Fig. 1

Pairwise comparison of GC content between aerobic and anaerobic prokaryotes. a Illustration of the difference between nonphylogenetically-controlled comparisons and phylogenetically-controlled comparison performed in this study. In a nonphylogenetically controlled comparison, the aerobes (including strain 1, species 7, species 8, and species 11) are compared to all the anaerobes (including strain 2, species 1–6, and species 9–10). However, only three changes in oxygen requirement are observed in the illustrated evolutionary tree. The differences in GC content between these three branches are likely to be associated with changes in the oxygen requirement. Therefore, only three pairs should be included in a phylogenetically controlled comparison. For branches having multiple strains/species with different evolutionary rates (e.g., species 4–8), we paired the slowly evolved aerobic strain/species with the slowly evolved anaerobic strain/species (species 6 vs species 7). In cases with two or more strains/species with identical divergence times, we preferentially selected the genomes in which more genes had been annotated. Next, the comparisons were duplicated using the dataset including the quickly evolved pairs (e.g., species 5 vs species 8 selected from species 4–8). Nearly identical results were obtained in the duplicated comparison. The results of the former are presented in Fig. 1b, c, and d and Table S1, and those of the latter are deposited as electronic supplementary material (Additional file 1: Figure S1 and Table S2). The choice of an anaerobe from species 4, 5 or 6 or an aerobe from species 7 or 8 did not alter the results. b Comparison of the GC content calculated from whole-genome sequences. c Comparison of GC content at the 4FDS of all protein-coding genes in each genome. d Comparison of GC content at the 4FDS of orthologous genes. The diagonal line represents cases in which aerobes and their paired anaerobes have the same GC content. Points above the line represent cases in which anaerobes have higher GC content than their paired aerobes, while points below the line indicate the reverse. All significance values were calculated using two-tailed Wilcoxon signed-rank tests