Fig. 5

Investigating the L. pneumophila pangenome through network graphs. A Genome-genome similarity network, coloured by ST. Nodes represent genomes, and edges are weighted by pairwise JSC. Two key ST36 clades are highlighted. Edges are filtered by JSC > 0.5 and using a k-NN = 10. B Same network as in A but coloured by sampling location. Same two key ST36 clades are highlighted. C Gene–gene similarity network; nodes represent genes, edges weighted by pairwise JSC. Edges are filtered by JSC > 0.55, and k-NN = 20. Clustering with MCLi = 1.50. Components of n < 10 removed for visual clarity. D Accessory gene distribution plots of the largest gene clusters associated with the division in ST36 between Swiss (reds and orange) and US (blues) genomes. Plots as described in Fig. 3. E 3D rendering of the pangenome synteny graph for L. pneumophila; coloured nodes correspond to the clusters in C, D. F Filtered and 2D view of the key region, with convergence of both Swiss and US-associated regions to the same core region