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

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 rep...

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Autores principales: O’Donnell, Samuel, Yue, Jia-Xing, Saada, Omar Abou, Agier, Nicolas, Caradec, Claudia, Cokelaer, Thomas, De Chiara, Matteo, Delmas, Stéphane, Dutreux, Fabien, Fournier, Téo, Friedrich, Anne, Kornobis, Etienne, Li, Jing, Miao, Zepu, Tattini, Lorenzo, Schacherer, Joseph, Liti, Gianni, Fischer, Gilles
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10412453/
https://www.ncbi.nlm.nih.gov/pubmed/37524789
http://dx.doi.org/10.1038/s41588-023-01459-y
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author O’Donnell, Samuel
Yue, Jia-Xing
Saada, Omar Abou
Agier, Nicolas
Caradec, Claudia
Cokelaer, Thomas
De Chiara, Matteo
Delmas, Stéphane
Dutreux, Fabien
Fournier, Téo
Friedrich, Anne
Kornobis, Etienne
Li, Jing
Miao, Zepu
Tattini, Lorenzo
Schacherer, Joseph
Liti, Gianni
Fischer, Gilles
author_facet O’Donnell, Samuel
Yue, Jia-Xing
Saada, Omar Abou
Agier, Nicolas
Caradec, Claudia
Cokelaer, Thomas
De Chiara, Matteo
Delmas, Stéphane
Dutreux, Fabien
Fournier, Téo
Friedrich, Anne
Kornobis, Etienne
Li, Jing
Miao, Zepu
Tattini, Lorenzo
Schacherer, Joseph
Liti, Gianni
Fischer, Gilles
author_sort O’Donnell, Samuel
collection PubMed
description 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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spelling pubmed-104124532023-08-11 Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae O’Donnell, Samuel Yue, Jia-Xing Saada, Omar Abou Agier, Nicolas Caradec, Claudia Cokelaer, Thomas De Chiara, Matteo Delmas, Stéphane Dutreux, Fabien Fournier, Téo Friedrich, Anne Kornobis, Etienne Li, Jing Miao, Zepu Tattini, Lorenzo Schacherer, Joseph Liti, Gianni Fischer, Gilles Nat Genet Article 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. Nature Publishing Group US 2023-07-31 2023 /pmc/articles/PMC10412453/ /pubmed/37524789 http://dx.doi.org/10.1038/s41588-023-01459-y Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
O’Donnell, Samuel
Yue, Jia-Xing
Saada, Omar Abou
Agier, Nicolas
Caradec, Claudia
Cokelaer, Thomas
De Chiara, Matteo
Delmas, Stéphane
Dutreux, Fabien
Fournier, Téo
Friedrich, Anne
Kornobis, Etienne
Li, Jing
Miao, Zepu
Tattini, Lorenzo
Schacherer, Joseph
Liti, Gianni
Fischer, Gilles
Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
title Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
title_full Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
title_fullStr Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
title_full_unstemmed Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
title_short Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
title_sort telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in saccharomyces cerevisiae
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10412453/
https://www.ncbi.nlm.nih.gov/pubmed/37524789
http://dx.doi.org/10.1038/s41588-023-01459-y
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