All publications

Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds.
Abhishek Dutta, Fabien Dutreux, Joseph Schacherer.
eLife. 2021. doi: 10.7554/eLife.70339

Species-wide transposable element repertoires retrace the evolutionary history of the Saccharomyces cerevisiae host.
Claudine Bleykasten-Grosshans, Roméo Fabrizio, Anne Friedrich, Joseph Schacherer. 
Molecular Biology and Evolution. 2021. doi: 10.1093/molbev/msab171

nPhase: an accurate and contiguous phasing method for polyploids.
Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich, Joseph Schacherer.
Genome Biology. 2021. doi: 10.1186/s13059-021-02342-x

Sex without crossing over in the yeast Saccharomycodes ludwigii
Ioannis A. Papaioannou, Fabien A. Dutreux, France A. Peltier, Hiromi Maekawa, Nicolas Delhomme, Amit Bardhan, Anne Friedrich, Joseph Schacherer, Michael Knop.
bioRxiv. 2021. doi: 10.1101/2021.04.22.440946

Evolution of quantitative trait locus hotspots in yeast species.
Peltier, E., Bibi-Triki, S., Dutreux, F., Caradec, C., Friedrich, A., Llorente, B., & Schacherer, J. 
bioRxiv. 2021. doi: 10.1101/2021.04.07.438839

Flor yeasts rewire the central carbon metabolism during wine alcoholic fermentation.
Peltier, E., Vion, C., Saada, O. A., Friedrich, A., Schacherer, J., & Marullo, P. 
bioRxiv. 2021. doi: 10.1101/2021.02.27.433177

High-throughput functional analysis of natural variants in yeast.
Yeh, C. C., Tsouris, A., Schacherer, J., & Dunham, M. J. 
bioRxiv. 2021. doi: 10.1101/2021.02.26.433108

Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species.
Eberlein, C., Saada, O. A., Friedrich, A., Albertin, W., & Schacherer, J.
bioRxiv. 2021. doi: 10.1101/2021.02.11.430840

CRISpy-Pop: A Web Tool for Designing CRISPR/Cas9-Driven Genetic Modifications in Diverse Populations.
Hayley R Stoneman, Russell L Wrobel, Michael Place, Michael Graham, David J Krause, Matteo De Chiara, Gianni Liti, Joseph Schacherer, Robert Landick, Audrey P Gasch, Trey K Sato, Chris Todd Hittinger.
G3 (Bethesda). 2020. doi: 10.1534/g3.120.401498

A yeast living ancestor reveals the origin of genomic introgressions.
Melania D'Angiolo, Matteo De Chiara, Jia-Xing Yue, Agurtzane Irizar, Simon Stenberg, Karl Persson, Agnès Llored, Benjamin Barré, Joseph Schacherer, Roberto Marangoni, Eric Gilson, Jonas Warringer, Gianni Liti.
Nature. 2020. doi: 10.1038/s41586-020-2889-1

Discordant evolution of mitochondrial and nuclear yeast genomes at population level.
Matteo De Chiara, Anne Friedrich, Benjamin Barré, Michael Breitenbach, Joseph Schacherer, Gianni Liti.
BMC Biology, 2020; doi: 10.1186/s12915-020-00786-4

Pervasive phenotypic impact of a large non-recombining introgressed region in yeast.
Christian Brion, Claudia Caradec, David Pflieger, Anne Friedrich, Joseph Schacherer.
Molecular Biology and Evolution, 2020; doi:10.1093/molbev/msaa101

High complexity and degree of genetic variation in Brettanomyces bruxellensis population.
Jean-Sébastien Gounot, Cécile Neuvéglise, Kelle C Freel, Hugo Devillers, Jure Piškur, Anne Friedrich, Joseph Schacherer.
Genome Biology and Evolution 2020; doi: 10.1093/gbe/evaa077

Domestication reprogrammed the budding yeast life cycle.
De Chiara, M., Barré, B., Persson, K., Chioma, A. O., Irizar, A., Schacherer, J., Warringer, J., & Liti, G.
bioRxiv. 2020. doi: 10.1101/2020.02.08.939314

Extensive impact of low-frequency variants on the phenotypic landscape at population-scale.
Téo Fournier, Omar Abou Saada, Jing Hou, Jackson Peter, Elodie Caudal, Joseph Schacherer.
eLife 2019;8:e49258 doi: 10.7554/eLife.49258

The induction of HAD-like phosphatases by multiple signaling pathways confers resistance to the metabolic inhibitor 2-deoxyglucose.
Quentin Defenouillère, Agathe Verraes, Clotilde Laussel, Anne Friedrich, Joseph Schacherer, Sébastien Léon.
Science Signaling 2019, doi: 10.1126/scisignal.aaw8000

