Signatures of optimal codon usage in metabolic genes inform budding yeast ecology
Fig 4
Closely related Kluyveromyces species exhibit differential codon optimization in the GAL pathway associated with isolation from dairy environments.
All 4 Kluyveromyces species were shown experimentally to metabolize galactose. (A) Species phylogeny of 4 closely related Kluyveromyces species. K. marxianus and K. lactis are both associated with dairy niches and have high codon optimization values in their GAL pathway genes. In contrast, K. aestuarii is associated with marine mud, and K. dobzhanskii is associated with flies. (B) The genome-wide distribution of codon optimization (stAI) values for the 4 Kluyveromyces species included in this study. The 50th and 75th percentiles are shown with black dashed lines. In the 2 species associated with dairy niches, the codon optimization for all 3 GAL genes falls in the top 25th percentile. In the 2 species not associated with dairy, the GAL genes fall below the top 25th percentile. Genes encoding ribosomal proteins are well established to rank among the most highly optimized genes within a genome. (C) The distribution of terminal synonymous (dS) branch lengths (in unrooted gene trees) calculated for the 651 BUSCO genes. All 3 GAL genes fall within the interquartile range for K. aestuarii and K. marxianus. In K. dobzhanskii, all 3 GAL genes lie above the 70th percentile with GAL1 in the upper quartile. In K. lactis, GAL7 falls below the interquartile range, while GAL10 lies above. The 50th and 75th percentiles are shown with black dashed lines. Underlying data can be found in Tables G–P S4 Data.