Abstract: This study aimed to establish a classification method for natural plasmids of Lactobacillus plantarum (L. plantarum) by using plasmid replication initiation protein (Rep) as a taxonomic marker. Fifty three plasmids encoding Rep in L. plantarum were divided into six plasmid types by the method of phylogenetic analysis, including five plasmid families and one novel replication type of plasmid. Then, the backbone sequence specific to each plasmid family was further proposed. Finally, a simple and effective classification method and criterion for L. plantarum natural plasmids was established. Compared with the previous classification methods based on plasmid function and incompatibility, this method displayed relatively better practicability and versatility.

Key words: Lactobacillus plantarum, plasmid, genome, replication initiation protein, replicon