Reshuffling yeast chromosomes with CRISPR/Cas9.
Aubin Fleiss, Samuel O'Donnell, Téo Fournier, Wenqing Lu, Nicolas Agier, Stéphane Delmas, Joseph Schacherer, Gilles Fischer.
PLoS Genet. 2019, doi: 10.1371/journal.pgen.1008332

RNAi as a tool to study virulence in the pathogenic yeast Candida glabrata.
Olena P. Ishchuk, Khadija Mohamed Ahmad, Katarina Koruza, Klara Bojanovič, Marcel Sprenger, Lydia Kasper, Sascha Brunke, Bernhard Hube, Torbjörn Säll, Thomas Hellmark, Birgitta Gullstrand, Christian Brion, Kelle Freel, Joseph Schacherer, Birgitte Regenberg, Wolfgang Knecht, Jure Piškur.
Front Microbiol. 2019, doi: 10.3389/fmicb.2019.01679

Quantitative Trait Nucleotides impacting the technological performances of industrial Saccharomyces cerevisiae strains.
Emilien Peltier, Anne Friedrich, Joseph Schacherer, Philippe Marullo.
Front. Genet. 2019, doi: 10.3389/fgene.2019.00683

Andre Goffeau's imprinting on second generation yeast "genomologists".
Cécile Fairhead, Gilles Fischer, Giani Liti, Cécile Neuveglise, Joseph Schacherer.
Yeast. 2019, doi: 10.1002/yea.3377

Incompatibilities in mismatch repair genes MLH1-PMS1 contribute to a wide range of mutation rates in human isolates of baker's yeast.
Vandana Raghavan, Duyen T. Bui, Najla Al-Sweel, Anne Friedrich, Joseph Schacherer, Charles F. Aquadro, Eric Alani.
Genetics. 2018, doi: 10.1534/genetics.118.301550

Genome evolution across 1,011 Saccharomyces cerevisiae isolates.
Jackson Peter, Matteo De Chiara, Anne Friedrich, Jia-Xing Yue, David Pflieger, Anders Bergström, Anastasie Sigwalt, Benjamin Barre, Kelle Freel, Agnès Llored, Corinne Cruaud, Karine Labadie, Jean-Marc Aury, Benjamin Istace, Kevin Lebrigand, Pascal Barbry, Stefan Engelen, Arnaud Lemainque, Patrick Wincker, Gianni Liti, Joseph Schacherer.
Nature. 2018, 556:339–344, doi: 10.1038/s41586-018-0030-5

Brettanomyces bruxellensis population survey reveals a diploid-triploid complex structured according to substrate of isolation and geographical distribution.
Marta Avramova, Alice Cibrario, Emilien Peltier, Monika Coton, Emmanuel Coton, Joseph Schacherer, Giuseppe Spano, Vittorio Capozzi, Giuseppe Blaiotta, Franck Salin, Marguerite Dols-Lafargue, Paul Grbin, Chris Curtin, Warren Albertin, Isabelle Masneuf-Pomarede.
Scientific Reports. 2018, doi: 10.1038/s41598-018-22580-7

Genetic backgrounds and hidden trait complexity in natural populations.
Téo Fournier, Joseph Schacherer.
Current Opinion in Genetics & Development. 2017, 47:48-53.

High-quality de novo genome assembly of the Dekkera bruxellensis yeast isolate using Nanopore MinION sequencing.
Téo Fournier, Jean-Sébastien Gounot, Kelle Freel, Corinne Cruaud, Arnaud Lemainque, Jean-Marc Aury, Patrick Wincker, Joseph Schacherer, Anne Friedrich.
G3. 2017, doi: 10.1534/g3.117.300128

Yeast-bacteria competition induced new metabolic traits through large-scale genomic rearrangements in Lachancea kluyveri.
Nerve Zhou, Samuele Bottagisi, Michael Katz, Joseph Schacherer, Anne Friedrich, Zoran Gojkovic, Krishna B. S. Swamy, Wolfgang Knecht, Concetta Compagno, Jure Piškur.
FEMS Yeast Research. 2017, doi: 10.1093/femsyr/fox060

Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts.
Christian Brion, Sylvain Legrand, Jackson Peter, Claudia Caradec, David Pflieger, Jing Hou, Anne Friedrich, Bertrand Llorente, Joseph Schacherer.
PLoS Genet. 2017, doi: 10.1371/journal.pgen.1006917

