Fig. 4

Syntenic connections within the S. aureus pangenome shows location of gene sets. A Full synteny network of S. aureus at 90% gene identity. Nodes represent genes and are sized according to the number of isolates in which they occur. Edges are weighted as the number of times two genes occur next to one another. Coloured by Louvain Cluster (LCi = 0.400). B “Phage” region (right-hand side of network in A), selected by retaining only nodes in clusters 1, 5, 6, 7 and 9. Coloured as in A. C 2D layout of the same region as in B, with common annotation highlighted alongside core genes. This network allows detailed inspection of phage integration sites with respect to core genes, accessory genes shared between common phage types, and putative novel factors carried on phage variants. Gene cluster 28 (see Fig. 3) is also found in this region. D Region, in context, that carries gene cluster 25 (orange; see Fig. 3) as a single syntenic set, inserted next to a near-core gene. Examples of gene cluster 3 (yellow) sets are also seen. E 2D layout of region from D (clusters 2 and 18). Smaller, focused networks aid navigation and investigation of specific gene locations and neighbours