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Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

Samuel O'donnell,Jia‐Xing Yue,O. A. Saada,Nicolas Agier,Claudia Caradec,T. Cokelaer,Matteo De Chiara,Stéphane Delmas,Fabien Dutreux,Téo Fournier,A. Friedrich,E. Kornobis,Jing Li,Zepu Miao,Lorenzo Tattini,J. Schacherer,Gianni Liti,Gilles Fischer

Published 2023 in Nature Genetics

ABSTRACT

Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising telomere-to-telomere assemblies of 142 strains representing phylogenetic and ecological diversity of the species characterizes its genome structural landscape. Pangenomes provide access to an accurate representation of the genetic diversity of species, both in terms of sequence polymorphisms and structural variants (SVs). Here we generated the Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising reference-quality genomes for 142 strains representing the species’ phylogenetic and ecological diversity. The ScRAP includes phased haplotype assemblies for several heterozygous diploid and polyploid isolates. We identified circa (ca.) 4,800 nonredundant SVs that provide a broad view of the genomic diversity, including the dynamics of telomere length and transposable elements. We uncovered frequent cases of complex aneuploidies where large chromosomes underwent large deletions and translocations. We found that SVs can impact gene expression near the breakpoints and substantially contribute to gene repertoire evolution. We also discovered that horizontally acquired regions insert at chromosome ends and can generate new telomeres. Overall, the ScRAP demonstrates the benefit of a pangenome in understanding genome evolution at population scale.

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