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Supplemental text: Statistical analysis of presence/absence of genes.

Fig. S1. Neighbor-joining cluster analysis based on phenotypic properties of the 185 L. plantarum strains using the product-moment coefficient and UPGMA (unweighted pair group method using arithmetic averages). Strains selected for gene content evaluation are highlighted with a blue square.

Fig. S2. Self-hybridization of WCFS1.

Fig. S3. A. M-A plot for WCFS1-WCFS1 (self) hybridization.

B. M-A plot for WCFS1-ATCC14917 hybridization.

C. M-A plot for WCFS1-DKO22 hybridization.

Fig. S4. Density distribution of probes on all microarrays. M-values of ±1 and ±2 are indicated with dashed lines.

Table S1. Genes present in all 42 L. plantarum strains, but not found in other lactic acid bacteria.

Table S2. Genes found only in the reference strain L. plantarum WCFS1, and not in the other 41 strains analysed.

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