From one genome to thousands, and beyond

Over the past three decades, Saccharomyces cerevisiae has gone from being the first eukaryote to have its genome fully sequenced to one of the most studied biological systems. Advances in sequencing technologies, functional genomics, and population genomics have expanded the scope of study from a single laboratory reference genome to thousands of natural isolates, and the species-wide pangenome. These advances have revealed vast genetic and structural diversity, shaped by evolution, ecology, and domestication, while large-scale experimental resources have made yeast a model organism of choice in systems biology. In this review, we trace this transition from a reference genome view to an understanding of diversity at the population level, highlighting how telomere-to-telomere assemblies, graph-pangenome, and multi-omics approaches are transforming our ability to link genomic variation to phenotype. Together, these advances place S. cerevisiae at the forefront of efforts to understand and predict genotype-phenotype relationships in eukaryotes.