Supporting Information

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Fig. 5. Genomic locations of IS 100 insertions and napA.

Fig. 6. Raw data with sSNPs. Black squares represent ancestral nucleotides present in Y. pseudotuberculosis, blue squares represent synonymous changes, and gray squares are missing data. Properties of 105 individual isolates, including strain designation, molecular grouping, original designation, country, and year of isolation are shown on the right.

Fig. 7. IS100 raw data. Red squares indicate the absence of the insertion site Y45, which corresponds to an IS1541 insertion that is lacking within Y. pseudotuberculosis. Black squares indicate an empty site, and blue squares indicate an IS100 insertion. Gray squares are missing data. Details on 131 Y. pestis and Y. pseudotuberculosis isolates, including strain designation, molecular grouping, original designation, country, and year of isolation are shown on the right.

Fig. 8. Neighbor joining analysis of 1.ORI isolates using MLVA-based genetic relationships. The data correspond to the 1.ORI branch that is collapsed in Fig. 3.

Exceptional Isolates. IP528 was assigned to 1.ORI.a although it has an empty site at Y14, different from other 1.ORI isolates, which contain an IS100 insertion at that location. IP537 was assigned to 1.ANT.a although it has an empty site at Y44, different from other 1.ANT isolates, which contain an IS100 insertion at that location. In both cases, these exceptions may represent excision of IS100 or the ancestral states before the acquisition of these IS100 insertions.

Two other exceptional isolates were assigned grouping designations, namely CO92 to group 1.ORI.c caused by sSNP s34 and IP619 to group 1.ORI.b caused by sSNP s36. It is not surprising that CO92 contains a unique sSNP because sSNPs were detected by genome comparisons against CO92. However, other experiments with IP619 have confirmed that it is unusual and contains multiple synonymous and nonsynonymous SNPs in various genes.

Nich51 was assigned to 1.ORI.a even though it contains an intact glpD gene, as shown by Motin et al. (1). glpD was not tested for any other isolates in our analysis.

1. Motin, V. L., Georgescu, A. M., Elliott, J. M., Hu, P., Worsham, P. L., Ott, L. L., Slezak, T. R., Sokhansanj, B. A., Regala, W. M., Brubaker, R. R., et al.. (2002) J. Bacteriol. 184, 1019-1027.