Figure 4.

Phylogenetic tree of RepFII repA1 gene from 18 IncFIIA plasmids. Core genome determination using both PGAP and Hal phylogenomics revealed that repA1 is the only gene conserved in all 18 plasmids. Trees constructed using output of PGAP and Hal phylogenomics are similar. Maximum likelihood (ML) method under the General Time Reversible plus Gamma model was used to construct the phylogenetic tree using MEGA5 supported with bootstrapping (1000 replicates). Bootstrap value with percentages equals or greater than 50% were shown on the branches and value less than 50% have been collapsed. FAB formula (F-:A-:B-) are indicated. All non ColV/BM plasmids were grouped together at cluster A and while all ColV/BM plasmids were grouped at cluster B. Black and white boxes indicate the presence and absence of specific plasmid features. Gray boxes^ab indicate the presence of specific plasmid features but are located at atypical plasmid sites. ^cThe ability to transfer for each plasmid was retrieved from their respective studies. Gray boxes^c indicate that the ability of the plasmid to transfer has not been reported before. Checkered gray boxes^c indicate that the plasmid is only transmissible in the presence of other plasmid and is not self-transmissible.