Replicon-resolved pangenomics reveals functional specialisation and genome evolution in Vibrio coralliilyticus

Multipartite genomes define the genus Vibrio, yet replicon specialisation remains poorly understood, particularly in environmental species. We developed a machine-learning classifier to assign draft contigs to putative replicons with high accuracy, integrating complete and draft genomes in comparative analyses. Independent implementation in Vibrio cholerae yielded similar performance, supporting broader applicability. Analysis of 41 Vibrio coralliilyticus genomes revealed functional specialisation between chromosomes despite similar proportions of core and flexible gene families. Chromosome I was enriched in essential cellular processes, central metabolism, motility and regulation, whereas chromosome II was enriched in environmental sensing, signal transduction, transport and interaction-associated functions. Chromosome I also exhibited greater plasticity, with more extensive homologous recombination and higher densities of mobile genetic elements and defence systems. Two previously undescribed conjugative megaplasmid lineages (254–628 kb) displayed contrasting adaptive repertoires. One was broadly distributed across hosts and geographic regions, encoding a conserved accessory repertoire including a giant multidomain putative effector predicted to mediate host interactions. The other was restricted to Mediterranean coral isolates, with an expanded mobilome and a conserved Sofic-like anti-phage defence system. Together, these findings show that functional specialisation can coexist with similar gene conservation patterns, while chromosomes and megaplasmids make complementary contributions to adaptation and genome evolution.