Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
Year: 2023
Type: article
Abstract: 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.
Source: Nature Genetics
Institutions: Centre National de la Recherche Scientifique, Sorbonne Université, Biologie Computationnelle, Quantitative et Synthétique, Institut de Biologie Paris-Seine, Inserm, Sun Yat-sen University, Université Côte d'Azur, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Génétique Moléculaire Génomique Microbiologie, Université de Strasbourg, Institut Pasteur, Department of Genomes & Genetics
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: hybrid
Estimated APC paid: $10,520
Funders: Agence Nationale de la Recherche, National Natural Science Foundation of China, Fondation pour la Recherche Médicale, Université de Strasbourg, Institut Universitaire de France, Guangdong Provincial Pearl River Talents Program, Basic and Applied Basic Research Foundation of Guangdong Province, H2020 European Research Council
Awards: G1764863541, Understanding the interplay between genomic Structural Variations and Phenotypes using the yeast model, Evolutionary innovation through Gain of Novel Genes, Inheritance, expressivity and epistasis hidden behind the phenotypic landscape of natural populations, G3344279351, G362680486, G4656594441, G4956680542, G5420063140, G593732207, G7428494302, G7475897207, G8365174397, G8800819381, G880779785
OpenAlex ID: W4385415902