Inheritance, expressivity and epistasis hidden behind the phenotypic landscape of natural populations

Información del proyecto

PhenomeNal

Identificador del acuerdo de subvención: 772505

DOI

10.3030/772505

Proyecto cerrado

Fecha de la firma de la CE 6 Marzo 2018

Fecha de inicio 1 Septiembre 2018

Fecha de finalización 28 Febrero 2025

Financiado con arreglo a

• EXCELLENT SCIENCE - European Research Council (ERC)

Coste total

€ 1 999 882,00

Aportación de la UE

€ 1 999 882,00

Coordinado por

UNIVERSITE DE STRASBOURG
France

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Publicaciones

Peer reviewed articles (29)

Species-Wide Transposable Element Repertoires Retrace the Evolutionary History of the Saccharomyces cerevisiae Host

Autores: Claudine Bleykasten-Grosshans, Romeo Fabrizio, Anne Friedrich, Joseph Schacherer
Publicado en: Molecular Biology and Evolution, Edición 38/10, 2021, Página(s) 4334-4345, ISSN 1537-1719
Editor: Oxford University Press
DOI: 10.1093/molbev/msab171

Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast

Autores: Elie M Teyssonniere, Yuichi Shichino, Mari Mito, Anne Friedrich, Shintaro Iwasaki, Joseph Schacherer
Publicado en: Nucleic Acids Research, Edición 52, 2024, Página(s) 2434-2445, ISSN 0305-1048
Editor: Oxford University Press
DOI: 10.1093/nar/gkae030

Towards accurate, contiguous and complete alignment-based polyploid phasing algorithms

Autores: Omar Abou Saada, Anne Friedrich, Joseph Schacherer
Publicado en: Genomics, Edición 114, 2024, Página(s) 110369, ISSN 0888-7543
Editor: Academic Press
DOI: 10.1016/j.ygeno.2022.110369

Non-additive genetic components contribute significantly to population-wide gene expression variation

Autores: Andreas Tsouris, Gauthier Brach, Joseph Schacherer, Jing Hou
Publicado en: Cell Genomics, Edición 4, 2024, Página(s) 100459, ISSN 2666-979X
Editor: Cell Genomics
DOI: 10.1016/j.xgen.2023.100459

Contrasting Genomic Evolution Between Domesticated and Wild<i>Kluyveromyces lactis</i>Yeast Populations

Autores: Anne Friedrich, Jean-Sébastien Gounot, Andreas Tsouris, Claudine Bleykasten, Kelle Freel, Claudia Caradec, Joseph Schacherer
Publicado en: Genome Biology and Evolution, Edición 15, 2023, ISSN 1759-6653
Editor: Oxford University Press
DOI: 10.1093/gbe/evad004

Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast

Autores: Élodie Caudal, Victor Loegler, Fabien Dutreux, Nikolaos Vakirlis, Élie Teyssonnière, Claudia Caradec, Anne Friedrich, Jing Hou, Joseph Schacherer
Publicado en: Nature Genetics, Edición 56, 2024, Página(s) 1278-1287, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/s41588-024-01769-9

Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

Autores: Elie Marcel Teyssonnière, Pauline Trébulle, Julia Muenzner, Victor Loegler, Daniela Ludwig, Fatma Amari, Michael Mülleder, Anne Friedrich, Jing Hou, Markus Ralser, Joseph Schacherer
Publicado en: Proceedings of the National Academy of Sciences, Edición 121, 2024, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2319211121

Lessons from the meiotic recombination landscape of the ZMM deficient budding yeast Lachancea waltii

Autores: Fabien Dutreux, Abhishek Dutta, Emilien Peltier, Sabrina Bibi-Triki, Anne Friedrich, Bertrand Llorente, Joseph Schacherer
Publicado en: PLOS Genetics, Edición 19, 2023, Página(s) e1010592, ISSN 1553-7404
Editor: PLOS Genetics
DOI: 10.1371/journal.pgen.1010592

