Fig. 4

Phylogenetic relationships predict a new sub cluster into the plasmid group B. a Phylogenetic analysis using the repA sequences only from plasmids, whose their complete sequences are available in the database. The neighbor-joining tree was constructed by MEGA 5 using the Jukes-Cantor model. Bootstrap values (1000 repetitions) are shown at the nodes. The plant host of isolation and the presence of some characteristic genes of the pPT23A family plasmids (such as copABCD and rulAB operon, and Type IV secretion system) are represented in the right columns beside each plasmid name. sht: sequence shorter than expected; imcomp: incomplete; *: rulA and rulB genes located at different positions and orientations. b Genomic diversity of the sub cluster of plasmids. Each plasmid is represented by an oval. The number of orthologous protein-coding genes shared by all plasmids (i. e., the core genes) is in the centre. Overlapping regions show the number of coding sequences (CDS) conserved only within the specified plasmids. Numbers in the non-overlapping portions of each oval show the number of CDS unique to each plasmid. Hypothetical proteins were not taking into account to this analysis