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

Informazioni relative al progetto

PhenomeNal

ID dell’accordo di sovvenzione: 772505

DOI

10.3030/772505

Progetto chiuso

Data della firma CE 6 Marzo 2018

Data di avvio 1 Settembre 2018

Data di completamento 28 Febbraio 2025

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 999 882,00

Contributo UE

€ 1 999 882,00

Coordinato da

UNIVERSITE DE STRASBOURG
France

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (29)

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

Autori: Claudine Bleykasten-Grosshans, Romeo Fabrizio, Anne Friedrich, Joseph Schacherer
Pubblicato in: Molecular Biology and Evolution, Numero 38/10, 2021, Pagina/e 4334-4345, ISSN 1537-1719
Editore: Oxford University Press
DOI: 10.1093/molbev/msab171

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

Autori: Elie M Teyssonniere, Yuichi Shichino, Mari Mito, Anne Friedrich, Shintaro Iwasaki, Joseph Schacherer
Pubblicato in: Nucleic Acids Research, Numero 52, 2024, Pagina/e 2434-2445, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkae030

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

Autori: Omar Abou Saada, Anne Friedrich, Joseph Schacherer
Pubblicato in: Genomics, Numero 114, 2024, Pagina/e 110369, ISSN 0888-7543
Editore: Academic Press
DOI: 10.1016/j.ygeno.2022.110369

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

Autori: Andreas Tsouris, Gauthier Brach, Joseph Schacherer, Jing Hou
Pubblicato in: Cell Genomics, Numero 4, 2024, Pagina/e 100459, ISSN 2666-979X
Editore: Cell Genomics
DOI: 10.1016/j.xgen.2023.100459

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

Autori: Anne Friedrich, Jean-Sébastien Gounot, Andreas Tsouris, Claudine Bleykasten, Kelle Freel, Claudia Caradec, Joseph Schacherer
Pubblicato in: Genome Biology and Evolution, Numero 15, 2023, ISSN 1759-6653
Editore: Oxford University Press
DOI: 10.1093/gbe/evad004

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

Autori: Élodie Caudal, Victor Loegler, Fabien Dutreux, Nikolaos Vakirlis, Élie Teyssonnière, Claudia Caradec, Anne Friedrich, Jing Hou, Joseph Schacherer
Pubblicato in: Nature Genetics, Numero 56, 2024, Pagina/e 1278-1287, ISSN 1061-4036
Editore: 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

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

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

Autori: Fabien Dutreux, Abhishek Dutta, Emilien Peltier, Sabrina Bibi-Triki, Anne Friedrich, Bertrand Llorente, Joseph Schacherer
Pubblicato in: PLOS Genetics, Numero 19, 2023, Pagina/e e1010592, ISSN 1553-7404
Editore: PLOS Genetics
DOI: 10.1371/journal.pgen.1010592

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

Autori: 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
Pubblicato in: Nature Genetics, Numero 55, 2023, Pagina/e 1390-1399, ISSN 1061-4036
Editore: 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

Autori: Omar Abou Saada, Andreas Tsouris, Chris Large, Anne Friedrich, Maitreya J. Dunham, Joseph Schacherer
Pubblicato in: Current Biology, Numero 32, 2024, Pagina/e 1350-1361.e3, ISSN 0960-9822
Editore: Cell Press
DOI: 10.1016/j.cub.2022.01.068

Natural proteome diversity links aneuploidy tolerance to protein turnover

Autori: 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
Pubblicato in: Nature, Numero 630, 2024, Pagina/e 149-157, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-024-07442-9

The dynamics of loss of heterozygosity events in genomes

Autori: Abhishek Dutta, Joseph Schacherer
Pubblicato in: EMBO Reports, 2025, ISSN 1469-3178
Editore: 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

Autori: Andreas Tsouris, Gauthier Brach, Anne Friedrich, Jing Hou, Joseph Schacherer
Pubblicato in: Molecular Systems Biology, Numero 20, 2024, Pagina/e 362-373, ISSN 1744-4292
Editore: Nature Publishing Group
DOI: 10.1038/s44320-024-00021-0

nPhase: an accurate and contiguous phasing method for polyploids

Autori: Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich, Joseph Schacherer
Pubblicato in: Genome Biology, Numero 22/1, 2021, ISSN 1474-760X
Editore: Springer Nature
DOI: 10.1186/s13059-021-02342-x

