Table S1. List of core chromosomal OGs (chrOGs) of the L. lactis genome. The list includes the genes in these chrOGs in the four reference genomes. The three different worksheets are sorted according to (i) our OG number, (ii) LaCOG number and (iii) functional annotation of the KF147 gene products.

Table S2. List of L. lactis-specific core chrOGs and genes.

Table S3. List of subspecies-specific and niche-specific chromosomal OGs.

Table S4. Annotation of variable gene clusters and genes.

Table S5. Known L. lactis plasmids represented on the CGH microarray.

Table S6. Predicted presence/absence of important known plasmid-located genes in 39 L. lactis strains.

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