Detecting positive selection in the budding yeast genome

Area of Science:

• Evolutionary genomics
• Molecular evolution
• Yeast biology

Background:

• Abundant genomic data enables fine-scale studies of yeast genome evolution.
• Understanding adaptive evolution in coding and promoter regions is crucial for deciphering strain divergence.

Purpose of the Study:

• To investigate the adaptive evolution of coding and promoter regions in three Saccharomyces cerevisiae strains.
• To determine if positive selection on coding regions is coupled with selection on promoter regions.

Main Methods:

• Maximum-likelihood approach to identify positively selected genes (PSG).
• Analysis of transcription-start sites to define core-promoter regions.
• Functional enrichment analysis of identified genes and promoters.

Main Results:

• Identified 76 positively selected genes (PSG) with biased biological functions and over-representation of charged amino acids.
• Identified 31 positively selected promoters, with associated genes enriched in transmembrane transporter function.
• Found no correlation between positively selected genes and promoter adaptation or expression variation, indicating uncoupled evolution.

Conclusions:

• Coding and promoter regions of Saccharomyces cerevisiae undergo independent adaptive evolution.
• Findings provide insights into the evolutionary mechanisms driving the divergence of yeast strains from different environments.