Phenotypic diagnosis of lineage and differentiation during sake yeast breeding.
Shinsuke Ohnuki, Hiroki Okada, Anne Friedrich, Yoichiro Kanno, Tetsuya Goshima, Hirokazu Hasuda, Masaaki Inahashi, Naoto Okazaki, Hiroyasu Tamura, Ryo Nakamura, Dai Hirata, Hisashi Fukuda, Hitoshi Shimoi, Katsuhiko Kitamoto, Daisuke Watanabe, Joseph Schacherer, Takeshi Akao, Yoshikazu Ohya.
G3. 2017, doi: 10.1534/g3.117.044099

Mismatch Repair Incompatibilities in Diverse Yeast Populations.
Duyen T. Bui, Anne Friedrich, Najla Al-Sweel, Gianni Liti, Joseph Schacherer, Charles F. Aquadro, Eric Alani.
Genetics. 2017, doi: 10.1534/genetics.116.199513

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer.
Benjamin Istace, Anne Friedrich, Léo d’Agata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, Sabrina Davidas, Corinne Cruaud, Gianni Liti, Arnaud Lemainque, Stefan Engelen, Patrick Wincker, Joseph Schacherer, Jean-Marc Aury.
Gigascience. 2017, doi: 10.1093/gigascience/giw018

Fitness trade-offs lead to suppressor tolerance in yeast.
Jing Hou, Joseph Schacherer.
Mol Biol Evol. 2016, doi: 10.1093/molbev/msw225

The hidden complexity of mendelian traits across natural yeast populations.
Jing Hou, Anastasie Sigwalt, Téo Fournier, David Pflieger, Jackson Peter, Jacky de Montigny, Maitreya J. Dunham, Joseph Schacherer.
Cell Reports. 2016, doi: 10.1016/j.celrep.2016.06.048

Dissection of quantitative traits by bulk segregant mapping in a protoploid yeast species.
Anastasie Sigwalt, Claudia Caradec C, Christian Brion, Jing Hou, Jacky de Montigny, Paul Jung, Gilles Fischer, Bertrand Llorente, Anne Friedrich, Joseph Schacherer.
FEMS Yeast Res. 2016, doi: 10.1093/femsyr/fow056

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus.
Nikolaos Vakirlis, Véronique Sarilar, Guénola Drillon, Aubin Fleiss, Nicolas Agier, Jean-Philippe Meyniel, Lou Blanpain, Alessandra Carbone, Hugo Devillers, Kenny Dubois, Alexandre Gillet-Markowska, Stéphane Graziani, Nguyen Huu-Vang, Marion Poirel, Cyrielle Reisser, Jonathan Schott, Joseph Schacherer, Ingrid Lafontaine, Bertrand Llorente, Cécile Neuvéglise and Gilles Fischer.
Genome Research.2016, doi: 10.1101/gr.204420.116

Beyond the simplicity of Mendelian inheritance.
Joseph Schacherer.
Comptes Rendus Biologies. 2016, doi:10.1016/j.crvi.2016.04.006

Species-wide survey reveals the various flavors of intraspecific reproductive isolation in yeast.
Jing Hou, Téo Fournier, Joseph Schacherer.
FEMS Yeast Res. 2016, doi: 10.1093/femsyr/fow048

Differences in environmental stress response between yeasts is consistent with species-specific lifestyles.
Christian Brion, David Pflieger, Sirine Souali-Crespo, Anne Friedrich, Joseph Schacherer.
Mol Biol Cell. 2016, doi: 10.1091/mbc

Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species.
Paul P. Jung, Anastasie Sigwalt, Shinsuke Ohnuki, Jacky de Montigny, Yoshikazu Ohya, Joseph Schacherer.
G3. 2016, doi: 10.1534/g3.115.026682

The hidden complexity of Mendelian traits across yeast natural populations.
Jing Hou, Anastasie Sigwalt, David Pflieger, Jackson Peter, Jacky de Montigny, Maitreya Dunham, Joseph Schacherer.
Biorxivpreprint. 2016, doi: 10.1101/039693

Whole-genome sequencing and intraspecific analysis of the yeast species Lachancea quebecensis.
Kelle C Freel, Anne Friedrich, Véronique Sarilar, Hugo Devillers, Cécile Neuvéglise, Joseph Schacherer.
Genome Biol Evol. 2016, doi:10.1093/gbe/evv262

On the Mapping of Epistatic Genetic Interactions in Natural Isolates: Combining Classical Genetics and Genomics.
Jing Hou, Joseph Schacherer.
Methods Mol Biol. 2016, 1361:345-60.

