, Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts, Cell, vol.166, issue.6, pp.1397-1410, 2016.
DOI : 10.1016/j.cell.2016.08.020
URL : https://doi.org/10.1016/j.cell.2016.08.020
, Population genomics of domestic and wild yeasts, Nature, vol.26, issue.7236, pp.337-341, 2009.
DOI : 10.1099/00207713-50-5-1931
, Life with 6000 Genes, Science, vol.274, issue.5287, pp.563-570, 1996.
DOI : 10.1126/science.274.5287.546
, in natural environments remote from human activity, Molecular Ecology, vol.16, issue.Botany, pp.5404-5417, 2012.
DOI : 10.1002/1097-0061(20000615)16:8<773::AID-YEA599>3.0.CO;2-1
, Remarkably ancient balanced polymorphisms in a multi-locus gene network, Nature, vol.5, issue.7285, pp.54-58, 2010.
DOI : 10.1126/science.274.5287.546
, Genus, G3: Genes|Genomes|Genetics, vol.1, issue.1, pp.11-25, 2011.
DOI : 10.1534/g3.111.000273
, Genome Sequence of the Lager Brewing Yeast, an Interspecies Hybrid, DNA Research, vol.16, issue.2, pp.115-129, 2009.
DOI : 10.1093/dnares/dsp003
, Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast, Proceedings of the National Academy of Sciences, vol.464, issue.7285, pp.14539-14544, 2011.
DOI : 10.1038/nature08791
, Comparative genomics of protoploid Saccharomycetaceae, Genome Res, vol.19, pp.1696-1709, 2009.
URL : https://hal.archives-ouvertes.fr/inria-00407511
, Genome evolution in yeasts, Nature, vol.316, issue.6995, pp.35-44, 2004.
DOI : 10.1093/nar/gkg056
URL : https://hal.archives-ouvertes.fr/hal-00104411
, Gene order evolution and paleopolyploidy in hemiascomycete yeasts, Proceedings of the National Academy of Sciences, vol.2, issue.5, pp.9272-9277, 2002.
DOI : 10.1038/35072009
URL : http://www.pnas.org/content/99/14/9272.full.pdf
, Insights into the Dekkera bruxellensis Genomic Landscape: Comparative Genomics Reveals Variations in Ploidy and Nutrient Utilisation Potential amongst Wine Isolates, PLoS Genetics, vol.29, issue.2, p.1004161, 2014.
DOI : 10.1371/journal.pgen.1004161.s014
, Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments, Genome Research, vol.22, issue.5
DOI : 10.1101/gr.130310.111
, Speciation driven by hybridization and chromosomal plasticity in a wild yeast, Nature Microbiology, vol.164, issue.1, p.15003, 2016.
DOI : 10.1186/1471-2148-7-214
, and its lager-brewing hybrids, Molecular Ecology, vol.20, issue.8, pp.2031-2045, 2014.
DOI : 10.1002/evan.20301
, Aneuploidy and copy number breakpoints in the genome of lager yeasts mapped by microarray hybridisation, Current Genetics, vol.45, issue.6, pp.360-370, 2004.
DOI : 10.1007/s00294-004-0504-x
, Extensive Copy Number Variation in Fermentation- Related Genes Among Saccharomyces cerevisiae Wine Strains
DOI : 10.1101/105502
, The Roles of Whole-Genome and Small-Scale Duplications in the Functional Specialization of Saccharomyces cerevisiae Genes, PLoS Genetics, vol.148, issue.1, p.1003176, 2013.
DOI : 10.1371/journal.pgen.1003176.s005
, Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118, Proceedings of the National Academy of Sciences, vol.12, issue.4
DOI : 10.1093/bioinformatics/12.4.357
, YEAST EVOLUTION AND COMPARATIVE GENOMICS, Annual Review of Microbiology, vol.59, issue.1, pp.135-153, 2005.
DOI : 10.1146/annurev.micro.59.030804.121400
, Yeast evolutionary genomics, Nature Reviews Genetics, vol.104, issue.7, pp.512-524, 2010.
DOI : 10.1038/nrg2689
, Polyploidy in fungi: evolution after whole-genome duplication, Proceedings of the Royal Society B: Biological Sciences, vol.142, issue.3, pp.2497-2509, 2012.
