Directed evolution for cell separation in budding yeast

Haploid and diploid natural isolates of the yeast Saccharomyces cerevisiae were evolved under a daily transfer protocol that selected against clumpy growth and for cell separation. For the haploid populations, whole genome sequencing revealed strong selection to deactivate AMN1 , a known regulator of cell separation, recapitulating evolution that likely occurred during the domestication of common lab strains. We also observed multiple mutational hits to the Rim101 pathway, which was not expected. Mutations to both AMN1 and the Rim101 pathway were strongly associated with cell separation. In the diploid populations, we observed the parallel emergence of a large partial deletion of chrIII, the so-called Hawthorn’s deletion. We show that this deletion is associated with reduced clumpy growth. The mechanism by which Hawthorne’s deletion affects cell separation is unknown but may be related to an effect on budding pattern.