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Publications

2017

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

Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C.
Caiti S. Heil, Joshua N. Burton, Ivan Liachko, Anne Friedrich, Noah A. Hanson, Cody L. Morris, Joseph Schacherer, Jay Shendure, James H. Thomas, Maitreya J. Dunham.
Yeast. 2017, doi: 10.1002/yea.3280.

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, https://doi.org/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, https://doi.org/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, https://doi.org/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, https://doi.org/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:https://doi.org/10.1093/gigascience/giw018.

2016

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: dx.doi.org/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: dx.doi.org/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.

2015

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: dx.doi.org/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 12615T, 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.

2014

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 (Hansenula fabianii).
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.

2013

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.

2012

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.

2011

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.

The Ty1 LTR-retrotransposon population in Saccharomyces cerevisiae genome: dynamics and sequence variations during mobility.
Claudine Bleykasten-Grosshans, Paul P Jung, Emilie S Fritsch, Serge Potier, Jacky de Montigny, Jean-Luc Souciet.
FEMS Yeast Res. 2011, 11(4):334-44.

2010

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

An unusual retinal phenotype associated with a novel mutation in RHO.
Audo I, Friedrich A, Mohand-Saïd S, Lancelot ME, Antonio A, Moskova-Doumanova V, Poch O, Bhattacharya S, Sahel JA, Zeitz C.
Arch Ophthalmol. 2010 Aug;128(8):1036-45.

SM2PH-db: an interactive system for the integrated analysis of phenotypic consequences of missense mutations in proteins involved in human genetic diseases.
Friedrich A, Garnier N, Gagnière N, Nguyen H, Albou LP, Biancalana V, Bettler E, Deléage G, Lecompte O, Muller J, Moras D, Mandel JL, Toursel T, Moulinier L, Poch O.
Hum Mutat. 2010 Feb;31(2):127-35.

2009

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.