Fig. 4

Heatmaps showing the presence (black) or absence (white) of pangenome genes in each E. faecium and E. lactis genome (A) and the fractions (%) of genomes harboring the pangenome genes in the respective E. faecium subclades I and II and E. lactis (B). Hierarchical clustering was performed using the Jaccard distance based on the presence or absence of pangenome genes. Colors indicate the taxonomic classifications (A) and isolation sources (B) of Enterococcus strains. COG classification of genes in regions 1, 2, and 3 (indicated by blue arrows) showing significant differences in the presence or absence of genes between E. faecium subclades I and II and E. lactis (C). The data are expressed as the average relative abundance per genome, with error bars indicating the standard deviations. C, energy production and conversion; D, cell division and chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme metabolism; I, lipid metabolism; J, translation, ribosomal structure, and biogenesis; K, transcription; L, DNA replication, recombination, and repair; M, cell envelope biogenesis and outer membrane; N, cell motility and secretion; O, post-translational modification, protein turnover, and chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolite biosynthesis, transport, and catabolism; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking, secretion, and vesicular transport; and V, defense mechanisms. The COG categories that exhibited a high enrichment (more than two times) in E. faecium subclade II genomes (or in E. lactis genomes) compared to E. faecium subclade I genomes and E. lactis genomes (or E. faecium subclade II genomes) are indicated with an asterisk (*)