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

Project Information

PhenomeNal

Grant agreement ID: 772505

DOI

10.3030/772505

Project closed

EC signature date 6 March 2018

Start date 1 September 2018

End date 28 February 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 999 882,00

EU contribution

€ 1 999 882,00

Coordinated by

UNIVERSITE DE STRASBOURG
France

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (29)

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

Author(s): Claudine Bleykasten-Grosshans, Romeo Fabrizio, Anne Friedrich, Joseph Schacherer
Published in: Molecular Biology and Evolution, Issue 38/10, 2021, Page(s) 4334-4345, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab171

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

Author(s): Elie M Teyssonniere, Yuichi Shichino, Mari Mito, Anne Friedrich, Shintaro Iwasaki, Joseph Schacherer
Published in: Nucleic Acids Research, Issue 52, 2024, Page(s) 2434-2445, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkae030

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

Author(s): Omar Abou Saada, Anne Friedrich, Joseph Schacherer
Published in: Genomics, Issue 114, 2024, Page(s) 110369, ISSN 0888-7543
Publisher: Academic Press
DOI: 10.1016/j.ygeno.2022.110369

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

Author(s): Andreas Tsouris, Gauthier Brach, Joseph Schacherer, Jing Hou
Published in: Cell Genomics, Issue 4, 2024, Page(s) 100459, ISSN 2666-979X
Publisher: Cell Genomics
DOI: 10.1016/j.xgen.2023.100459

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

Author(s): Anne Friedrich, Jean-Sébastien Gounot, Andreas Tsouris, Claudine Bleykasten, Kelle Freel, Claudia Caradec, Joseph Schacherer
Published in: Genome Biology and Evolution, Issue 15, 2023, ISSN 1759-6653
Publisher: Oxford University Press
DOI: 10.1093/gbe/evad004

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

Author(s): Élodie Caudal, Victor Loegler, Fabien Dutreux, Nikolaos Vakirlis, Élie Teyssonnière, Claudia Caradec, Anne Friedrich, Jing Hou, Joseph Schacherer
Published in: Nature Genetics, Issue 56, 2024, Page(s) 1278-1287, ISSN 1061-4036
Publisher: 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

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

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

Author(s): Fabien Dutreux, Abhishek Dutta, Emilien Peltier, Sabrina Bibi-Triki, Anne Friedrich, Bertrand Llorente, Joseph Schacherer
Published in: PLOS Genetics, Issue 19, 2023, Page(s) e1010592, ISSN 1553-7404
Publisher: PLOS Genetics
DOI: 10.1371/journal.pgen.1010592

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

Author(s): 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
Published in: Nature Genetics, Issue 55, 2023, Page(s) 1390-1399, ISSN 1061-4036
Publisher: 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

Author(s): Omar Abou Saada, Andreas Tsouris, Chris Large, Anne Friedrich, Maitreya J. Dunham, Joseph Schacherer
Published in: Current Biology, Issue 32, 2024, Page(s) 1350-1361.e3, ISSN 0960-9822
Publisher: Cell Press
DOI: 10.1016/j.cub.2022.01.068

Natural proteome diversity links aneuploidy tolerance to protein turnover

Author(s): 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
Published in: Nature, Issue 630, 2024, Page(s) 149-157, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-024-07442-9

The dynamics of loss of heterozygosity events in genomes

Author(s): Abhishek Dutta, Joseph Schacherer
Published in: EMBO Reports, 2025, ISSN 1469-3178
Publisher: 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

Author(s): Andreas Tsouris, Gauthier Brach, Anne Friedrich, Jing Hou, Joseph Schacherer
Published in: Molecular Systems Biology, Issue 20, 2024, Page(s) 362-373, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.1038/s44320-024-00021-0

nPhase: an accurate and contiguous phasing method for polyploids

Author(s): Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich, Joseph Schacherer
Published in: Genome Biology, Issue 22/1, 2021, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-021-02342-x

