Pan-Genome Analysis and Search for Virulence Genes

The pan-genome analysis of the 64-genome P. gingivalis was performed through the Roary v3.7.0 pipeline (Page et al., 2015). For virulence gene identification, a homology search of predicted protein sequences in CP3 and H3 genomes against the most characterized virulence genes identified in P. gingivalis available in the literature was performed, using CRB-Blast v0.6.6 (https://github.com/cboursnell/crb-blast). Also, virulence genes were identified in the 64-genome dataset using pan-genome results to evaluate presence/absence and protein sequence variation of these genes. According to shared and unique genes between CP3 and H3 genomes, a Venn diagram was plotted using the VennDiagram R package (https://cran.r-project.org/package=VennDiagram). The inferred phylogenetic tree was annotated based on the presence/absence of the virulence genes that are part of the accessory genome, using the pheatmap R package and FigTree.