Figure 3
(A) Pangenome analysis of Entomospira species conducted in Pirate13. Shared gene presence per isolate for different percent identity thresholds (50%, 75%, 90%, 95%) were calculated. Gene family presence is indicated by colored columns according to threshold. The scale shows a color gradient for identity thresholds used in the analysis. 97% of the genes shared by all four genomes lie in the range between 50 and 70% identity. The heatmap also shows that shared genes above a 95% identity occur only in BR149 and BR151. (B) COG categories14,15 identified in the shared genes (left panel) and in the accessory set of genes (right panel). One-letter abbreviations for the functional categories: 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, including ribosome structure and biogenesis; K, transcription; L, replication, recombination and repair; M, cell wall structure and biogenesis and outer membrane; N, secretion, motility and chemotaxis; O, molecular chaperones and related functions; P, inorganic ion transport and metabolism; Q, Secondary metabolites biosynthesis, transport, and catabolism; R, general functional prediction only; S, no functional prediction; T, signal transduction; U, intracellular trafficking, secretion, and vesicular transport; V, defense mechanisms. (C) For each genome we assessed whether the shared genes are located on the chromosome or on plasmids, shared genes location in the left panel and accessory genes location in right panel.