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

Autores: Samuel O’Donnell, Jia-Xing Yue, Omar Abou Saada, Nicolas Agier, Claudia Caradec, Thomas Cokelaer, Matteo De Chiara, Stéphane Delmas, Fabien Dutreux, Téo Fournier, Anne Friedrich, Etienne Kornobis, Jing Li, Zepu Miao, Lorenzo Tattini, Joseph Schacherer, Gianni Liti, Gilles Fischer
Publicado en: Nature Genetics, Edición 55, 2023, Página(s) 1390-1399, ISSN 1061-4036
Editor: Nature Publishing Group
DOI: 10.1038/s41588-023-01459-y

Phased polyploid genomes provide deeper insight into the multiple origins of domesticated Saccharomyces cerevisiae beer yeasts

Autores: Omar Abou Saada, Andreas Tsouris, Chris Large, Anne Friedrich, Maitreya J. Dunham, Joseph Schacherer
Publicado en: Current Biology, Edición 32, 2024, Página(s) 1350-1361.e3, ISSN 0960-9822
Editor: Cell Press
DOI: 10.1016/j.cub.2022.01.068

Natural proteome diversity links aneuploidy tolerance to protein turnover

Autores: Julia Muenzner, Pauline Trébulle, Federica Agostini, Henrik Zauber, Christoph B. Messner, Martin Steger, Christiane Kilian, Kate Lau, Natalie Barthel, Andrea Lehmann, Kathrin Textoris-Taube, Elodie Caudal, Anna-Sophia Egger, Fatma Amari, Matteo De Chiara, Vadim Demichev, Toni I. Gossmann, Michael Mülleder, Gianni Liti, Joseph Schacherer, Matthias Selbach, Judith Berman, Markus Ralser
Publicado en: Nature, Edición 630, 2024, Página(s) 149-157, ISSN 0028-0836
Editor: Nature Publishing Group
DOI: 10.1038/s41586-024-07442-9

The dynamics of loss of heterozygosity events in genomes

Autores: Abhishek Dutta, Joseph Schacherer
Publicado en: EMBO Reports, 2025, ISSN 1469-3178
Editor: EMBO
DOI: 10.1038/s44319-024-00353-w

Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast

Autores: Andreas Tsouris, Gauthier Brach, Anne Friedrich, Jing Hou, Joseph Schacherer
Publicado en: Molecular Systems Biology, Edición 20, 2024, Página(s) 362-373, ISSN 1744-4292
Editor: Nature Publishing Group
DOI: 10.1038/s44320-024-00021-0

nPhase: an accurate and contiguous phasing method for polyploids

Autores: Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich, Joseph Schacherer
Publicado en: Genome Biology, Edición 22/1, 2021, ISSN 1474-760X
Editor: Springer Nature
DOI: 10.1186/s13059-021-02342-x

Loss of Heterozygosity Spectrum Depends on Ploidy Level in Natural Yeast Populations

Autores: Abhishek Dutta, Fabien Dutreux, Joseph Schacherer
Publicado en: Molecular Biology and Evolution, Edición 39, 2022, ISSN 0737-4038
Editor: Oxford University Press
DOI: 10.1093/molbev/msac214

Loss-of-function mutation survey revealed that genes with background-dependent fitness are rare and functionally related in yeast

Autores: Elodie Caudal, Anne Friedrich, Arthur Jallet, Marion Garin, Jing Hou, Joseph Schacherer
Publicado en: Proceedings of the National Academy of Sciences, Edición 119, 2022, ISSN 0027-8424
Editor: National Academy of Sciences
DOI: 10.1073/pnas.2204206119

High complexity and degree of genetic variation in Brettanomyces bruxellensis population

Autores: Jean-Sébastien Gounot, Cécile Neuvéglise, Kelle C Freel, Hugo Devillers, Jure Piškur, Anne Friedrich, Joseph Schacherer
Publicado en: Genome Biology and Evolution, 2020, ISSN 1759-6653
Editor: Oxford University Press
DOI: 10.1093/gbe/evaa077

Discordant evolution of mitochondrial and nuclear yeast genomes at population level

Autores: Matteo De Chiara, Anne Friedrich, Benjamin Barré, Michael Breitenbach, Joseph Schacherer, Gianni Liti
Publicado en: BMC Biology, Edición 18/1, 2020, ISSN 1741-7007
Editor: BioMed Central
DOI: 10.1186/s12915-020-00786-4

