Fig. 4: The network of cliques.

Cliques, represented as vertices, are connected with an edge if the average Jaccard index (JI) between plasmids of two cliques is >0.01. The colour of the edges indicates the average JI, while the width is proportional to the number of connections between a pair of cliques. The shape and colour of the cliques indicates the phylum of the predominant bacterial host. The size and the transparency are proportional to the clique size and the internal JI, respectively. The cliques form multiple clusters, which have been named based on the genus of the bacterial host characteristic for a particular cluster. There are two exceptions—the Proteobacteria and the Dairy (Lactic) cluster whose respective genera distributions have been provided. The most common GO biological functions of the genes found on plasmids of Proteobacteria, Staphylococcus, Enterococcus and Dairy clusters were further assessed. During the assessment, the respective frequencies of the genes were considered. In case of Proteobacteria, the bar chart distribution of the biological functions is provided. The shared and core gene content of Staphylococcus, Enterococcus and Dairy clusters is presented in the Venn diagram with the numbers in the diagram indicating the number of core and shared genes.