Signatures of optimal codon usage in metabolic genes inform budding yeast ecology
Fig 1
The GAL pathway and the distribution of galactose metabolism, GAL genes, and preferred codon usage across the Saccharomycotina.
(A) The 3 enzymes of the GAL pathway metabolize galactose into glucose-1-phosphate, which can then enter glycolysis after being converted into glucose-6-phosphate. (B) Various features of galactose metabolism plotted on a phylogeny of the budding yeast subphylum Saccharomycotina; the 12 major clades of the subphylum are color coded. The presence and codon optimization (measured by estAI) of the 3 GAL genes are represented in the inner 3 rings. Clades with 3 or more species without a complete GAL pathway were condensed and are shown as triangles; for the full tree, see S1 Fig. The GAL clusters in the Dipodascaceae/Trichomonascaceae, Pichiaceae, and Phaffomycetaceae were recently found to have likely originated from horizontal gene transfer events from the CUG-Ser1 clade [72]. We did not identify any GAL genes from species in the CUG-Ser2 clade or the family Saccharomycodaceae. In every other major clade examined, we identified complete and clustered occurrences of the GAL pathway (filled-in blue squares and circles, respectively.) High codon optimization (darker colors) in the GAL pathway is not restricted to any one major clade. The ability to metabolize galactose (filled-in green triangle) was assessed either experimentally in this study or taken from the literature. In some instances, where only literature data were available, there were conflicting or variable reports of galactose metabolism (5 species; empty green triangles). The majority of species in the Saccharomycotina have also been shown to have genome-wide selection on codon usage (denoted by the yellow stars) [59]. Species names and ecological information can be found in S1 Fig and Table A S1 Data.