Population genomics of yeasts: Towards a comprehensive view across a broad evolutionary scale.
Jackson Peter, Joseph Schacherer.
Yeast. 2015, doi: 10.1002/yea.3142

Lachancea quebecensis sp. nov., a yeast species consistently isolated from tree bark in the Canadian province of Québec.
Kelle C. Freel,  Guillaume Charron,  Jean-Baptiste Leducq,  Christian R Landry, Joseph Schacherer.
Int J Syst Evol Microbiol. 2015, doi: 10.1099/ijsem.0.000426

Negative epistasis: a route to intraspecific reproductive isolation in yeast?
Jing Hou, Joseph Schacherer.
Curr Genet. 2015, doi 10.1007/s00294-015-0505-y

Comprehensive survey of condition-specific reproductive isolation reveals genetic incompatibility in yeast.
Jing Hou, Anne Friedrich, Jean-Sébastien Gounot, Joseph Schacherer.
Nat Commun. 2015, 26 (6):7214.

Mitochondrial genome evolution in yeasts: an all-encompassing view.
Kelle C. Freel, Anne Friedrich, Joseph Schacherer.
FEMS Yeast Res. 2015, doi: 10.1093/femsyr/fov023

Evolution of intraspecific transcriptomic landscapes in yeasts.
Christian Brion, David Pflieger, Anne Friedrich and Joseph Schacherer.
Nucl Acids Res. 2015, doi: 10.1093/nar/gkv363

Draft genome sequence of Lachancea lanzarotensis CBS 12615^T, an ascomycetous yeast isolated from grapes.
Véronique Sarilar, Hugo Devillers, Kelle C. Freel, Joseph Schacherer, Cécile Neuvéglise.
Genome Announc. 2015, 3 (2):e00292-15.

Population genomics reveals chromosome-scale heterogeneous evolution in a protoploid yeast.
Anne Friedrich, Paul Jung, Cyrielle Reisser, Gilles Fischer, Joseph Schacherer.
Mol Biol Evol. 2015, 32 (1):184-192.

Evolutionary dynamics of hAT DNA transposon families in Saccharomycetaceae.
Véronique Sarilar, Claudine Bleykasten-Grosshans, Cécile Neuvéglise.
Genome Biol Evol. 2015, 7 (1):172-190.

Population genomic analysis reveals highly conserved mitochondrial genomes in the yeast species Lachancea thermotolerans.
Kelle C Freel, Anne Friedrich, Jing Hou, Joseph Schacherer.
Genome Biol Evol. 2014, 6 (10):2586-2594.

Genome sequence of the yeast Cyberlindnera fabianii (Hansenulafabianii).
Kelle C Freel, Véronique Sarilar, Cécile Neuvéglise , Hugo Devillers, Anne Friedrich, Joseph Schacherer.
Genome Announc. 2014, 7:2(4).

Chromosomal rearrangements as a major mechanism in the onset of reproductive isolation in Saccharomyces cerevisiae.
Jing Hou, Anne Friedrich, Jacky de Montigny, Joseph Schacherer.
Current Biology. 2014, 24(10):1153-9.

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.
Kunze G, Gaillardin C, Czernicka M, Durrens P, Martin T, Böer E, Gabaldón T, Cruz JA, Talla E, Marck C, Goffeau A, Barbe V, Baret P, Baronian K, Beier S, Bleykasten C, Bode R, Casaregola S, Despons L, Fairhead C, Giersberg M, Gierski PP, Hähnel U, Hartmann A, Jankowska D, Jubin C, Jung P, Lafontaine I, Leh-Louis V, Lemaire M, Marcet-Houben M, Mascher M, Morel G, Richard GF, Riechen J, Sacerdot C, Sarkar A, Savel G, Schacherer J, Sherman DJ, Stein N, Straub ML, Thierry A, Trautwein-Schult A, Vacherie B, Westhof E, Worch S, Dujon B, Souciet JL, Wincker P, Scholz U, Neuvéglise C.
Biotechnol Biofuels. 2014, 7:66.

Single-cell phenomics reveals intra-species variation of phenotypic noise in yeast.
Gaël Yvert, Shinsuke Ohnuki, Satoru Nogami, Yasutaka Imanaga, Steffen Fehrmann, Joseph Schacherer and Yoshikazu Ohya.
BMC Systems Biology. 2013, 7:54.

Genome-wide analysis of intraspecific transposon diversity in yeast.
Claudine Bleykasten-Grosshans, Anne Friedrich, Joseph Schacherer.
BMC Genomics. 2013, 14:399.

Genetic basis of ammonium toxicity resistance in a sake strain of yeast: a mendelian case.
Cyrielle Reisser, Cynthia Dick, Leonid Kruglyak, David Botstein, Joseph Schacherer, David Hess.
G3 (Bethesda). 2013, 3:733-740.

