Fig. 1: Maximum likelihood phylogenetic tree of 936 Lm genomes from New York State and the distribution of annotated genetic elements of interest.

Each row of the matrix represents a genome assembly, whose phylogenetic lineage and clonal complex (CC) are indicated by the first and second row colors on the left of the matrix, respectively. Only CCs represented by at least 30 genomes have individual colors, while less common CCs alternate between two shades of gray. Each column represents an annotated genetic element, with specific names found at the bottom of the matrix. These genetic elements are grouped by colored blocks, shown at the top of the matrix. Blanks indicate the absence of the genetic element of interest in the genome assembly. Regarding inlA, colors inside the matrix indicate whether the gene was found truncated or full-length. Regarding hypervirulence factors, colors indicate whether all genes comprising the Listeria pathogenicity island (LIPI) were found. Regarding the other genetic elements, colors indicate in which DNA vehicle the genetic element is found in the genome. The category “multiple” in the gene columns refers to a gene that was detected multiple times in the same genome, but in different DNA vehicles. “multiple” in the phage column refers to the four genomes that harbor plasmidic phages in addition to other phages. For better visualization, the outgroup (Listeria innocua, Accession number: GCF_028596125) is not shown. Source data for the matrix are provided in Supplementary Data 2.