DOI : 10.1016/j.ympev.2004.04.018
URL : http://rspb.royalsocietypublishing.org/content/royprsb/279/1738/2497.full.pdf
, Recent Evolution of the Human Pathogen Cryptococcus neoformans by Intervarietal Transfer of a 14-Gene Fragment, Molecular Biology and Evolution, vol.23, issue.10, pp.1879-1890, 2006.
DOI : 10.1093/molbev/msl070
, Insights into the Life Cycle of Yeasts from the CTG Clade Revealed by the Analysis of the Millerozyma (Pichia) farinosa Species Complex, PLoS ONE, vol.78, issue.5, p.35842, 2012.
DOI : 10.1371/journal.pone.0035842.s008
URL : https://hal.archives-ouvertes.fr/hal-01190781
, Sequence Diversity, Reproductive Isolation and Species Concepts in Saccharomyces, Genetics, vol.174, issue.2, pp.839-850, 2006.
DOI : 10.1534/genetics.106.062166
URL : http://www.genetics.org/content/genetics/174/2/839.full.pdf
, A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum, Nature Communications, vol.22, p.4044, 2014.
DOI : 10.1101/gr.130310.111
URL : https://hal.archives-ouvertes.fr/hal-01002466
, Molecular genetic study of introgression betweenSaccharomyces bayanus andS. cerevisiae, Yeast, vol.22, issue.14, pp.1099-1115, 2005.
DOI : 10.1016/S0723-2020(99)80041-1
, Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts, Microbiology and Molecular Biology Reviews, vol.76, issue.4, pp.721-760, 2012.
DOI : 10.1128/MMBR.00022-12
, Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts, Molecular Biology and Evolution, vol.32, issue.7, p.57, 2015.
DOI : 10.1093/molbev/msv057
, Amplification of a Zygosaccharomyces bailii DNA Segment in Wine Yeast Genomes by Extrachromosomal Circular DNA Formation, PLoS ONE, vol.24, issue.3, p.17872, 2011.
DOI : 10.1371/journal.pone.0017872.s002
URL : https://hal.archives-ouvertes.fr/hal-01222409
, Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression, PLoS Genetics, vol.7, issue.3, p.1003366, 2013.
DOI : 10.1371/journal.pgen.1003366.s010
, Adaptive Horizontal Gene Transfers between Multiple Cheese-Associated Fungi, Current Biology, vol.25, issue.19, pp.2562-2569, 2015.
DOI : 10.1016/j.cub.2015.08.025
URL : https://hal.archives-ouvertes.fr/hal-01302701
, Adaptation by introgression, Journal of Biology, vol.8, issue.9, p.82, 2009.
DOI : 10.1186/jbiol176
URL : https://doi.org/10.1186/jbiol176
, Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA, Nature, vol.329, issue.7513, pp.194-197, 2014.
DOI : 10.1126/science.1189406
, Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders, BMC Evolutionary Biology, vol.9, issue.1, p.176, 2009.
DOI : 10.1186/1471-2148-9-176
, Detecting Adaptive Trait Introgression Between Iris fulva and I. brevicaulis in Highly Selective Field Conditions, Genetics, vol.172, issue.4, pp.2481-2489, 2006.
DOI : 10.1534/genetics.105.053538
URL : http://www.genetics.org/content/genetics/172/4/2481.full.pdf
, The origin of the domestic pig: independent domestication and subsequent introgression, Genetics, vol.154, pp.1785-1791, 2000.
, Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome, PLoS ONE, vol.38, issue.5, p.10780, 2010.
DOI : 10.1371/journal.pone.0010780.s009
, The Genetics of Non-conventional Wine Yeasts: Current Knowledge and Future Challenges, Frontiers in Microbiology, vol.151, issue.166, 2016.
DOI : 10.1016/j.ijfoodmicro.2011.08.026
, isolated from Amarone wine, Journal of Applied Microbiology, vol.1, issue.1, pp.210-218, 2009.
DOI : 10.1002/j.2050-0416.2003.tb00602.x
, Predominance of Saccharomyces uvarum during spontaneous alcoholic fermentation, for three consecutive years, in an Alsatian winery, Journal of Applied Microbiology, vol.43, issue.6, pp.1140-1148, 2004.
DOI : 10.1007/BF00173729
, Genetic identification of Saccharomyces bayanus var. uvarum, a cider-fermenting yeast, International Journal of Food Microbiology, vol.65, issue.3, pp.163-71, 2001.