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

Author(s): Abhishek Dutta, Fabien Dutreux, Joseph Schacherer
Published in: Molecular Biology and Evolution, Issue 39, 2022, ISSN 0737-4038
Publisher: 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

Author(s): Elodie Caudal, Anne Friedrich, Arthur Jallet, Marion Garin, Jing Hou, Joseph Schacherer
Published in: Proceedings of the National Academy of Sciences, Issue 119, 2022, ISSN 0027-8424
Publisher: National Academy of Sciences
DOI: 10.1073/pnas.2204206119

High complexity and degree of genetic variation in Brettanomyces bruxellensis population

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

Discordant evolution of mitochondrial and nuclear yeast genomes at population level

Author(s): Matteo De Chiara, Anne Friedrich, Benjamin Barré, Michael Breitenbach, Joseph Schacherer, Gianni Liti
Published in: BMC Biology, Issue 18/1, 2020, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-020-00786-4

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

Author(s): Téo Fournier, Omar Abou Saada, Jing Hou, Jackson Peter, Elodie Caudal, Joseph Schacherer
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.49258

Pervasive Phenotypic Impact of a Large Nonrecombining Introgressed Region in Yeast

Author(s): Christian Brion, Claudia Caradec, David Pflieger, Anne Friedrich, Joseph Schacherer
Published in: Molecular Biology and Evolution, 2020, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa101

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

Author(s): Arthur Jallet, Anne Friedrich, Joseph Schacherer
Published in: G3: Genes, Genomes, Genetics, Issue 13, 2024, ISSN 2160-1836
Publisher: Genetics Society of America
DOI: 10.1093/g3journal/jkad115

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

Author(s): Andreas Tsouris, Téo Fournier, Anne Friedrich, Jing Hou, Maitreya J. Dunham, Joseph Schacherer
Published in: PLOS Genetics, Issue 20, 2024, Page(s) e1011119, ISSN 1553-7404
Publisher: PLOS Genetics
DOI: 10.1371/journal.pgen.1011119

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

Author(s): Abhishek Dutta, Fabien Dutreux, Joseph Schacherer
Published in: eLife, Issue 10, 2021, ISSN 2050-084X
Publisher: 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

Author(s): Jackson Peter, Anne Friedrich, Gianni Liti, Joseph Schacherer
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, Issue 377, 2023, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2020.0514

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

Author(s): Victor Loegler, Anne Friedrich, Joseph Schacherer
Published in: G3 Genes|Genomes|Genetics, 2024, ISSN 2160-1836
Publisher: 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

Author(s): Chris Eberlein, Omar Abou Saada, Anne Friedrich, Warren Albertin, Joseph Schacherer
Published in: Genome Research, Issue 31, 2023, Page(s) 2316-2326, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.275380.121

Copy number variation alters local and global mutational tolerance

Author(s): Grace Avecilla, Pieter Spealman, Julia Matthews, Elodie Caudal, Joseph Schacherer, David Gresham
Published in: Genome Research, Issue 33, 2023, Page(s) 1340-1353, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.277625.122

Multiple independent losses of crossover interference during yeast evolutionary history

Author(s): Abhishek Dutta, Fabien Dutreux, Marion Garin, Claudia Caradec, Anne Friedrich, Gauthier Brach, Pia Thiele, Maxime Gaudin, Bertrand Llorente, Joseph Schacherer
Published in: PLOS Genetics, Issue 20, 2024, Page(s) e1011426, ISSN 1553-7404
Publisher: PLOS Genetics
DOI: 10.1371/journal.pgen.1011426

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

Author(s): Emilien Peltier, Sabrina Bibi-Triki, Fabien Dutreux, Claudia Caradec, Anne Friedrich, Bertrand Llorente, Joseph Schacherer
Published in: G3 Genes|Genomes|Genetics, Issue 11/9, 2021, ISSN 2160-1836
Publisher: Genetics Society of America
DOI: 10.1093/g3journal/jkab242