Extensive impact of low-frequency variants on the phenotypic landscape at population-scale

Autores: Téo Fournier, Omar Abou Saada, Jing Hou, Jackson Peter, Elodie Caudal, Joseph Schacherer
Publicado en: eLife, Edición 8, 2019, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.49258

Pervasive Phenotypic Impact of a Large Nonrecombining Introgressed Region in Yeast

Autores: Christian Brion, Claudia Caradec, David Pflieger, Anne Friedrich, Joseph Schacherer
Publicado en: Molecular Biology and Evolution, 2020, ISSN 0737-4038
Editor: Oxford University Press
DOI: 10.1093/molbev/msaa101

Impact of the acquired subgenome on the transcriptional landscape in <i>Brettanomyces bruxellensis</i> allopolyploids

Autores: Arthur Jallet, Anne Friedrich, Joseph Schacherer
Publicado en: G3: Genes, Genomes, Genetics, Edición 13, 2024, ISSN 2160-1836
Editor: Genetics Society of America
DOI: 10.1093/g3journal/jkad115

Species-wide survey of the expressivity and complexity spectrum of traits in yeast

Autores: Andreas Tsouris, Téo Fournier, Anne Friedrich, Jing Hou, Maitreya J. Dunham, Joseph Schacherer
Publicado en: PLOS Genetics, Edición 20, 2024, Página(s) e1011119, ISSN 1553-7404
Editor: PLOS Genetics
DOI: 10.1371/journal.pgen.1011119

Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds

Autores: Abhishek Dutta, Fabien Dutreux, Joseph Schacherer
Publicado en: eLife, Edición 10, 2021, ISSN 2050-084X
Editor: eLife Sciences Publications
DOI: 10.7554/elife.70339

Extensive simulations assess the performance of genome-wide association mapping in various<i>Saccharomyces cerevisiae</i>subpopulations

Autores: Jackson Peter, Anne Friedrich, Gianni Liti, Joseph Schacherer
Publicado en: Philosophical Transactions of the Royal Society B: Biological Sciences, Edición 377, 2023, ISSN 0962-8436
Editor: Royal Society of London
DOI: 10.1098/rstb.2020.0514

Overview of the Saccharomyces cerevisiae population structure through the lens of 3,034 genomes

Autores: Victor Loegler, Anne Friedrich, Joseph Schacherer
Publicado en: G3 Genes|Genomes|Genetics, 2024, ISSN 2160-1836
Editor: Genetics Society of America
DOI: 10.1093/g3journal/jkae245

Different trajectories of polyploidization shape the genomic landscape of the<i>Brettanomyces bruxellensis</i>yeast species

Autores: Chris Eberlein, Omar Abou Saada, Anne Friedrich, Warren Albertin, Joseph Schacherer
Publicado en: Genome Research, Edición 31, 2023, Página(s) 2316-2326, ISSN 1088-9051
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.275380.121

Copy number variation alters local and global mutational tolerance

Autores: Grace Avecilla, Pieter Spealman, Julia Matthews, Elodie Caudal, Joseph Schacherer, David Gresham
Publicado en: Genome Research, Edición 33, 2023, Página(s) 1340-1353, ISSN 1088-9051
Editor: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.277625.122

Multiple independent losses of crossover interference during yeast evolutionary history

Autores: Abhishek Dutta, Fabien Dutreux, Marion Garin, Claudia Caradec, Anne Friedrich, Gauthier Brach, Pia Thiele, Maxime Gaudin, Bertrand Llorente, Joseph Schacherer
Publicado en: PLOS Genetics, Edición 20, 2024, Página(s) e1011426, ISSN 1553-7404
Editor: PLOS Genetics
DOI: 10.1371/journal.pgen.1011426

Dissection of quantitative trait loci in the Lachancea waltii yeast species highlights major hotspots

Autores: Emilien Peltier, Sabrina Bibi-Triki, Fabien Dutreux, Claudia Caradec, Anne Friedrich, Bertrand Llorente, Joseph Schacherer
Publicado en: G3 Genes|Genomes|Genetics, Edición 11/9, 2021, ISSN 2160-1836
Editor: Genetics Society of America
DOI: 10.1093/g3journal/jkab242