A stepwise route to polyploidy in yeast

Polyploidy is a ubiquitous biological phenomenon that promotes genetic innovation and adaptation1. In the budding yeast Saccharomyces cerevisiae, polyploid strains are widespread in natural, industrial, and clinical niches, yet their origin is unclear2-4. Here, we identify a novel mechanism of stepwise polyploidization that involves a Sporulate-Endoreplicate-Mate (SEM) sequence. We show that spore endoreplication during germination doubles the genome while preserving mating competence, enabling incremental increases in ploidy through mating with a non-endoreplicated spore from the same ascus. We experimentally demonstrate the transition from diploidy to triploidy and from triploidy to tetraploidy. Stepwise polyploidization thus positions triploids as central intermediates in ploidy evolution rather than evolutionary dead-ends. We further show that spores from intact asci can spontaneously undergo one or two successive SEM cycles and generate novel triploid and tetraploid strains without genetic manipulation. Natural polyploids harbor specific genomic features that are consistent with the SEM mechanism, including the prevalence of triploidy, extensive aneuploidy, pervasive heterozygosity, and a strong association with heterothallism4-11. Together, our findings establish stepwise polyploidization through iterative SEM cycles as the predominant natural route to polyploidy in S. cerevisiae.