Figure 2. Codon-pair contexts are highly conserved.
A) Codon-context conservation in fungi was determined by calculating the percentage of preferred or repressed codon contexts that showed bias conservation in the aligned sequences of each organism versus S. cerevisiae (red bars in the graphs). The percentage of conservation of the first codon of the pair between both sequences is shown in blue bars. This allows for comparison of codon-context and first codon conservation in the alignments. The graphs are organized according to the fungal phylogenetic tree described by Fitzpatrick and colleagues [39]. One fungal species was chosen for each branch of the tree, as follows: Zygomycota/Basidiomycota – C. neoformans; Schizosaccharomyces – S. pombe; Eurotiomycetes – A. fumigatus; Sordariomycetes/Leotiomycetes – N. crassa; Candida – C. tropicalis; Saccharomyces – S. mikatae; Kluyveromyces – E. gossypii. B) The same approach was used to compare codon-context and first codon conservation in a group of bacteria, archaea and high eukaryotes (see Figure S1), using E. coli, M. jannaschii and H. sapiens as reference organisms, respectively. In order to determine the statistical significance of the data the plots were tested using two-tailed T-student tests for paired samples, and all organisms showed significantly higher conservation of codon contexts than first codon conservation (10−35<p<10−7).