Large extrachromosomal replicons are widespread across bacterial lineages and show coordinated replication termination and spatial coupling with the chromosome

Bacterial genomes frequently harbor extrachromosomal replicons (ERs) that promote genome plasticity and adaptation, ranging from small plasmids to chromosome-scale replicons. In a few model organisms, including Vibrio cholerae and Agrobacterium tumefaciens, large ERs are coordinated with chromosome replication and cell-cycle organization by specific molecular mechanisms. Whether this applies broadly across bacteria remains unknown. Here, we analyzed more than 40,000 complete bacterial genomes to update the distribution of ERs across bacterial taxa. Their GC content converged toward that of the chromosome with increasing ER size, revealing a size-dependent trend toward chromosomal composition. Such large ERs were found as conserved genomic features in many distinct genera, consistent with independent acquisition and long-term maintenance. We selected representative strains from these lineages, spanning five taxonomic classes across three bacterial phyla, to investigate replication dynamics and spatial organization. Marker frequency analysis showed that these large ERs are maintained at the same copy number as the chromosome and often complete replication synchronously. Chromosome conformation capture further revealed frequent ER-chromosome contacts, including origin-origin interactions and extended contacts along replicated arms. Together, this exploratory study lays the groundwork for uncovering new mechanisms coordinating large-ER maintenance with the bacterial chromosome.