Signatures of optimal codon usage in metabolic genes inform budding yeast ecology
Fig 3
Codon optimization in the GAL pathway is correlated with specific ecological niches in 2 different major clades of budding yeasts.
p-values less than 0.01 are indicated with ** and less than 0.05 with *. (A) In the CUG-Ser1 clade, species associated with a human niche or human and insect niches (13 species) have significantly higher codon usage optimization values in all GAL genes (p-values of 0.022, 0.028, and 0.006 for GAL1, GAL10, and GAL7, respectively) when compared to species that are associated with insect niches but not human niches (44 species). Only 11 species were not associated with either human or insect niches. (B) In the Saccharomycetaceae, species associated with only dairy niches (5 species) have significantly higher codon usage optimization values in all of the GAL genes (p-values of 0.010, 0.002, and 0.014 for GAL1, GAL10, and GAL7, respectively) versus species associated with only alcohol niches (14 species). A total of 9 species are associated with both dairy and alcohol niches. Underlying data can be found in Tables E and F S4 Data.