Comparative mitochondrial genomics within and among yeast species of the Lachancea genus.
Anne Friedrich, Paul P Jung, Jing Hou, Cécile Neuvéglise, Joseph Schacherer.
PLoS One. 2012, 7(10):e47834.

Mitochondrial genome evolution in a single protoploid yeast species.
Paul P Jung, Anne Friedrich, Cyrielle Reisser, Jing Hou, Joseph Schacherer.
G3 (Bethesda). 2012, 2(9):1103-11.

Pichia sorbitophila, an interspecies yeast hybrid, reveals early steps of genome resolution after polyploidization.
Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casarégola S, Neuvéglise C, Fairhead C, Marck C, Cruz JA, Straub ML, Kugler V, Sacerdot C, Uzunov Z, Thierry A, Weiss S, Bleykasten C, De Montigny J, Jacques N, Jung P, Lemaire M, Mallet S, Morel G, Richard GF, Sarkar A, Savel G, Schacherer J, Seret ML, Talla E, Samson G, Jubin C, Poulain J, Vacherie B, Barbe V, Pelletier E, Sherman DJ, Westhof E, Weissenbach J, Baret PV, Wincker P, Gaillardin C, Dujon B, Souciet JL.
G3 (Bethesda). 2012, 2(2):299-311.

The rise of yeast population genomics.
Giani Liti, Joseph Schacherer.
C R Biol. 2011, 334(8-9):612-9.

Transposable elements in yeasts.
Claudine Bleykasten-Grosshans, Cécile Neuvéglise.
C R Biol. 2011, 334(8-9):679-86.

Ploidy influences cellular responses to gross chromosomal rearrangements in Saccharomyces cerevisiae.
Paul P Jung, Emilie S Fritsch, Corinne Blugeon, Jean-Luc Souciet, Serge Potier, Sophie Lemoine, Joseph Schacherer, Jacky de Montigny.
BMC Genomics. 2011, 12:331.

Complete mitochondrial genome sequence of the yeast Pichia farinosa and comparative analysis of closely related species.
Jung PP, Friedrich A, Souciet JL, Louis V, Potier S, de Montigny J, Schacherer J.
Curr Genet. 2010 Dec;56(6):507-15

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae.
Schacherer J, Shapiro JA, Ruderfer DM, Kruglyak L.
Nature. 2009 Mar 19;458(7236):342-5.

The complete mitochondrial genome of the yeast Pichia sorbitophila.
Jung PP, Schacherer J, Souciet JL, Potier S, Wincker P, de Montigny J.
FEMS Yeast Res. 2009 Sep;9(6):903-10.

Comparative genomics of protoploid Saccharomycetaceae.
Génolevures Consortium, Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E, Wincker P, Jubin C, Poulain J, Barbe V, Ségurens B, Artiguenave F, Anthouard V, Vacherie B, Val ME, Fulton RS, Minx P, Wilson R, Durrens P, Jean G, Marck C, Martin T, Nikolski M, Rolland T, Seret ML, Casarégola S, Despons L, Fairhead C, Fischer G, Lafontaine I, Leh V, Lemaire M, de Montigny J, Neuvéglise C, Thierry A, Blanc-Lenfle I, Bleykasten C, Diffels J, Fritsch E, Frangeul L, Goëffon A, Jauniaux N, Kachouri-Lafond R, Payen C, Potier S, Pribylova L, Ozanne C, Richard GF, Sacerdot C, Straub ML, Talla E.
Genome Res. 2009 Oct;19(10):1696-709.

Influence of genetic background on the occurrence of chromosomal rearrangements in Saccharomyces cerevisiae.
Fritsch ES, Schacherer J, Bleykasten-Grosshans C, Souciet JL, Potier S, de Montigny J.
BMC Genomics. 2009 Mar 6;10:99.

Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.
Sherman DJ, Martin T, Nikolski M, Cayla C, Souciet JL, Durrens P; Génolevures Consortium.
Nucleic Acids Res. 2009 Jan;37(Database issue):D550-4.

Spontaneous duplications in diploid Saccharomyces cerevisiae cells.
Schacherer J, Tourrette Y, Potier S, Souciet JL, de Montigny J.
DNA Repair (Amst). 2007 Oct 1;6(10):1441-52.

Spontaneous deletions and reciprocal translocations in Saccharomyces cerevisiae: influence of ploidy.
Tourrette Y, Schacherer J, Fritsch E, Potier S, Souciet JL, de Montigny J.
Mol Microbiol. 2007 Apr;64(2):382-95.