DOI : 10.1016/S0168-1605(00)00515-8
, Natural Populations of Saccharomyces kudriavzevii in Portugal Are Associated with Oak Bark and Are Sympatric with S. cerevisiae and S. paradoxus, Applied and Environmental Microbiology, vol.74, issue.7, pp.2144-2152, 2008.
DOI : 10.1128/AEM.02396-07
, The ecology and evolution of non-domesticated Saccharomyces species, Yeast, vol.31, pp.449-62, 2014.
, Hybridization within Saccharomyces Genus Results in Homoeostasis and Phenotypic Novelty in Winemaking Conditions, PLOS ONE, vol.6, issue.10, p.123834, 2015.
DOI : 10.1371/journal.pone.0123834.s010
, Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads, Genome Research, vol.21, issue.6, pp.936-945, 2011.
DOI : 10.1101/gr.111120.110
, The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009.
DOI : 10.1093/bioinformatics/btp352
URL : https://academic.oup.com/bioinformatics/article-pdf/25/16/2078/531810/btp352.pdf
, The variant call format and VCFtools, Bioinformatics, vol.27, issue.15, 2011.
DOI : 10.1093/bioinformatics/btr330
URL : https://academic.oup.com/bioinformatics/article-pdf/27/15/2156/1125001/btr330.pdf
, A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff, Fly, vol.8, issue.2, pp.80-92, 2012.
DOI : 10.1101/gr.4086505
, Genome sequence assembly using trace signals and additional sequence information, Ger. Conf. Bioinforma, 1999.
, simNGS and simLibrary?software for simulating next-gen sequencing data, 2012.
, High-quality draft assemblies of mammalian genomes from massively parallel sequence data, Proceedings of the National Academy of Sciences, vol.462, issue.7269, 2011.
DOI : 10.1038/462021a
, C-Sibelia: an easy-to-use and highly accurate tool for bacterial genome comparison, F1000Research, vol.174, 1000.
DOI : 10.1111/j.1574-6968.1999.tb13575.x
URL : https://doi.org/10.12688/f1000research.2-258.v1
, Microsatellite analysis of Saccharomyces uvarum diversity, FEMS Yeast Res, vol.16, 2016.
, The [chi-squared] test of goodness of fit, Ann. Math. Stat, vol.25, pp.315-345, 1952.
, SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform, Current Protocols in Human Genetics, vol.357, 2009.
DOI : 10.1002/0471142905.hg0212s60
, Characterization of two forms of asparaginase in Saccharomyces cerevisiae, J. Biol. Chem, vol.253, pp.1297-1304, 1978.
, The amino-acids of apple juices and ciders, Journal of the Science of Food and Agriculture, vol.179, issue.3, pp.122-131, 1957.
DOI : 10.1002/j.2050-0416.1954.tb02779.x
, Grape, apple and pineapple juice characterisation and detection of mixtures, Journal of the Science of Food and Agriculture, vol.70, issue.1, pp.47-53, 1992.
DOI : 10.1002/jsfa.2740600109
, strains, FEMS Yeast Research, vol.7, issue.6, pp.941-952, 2007.
DOI : 10.1111/j.1567-1364.2007.00252.x
URL : https://hal.archives-ouvertes.fr/ensl-00186849
, Fzf1p ofSaccharomyces cerevisiae is a positive regulator ofSSU1 transcription and its first zinc finger region is required for DNA binding, Yeast, vol.25, issue.6, pp.473-480, 1999.
DOI : 10.1128/MCB.12.5.1940
, Formation of hydrogen sulfide and glutathione during fermentation of white grape musts, Am. J. Enol. Vitic, vol.51, pp.91-97, 2000.
, Divergence of the Yeast Transcription Factor FZF1 Affects Sulfite Resistance, PLoS Genetics, vol.86, issue.6, 2012.
DOI : 10.1371/journal.pgen.1002763.s007
, Genomic signatures of adaptation to wine biological aging conditions in biofilm-forming flor yeasts, Mol. Ecol, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01608516
, Advances in Quantitative Trait Analysis in Yeast, PLoS Genetics, vol.8, issue.8, 2012.
DOI : 10.1371/journal.pgen.1002912.g003
URL : https://doi.org/10.1371/journal.pgen.1002912
, Reassessment of phenotypic traits for Saccharomyces bayanus var. uvarum wine yeast strains, International Journal of Food Microbiology, vol.139, issue.1-2, pp.79-86, 2010.
DOI : 10.1016/j.ijfoodmicro.2010.01.038