Fig. 3.

Status of known Y. pestis virulence factors in newly reported genomes. Heatmaps displaying the presence or absence of 159 known virulence factors (Dataset S3) in Y. pestis genes of the chromosome (n = 115), and the pCD1 (n = 37), pMT1 (n = 6), and pPCP1 (n = 1) plasmids. Yellow represents 100% of the gene covered at least 1X while black represents 0% of the gene covered. Genomes are ordered based on their phylogenetic placement with the outgroup Y. pseudo (Y. pseudotuberculosis IP32593) at the bottom. The numbered box highlights the yapC gene, whose loss is part of deletion event 1 (SI Appendix, Fig. S5). The heatmaps were produced using the ggplot2 (39) and ggpubr (42) packages in R v3.6 (43).