In Silico Prediction of a Divergent Candidate FII-Related Replicon Among the Serratia Plasmid Lineage

The replication region, replicon, is the most important module of plasmids that controls their replication and consequently their existence. Currently, a large number of replicon types with different architectures have been characterized, serving as a basis for plasmid classification and replicon typing. Despite ongoing research to characterize the replicative apparatus of plasmids, they remain unidentified by the replication system. Fifty replicons were studied in Serratia bacterial plasmids that were untypable or showed contradictory identification results by the replication system. These replicons shared a possibly new gene for the replication initiation protein repA. But a varying arrangement of the copA and copB genes typical of the FII and FIC replicons was observed. Comparative genomic and phylogenetic analysis revealed new insights into their possible evolution from the FII type. Based on these results, we propose a divergent candidate FII-related replicon type among Serratia plasmids. The obtained findings are discussed through the prism of the two phases of evolution’s general model. The results provide new insights into plasmid classification by replication system, plasmid replicons evolution, and bacterial plasmid typing.