Fig. 2

Genomic and phylogenomic features of S. thermophilus. A Core and pan-genome size evolution in S. thermophilus isolates according to the number of genomes. Each point represents the number of protein families conserved between genomes. All of the points are plotted as a function of the strain number (x). The deduced pan-genome size is y = 1920.3 × ^0.3052 (R2 = 0.9972). B. The distribution of core and accessory proteins according to the COG classification. The x-axis indicates the percentage of proteins in various COG categories. (A) RNA processing and modification; (C) Energy production and conversion; (D) Cell cycle control, cell division, chromosome partitioning; (E) Amino acid transport and metabolism; (F) Nucleotide transport and metabolism; (G) Carbohydrate transport and metabolism; (H) Coenzyme transport and metabolism; (I) Lipid transport and metabolism; (J) Translation, ribosomal structure and biogenesis; (K) Transcription; (L) Replication, recombination, and repair; (M) Cell wall/membrane/envelope biogenesis; (N) Cell motility; (O) Posttranslational modification, protein turnover, chaperones; (P) Inorganic ion transport and metabolism; (Q) Secondary metabolites biosynthesis, transport, and catabolism; (S) Function unknown; (T) Signal transduction mechanisms; (U) Intracellular trafficking and secretion; (V) Defense mechanisms. C Word cloud of pseudogenes annotations. Annotation of pseudogenes provided by MicroScope was filtered to remove non-informative words (see Methods section for the complete list of removed words). Word size is calculated accordingly to its occurrence. D Heatmap showing the pairwise percentage of differences (% differences) between core proteome of the 79 STH strains. Strains were clustered into three clusters (a, b, c). Subgroups within the clusters are also identified (b1, b2, c1, c2, and c3)