Comparative genomic analyses of 28 selected Acidithiobacillus strains. a Phylogeny based on concatenated proteins of Acidithiobacillus genomes and orthologous proteins shared by Acidithiobacillus spp. using CVTree3 with a composition vector approach. The topology of phylogenomic tree was shown, and Achromobacter xylosoxidans A8 was used as outgroup. Type strains are shown in red triangles. Specially, the redefined species are shown in the phylogenomic tree, and their former names can be also found in brackets. Numbers at internal nodes represent the number of possible ancestral genes as retrieved under the GD-FR-CWP model. Numbers on the branches and at the end of branches indicate the number of gain (red) and loss (blue) genes, and the extant counts of genes, respectively. For core genome-based phylogeny, the species are numbered in sequence. b Venn diagram representing the orthologous and non-orthologous genes of Acidithiobacillus spp. The number of orthologous genes shared by 28 Acidithiobacillus genomes and the strain-specific genes are shown in the center circle and petals, respectively. c COG assignments of core, accessory, and unique genes. Abbreviations: 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; V, defense mechanisms; T, signal transduction mechanisms; M, cell wall/membrane/envelope biogenesis; N, cell motility; U, intracellular trafficking, secretion, and vesicular transport; O, posttranslational modification, protein turnover, chaperones; 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 and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown. d Mathematical extrapolation for the estimation of size of Acidithiobacillus pan-genome and core genome. Detailed description for calculation is shown in section Model Extrapolation for Acidithiobacillus Pan-Genome.