Maximum likelihood phylogenetic tree generated from 16,097 core genome SNPs differentiating all 188 isolates sequenced in this study (Fig. S1), SNP count boxplots (Fig. S2), maximum likelihood phylogenetic tree generated from 14,846 core and accessory genome SNPs called in Cortex_var for all 179 lineage I isolates (Fig. S3), strain sequences in the study (Table S1), genome sequence and assembly metrics (Table S2), additional genomes used in the kSNP analysis (Table S3), gene presence/absence enrichment analysis for selected groups of isolates (Table S4), phylogenetic model selection by path sampling (Table S5), presence or absence of previously described L. monocytogenes plasmids among sequenced isolates (Table S6), and genes significantly enriched in the 38 strains in SNP group 1 not from store 16 (Table S7).
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