In this Nature Genetics article, the scientists describe the construction of an exhaustive genomic dataset comprising the complete and uninterrupted telomere-to-telomere genome assemblies  of 142  isolates of the  baker's yeast, Saccharomyces cerevisiae. These strains were carefully chosen to represent the full phylogenetic, ecological and geographical diversity of the species, as well as its natural diversity in terms of ploidy and heterozygosity. This unprecedented dataset, called ScRAP for Saccharomyces cerevisiae Reference Assembly Panel, provides access to a more detailed level of genetic knowledge than that achieved in any other organism, including humans.  It is not just a simple catalogue of similarities and differences between genomes as the ScRAP provides new biological insights into the mechanisms by which genomes evolve.

A major advance has been the identification of the different structural variants resulting from the accumulation of large chromosomal rearrangements and the measurement of their quantitative impact on the transcription of neighbouring genes and on the evolution of the gene repertoire. The description of the diversity of chromosome structure has been extended to the study of variations in telomere length, as well as the reconstruction of the mobility of transposable elements, which accounts for 40% of structural variants.

These results highlight many unexpected discoveries that do not simply provide a more detailed view of what the scientific community already knows. This work also brings to light new observations that the field had not previously thought of, or for which there were clearly no exploitable data. Among the many contributions of this study, the scientists were able to demonstrate the horizontal transfer of large chromosomal regions from other yeast species, which are integrated at the ends of chromosomes. They generate new telomeres with structures that make the transition between the telomeric repeat pattern of the donor species and the repeat pattern of S. cerevisiae. The authors also discovered horizontal transfer of entire chromosomes, calling into question current models of hybridisation between related species. This work has also made it possible to reconstruct the evolutionary history of tRNA gene families, showing that, like protein-coding genes, the tRNA gene repertoire undergoes losses and gains, and that subtelomeric regions serve as a cradle for these phenomena.

Each of these stories is a new discovery demonstrating the need to replace the use of a single reference genome with a pangenome unifying numerous genomes representative of the species' phylogenetic diversity and providing a complete map of the population's genetic diversity.