) are multi-protein assemblies regulating bacterial motility and cellular functions. Despite extensive study of chemotaxis in Vibrio cholerae, a comprehensive evolutionary analysis of CSSs across order Vibrionales has been lacking. Using 116 curated representative genomes across 28 Vibrio clades and ~10,000 RefSeq/metagenome-assembled genomes, we characterized the chemosensory toolkit of Vibrionales. CheA-based phylogenetics, CSS architecture, sequence similarity networks, structural comparisons, and synteny analysis identified four discrete CSS types: F6, F7, F9, and a novel lineage, F8. F6 is universally conserved on chromosome I and essential for flagellar motility, while F7, F8, and F9 show patchy, replicon-flexible distributions reflecting lineage-specific retention or horizontal acquisition. F6, F7, and F8 were vertically inherited from Gammaproteobacteria; F9 was horizontally acquired from Alphaproteobacteria. Structural analysis reveals conserved CheA folds despite sequence divergence, with lineage-specific domain insertions in F8 and F9. Collectively, this study reveals a two-tier chemosensory architecture within order Vibrionales, 1) a chromosomally stable F6 motility core under purifying selection, 2) overlaid by dynamically evolving F7, F8, and F9 accessory systems, wherein multipartite genome organization itself serves as an evolutionary substrate for sensory innovation, enabling rapid niche adaptation without compromising core chemotactic fidelity. Importance Bacteria actively navigate their environments using molecular sensors called chemosensory systems, moving toward nutrients and away from harm. In Vibrio bacteria, which cause cholera and serious seafood-borne infections, these same sensors help bacteria locate and colonize the human gut, making them direct contributors to disease. Yet how systems evolved across the broader Vibrio family remained unknown. By analyzing over 10,000 Vibrio genomes, this study maps CSS diversity order-wide, identifies a previously uncharacterized system (F8), and reveals how the bacteria’s distinctive two-chromosome genome enables flexible, niche-tailored sensory assembly. These findings expose key signaling proteins, CheA and MCP, as promising drug targets to disarm Vibrio pathogens by crippling their ability to sense and colonize the human host. Competing Interest Statement The authors have declared no competing interest.