Extended Data Fig. 3: Principal component analysis (PCA) of phylogroup clustering in Y. pestis and comparison of synteny diversity with Y. pseudotuberculosis.
From: Insights into Yersinia pestis evolution through rearrangement analysis of 242 complete genomes
a, PCA cumulative variance plot of 178 synteny block adjacencies associated with rearrangements. The first six principal components (PCs) accounted for over 60.2% of the variance. b, PCA cumulative variance plot of 3,185 single nucleotide polymorphisms (SNPs) and clustering of Y. pestis phylogroups on PC1 and PC2. The first six PCs accounted for 69.8% of the variance. The shaded area represents the cluster of early-diverging 0.PE phylogroups, including 0.PE7, 0.PE2, 0.PE4A, 0.PE4B, and 0.PE4C. c, PCA cumulative variance plot of 2,023 indels and clustering of Y. pestis phylogroups on PC1 and PC2. The first six PCs accounted for 58.6% of the variance. The shaded area represents the cluster of early-diverging 0.PE phylogroups, including 0.PE7, 0.PE2, 0.PE4A, 0.PE4B, and 0.PE4C. d, Synteny diversity comparison between 242 Y. pestis and 25 Y. pseudotuberculosis strains. A sliding window analysis was performed using the IP32953 chromosome as the reference. Synteny diversity in 50-kb windows (10-kb steps) is visualized in purple for Y. pestis and orange for Y. pseudotuberculosis, with 5-kb windows (1-kb steps) in grey for both.
