Fig. 1

Pan and core genome analysis. a The pan-genome of the 73 Salmonella Typhi isolates contains 6602 genes. The pan-genome can be further divided into the unique genome (orange), dispensable genome (red) and core genome (blue), depending on how many isolates share a given gene. b Core and pan-genome curves. The number of core genes stabilizes after the addition of the tenth genome. The pan-genome is open according to the fitting parameter γ = 0.67. c Distribution of genes in the unique, dispensable and core genomes on in each COG class. COG classes are as follows: [J] Translation, ribosomal structure and biogenesis; [A] RNA processing and modification; [K] Transcription; [L] Replication, recombination and repair; [B] Chromatin structure and dynamics; [D] Cell cycle control, cell division, chromosome partitioning; [Y] Nuclear structure; [V] Defense mechanisms; [T] Signal transduction mechanisms; [M] Cell wall/membrane/envelope biogenesis; [N] Cell motility; [Z] Cytoskeleton; [W] Extracellular structures; [U] Intracellular trafficking, secretion, and vesicular transport; [O] Post-translational modification, protein turnover, chaperones; [X] Mobilome: prophages, transposons; [C] Energy production and conversion; [G] Carbohydrate transport and metabolism; [E] Amino acid transport and metabolism; [F] Nucleotide transport and metabolism; [H] Coenzyme transport and metabolism; [I] Lipid transport and metabolism; [P] Inorganic ion transport; [Q] Secondary metabolites biosynthesis, transport and catabolism; [R] General function prediction only; [S] Function unknown; [−] Unclassified