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

Autori: Abhishek Dutta, Fabien Dutreux, Joseph Schacherer
Pubblicato in: Molecular Biology and Evolution, Numero 39, 2022, ISSN 0737-4038
Editore: 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

Autori: Elodie Caudal, Anne Friedrich, Arthur Jallet, Marion Garin, Jing Hou, Joseph Schacherer
Pubblicato in: Proceedings of the National Academy of Sciences, Numero 119, 2022, ISSN 0027-8424
Editore: National Academy of Sciences
DOI: 10.1073/pnas.2204206119

High complexity and degree of genetic variation in Brettanomyces bruxellensis population

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

Discordant evolution of mitochondrial and nuclear yeast genomes at population level

Autori: Matteo De Chiara, Anne Friedrich, Benjamin Barré, Michael Breitenbach, Joseph Schacherer, Gianni Liti
Pubblicato in: BMC Biology, Numero 18/1, 2020, ISSN 1741-7007
Editore: BioMed Central
DOI: 10.1186/s12915-020-00786-4

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

Autori: Téo Fournier, Omar Abou Saada, Jing Hou, Jackson Peter, Elodie Caudal, Joseph Schacherer
Pubblicato in: eLife, Numero 8, 2019, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.49258

Pervasive Phenotypic Impact of a Large Nonrecombining Introgressed Region in Yeast

Autori: Christian Brion, Claudia Caradec, David Pflieger, Anne Friedrich, Joseph Schacherer
Pubblicato in: Molecular Biology and Evolution, 2020, ISSN 0737-4038
Editore: Oxford University Press
DOI: 10.1093/molbev/msaa101

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

Autori: Arthur Jallet, Anne Friedrich, Joseph Schacherer
Pubblicato in: G3: Genes, Genomes, Genetics, Numero 13, 2024, ISSN 2160-1836
Editore: Genetics Society of America
DOI: 10.1093/g3journal/jkad115

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

Autori: Andreas Tsouris, Téo Fournier, Anne Friedrich, Jing Hou, Maitreya J. Dunham, Joseph Schacherer
Pubblicato in: PLOS Genetics, Numero 20, 2024, Pagina/e e1011119, ISSN 1553-7404
Editore: PLOS Genetics
DOI: 10.1371/journal.pgen.1011119

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

Autori: Abhishek Dutta, Fabien Dutreux, Joseph Schacherer
Pubblicato in: eLife, Numero 10, 2021, ISSN 2050-084X
Editore: 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

Autori: Jackson Peter, Anne Friedrich, Gianni Liti, Joseph Schacherer
Pubblicato in: Philosophical Transactions of the Royal Society B: Biological Sciences, Numero 377, 2023, ISSN 0962-8436
Editore: Royal Society of London
DOI: 10.1098/rstb.2020.0514

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

Autori: Victor Loegler, Anne Friedrich, Joseph Schacherer
Pubblicato in: G3 Genes|Genomes|Genetics, 2024, ISSN 2160-1836
Editore: 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

Autori: Chris Eberlein, Omar Abou Saada, Anne Friedrich, Warren Albertin, Joseph Schacherer
Pubblicato in: Genome Research, Numero 31, 2023, Pagina/e 2316-2326, ISSN 1088-9051
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.275380.121

Copy number variation alters local and global mutational tolerance

Autori: Grace Avecilla, Pieter Spealman, Julia Matthews, Elodie Caudal, Joseph Schacherer, David Gresham
Pubblicato in: Genome Research, Numero 33, 2023, Pagina/e 1340-1353, ISSN 1088-9051
Editore: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.277625.122

Multiple independent losses of crossover interference during yeast evolutionary history

Autori: Abhishek Dutta, Fabien Dutreux, Marion Garin, Claudia Caradec, Anne Friedrich, Gauthier Brach, Pia Thiele, Maxime Gaudin, Bertrand Llorente, Joseph Schacherer
Pubblicato in: PLOS Genetics, Numero 20, 2024, Pagina/e e1011426, ISSN 1553-7404
Editore: PLOS Genetics
DOI: 10.1371/journal.pgen.1011426

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

Autori: Emilien Peltier, Sabrina Bibi-Triki, Fabien Dutreux, Claudia Caradec, Anne Friedrich, Bertrand Llorente, Joseph Schacherer
Pubblicato in: G3 Genes|Genomes|Genetics, Numero 11/9, 2021, ISSN 2160-1836
Editore: Genetics Society of America
DOI: 10.1093/g3journal/jkab242