Michel RH, McGovern PE, Badler VR. Chemical evidence for ancient beer. Nature. 1992;360(6399):24.
Article
Google Scholar
Fay JC, Benavides JA. Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet. 2005;1(1):e5.
Article
CAS
PubMed Central
Google Scholar
Edgardo A, Carolina P, Manuel R, Juanita F, Baeza J. Selection of thermotolerant yeast strains Saccharomyces cerevisiae for bioethanol production. Enzym Microb Technol. 2008;43(2):120–3.
Article
CAS
Google Scholar
Marsit S, Dequin S. Diversity and adaptive evolution of Saccharomyces wine yeast: a review. FEMS Yeast Res. 2015;15(7):fov067.
Rozpędowska E, Hellborg L, Ishchuk OP, Orhan F, Galafassi S, Merico A, Woolfit M, Compagno C, Piškur J. Parallel evolution of the make–accumulate–consume strategy in Saccharomyces and Dekkera yeasts. Nat Commun. 2011;2:302.
Article
CAS
PubMed
Google Scholar
Smith MT. Chapter 89 - Brettanomyces Kufferath & van Laer (1921). In: Kurtzman CP, Fell JW, Boekhout T, editors. The Yeasts (Fifth Edition). Edited by. London: Elsevier; 2011. p. 983–6.
Google Scholar
Peter G, Dlauchy D, Tobias A, Fulop L, Podgorsek M, Cadez N. Brettanomyces acidodurans sp. nov., a new acetic acid producing yeast species from olive oil. Antonie Van Leeuwenhoek. 2017;110(5):657–64.
Article
CAS
PubMed
Google Scholar
Yamada Y, Matsuda M, Maeda K, Mikata K. The phylogenetic relationships of species of the genus Dekkera van der Walt based on the partial sequences of 18S and 26S ribosomal RNAs (Saccharomycetaceae). Biosci Biotechnol Biochem. 1994;58(10):1803–8.
Article
CAS
PubMed
Google Scholar
Yamada Y, Matsuda M, Mikata K. The phylogenetic relationships ofEeniella nana Smith, Batenburg-van der Vegte et Scheffers based on the partial sequences of 18S and 26S ribosomal RNAs (Candidaceae). J Ind Microbiol. 1995;14(6):456–60.
Article
CAS
PubMed
Google Scholar
Röder C, König H, Fröhlich J. Species-specific identification of Dekkera/Brettanomyces yeasts by fluorescently labeled DNA probes targeting the 26S rRNA. FEMS Yeast Res. 2007;7(6):1013–26.
Article
CAS
PubMed
Google Scholar
Chatonnet P, Dubourdie D, Boidron J-N, Pons M. The origin of ethylphenols in wines. J Sci Food Agric. 1992;60(2):165–78.
Article
CAS
Google Scholar
Chatonnet P, Dubourdieu D, Boidron JN. The Influence of Brettanomyces/Dekkera sp. Yeasts and Lactic Acid Bacteria on the Ethylphenol Content of Red Wines. Am J Enology Viticulture. 1995;46(4):463.
CAS
Google Scholar
Van Oevelen D, Spaepen M, Timmermans P, Verachtert H. Microbiological aspects of spontaneous wort fermentation in the production of lambic and gueuze. J Inst Brew. 1977;83(6):356–60.
Article
Google Scholar
Spaepen M, Van Oevelen D, Verachtert H. Fatty acids and esters produced during the spontaneous fermentation of lambic and gueuze. J Inst Brew. 1978;84(5):278–82.
Article
CAS
Google Scholar
Basso RF, Alcarde AR, Portugal CB. Could non-Saccharomyces yeasts contribute on innovative brewing fermentations? Food Res Int. 2016;86:112–20.
Article
CAS
Google Scholar
De Souza Liberal AT, Basílio ACM, Do Monte Resende A, BTV B, Da Silva-Filho EA, JOF DM, Simões DA, De Morais MA Jr. Identification of Dekkera bruxellensis as a major contaminant yeast in continuous fuel ethanol fermentation. J Appl Microbiol. 2007;102(2):538–47.
Article
CAS
PubMed
Google Scholar
Reis ALS, de Fátima Rodrigues de Souza R, RRN BT, FCB L, PMG P, Vidal EE, de Morais MA. Oxygen-limited cellobiose fermentation and the characterization of the cellobiase of an industrial Dekkera/Brettanomyces bruxellensis strain. SpringerPlus. 2014;3(1):38.
Article
CAS
PubMed
PubMed Central
Google Scholar
Curtin CD, Borneman AR, Chambers PJ, Pretorius IS. De-novo assembly and analysis of the heterozygous triploid genome of the wine spoilage yeast Dekkera bruxellensis AWRI1499. PLoS One. 2012;7(3):e33840.
Article
CAS
PubMed
PubMed Central
Google Scholar
Albertin W, Panfili A, Miot-Sertier C, Goulielmakis A, Delcamp A, Salin F, Lonvaud-Funel A, Curtin C, Masneuf-Pomarede I. Development of microsatellite markers for the rapid and reliable genotyping of Brettanomyces bruxellensis at strain level. Food Microbiol. 2014;42:188–95.
Article
CAS
PubMed
Google Scholar
Borneman AR, Zeppel R, Chambers PJ, Curtin CD. Insights into the Dekkera bruxellensis genomic landscape: comparative genomics reveals variations in Ploidy and nutrient utilisation potential amongst wine isolates. PLoS Genet. 2014;10(2):e1004161.
Article
CAS
PubMed
PubMed Central
Google Scholar
Crauwels S, Zhu B, Steensels J, Busschaert P, De Samblanx G, Marchal K, Willems KA, Verstrepen KJ, Lievens B. Assessing genetic diversity among genus-species Brettanomyces yeasts by DNA fingerprinting and whole-genome sequencing. Appl Environ Microbiol. 2014;80(14):4398.
Article
CAS
PubMed
PubMed Central
Google Scholar
Varela C, Lleixà J, Curtin C, Borneman A. Development of a genetic transformation toolkit for Brettanomyces bruxellensis. FEMS Yeast Res. 2018;18(7):foy070.
Varela C, Bartel C, Roach M, Borneman A, Curtin C. Brettanomyces bruxellensis SSU1 haplotypes confer different levels of sulfite tolerance when expressed in a Saccharomyces cerevisiae SSU1 null mutant. Appl Environ Microbiol. 2019;85(4):e02429–18.
CAS
PubMed
PubMed Central
Google Scholar
Fournier T, Gounot J-S, Freel K, Cruaud C, Lemainque A, Aury J-M, Wincker P, Schacherer J, Friedrich A. High-Quality de Novo Genome Assembly of the Dekkera bruxellensis Yeast Using Nanopore MinION Sequencing. G3. 2017;7(10):3243–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vervoort Y, Herrera-Malaver B, Mertens S, Guadalupe Medina V, Duitama J, Michiels L, Derdelinckx G, Voordeckers K, Verstrepen KJ. Characterization of the recombinant Brettanomyces anomalus β-glucosidase and its potential for bioflavouring. J Appl Microbiol. 2016;121(3):721–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Avramova M, Cibrario A, Peltier E, Coton M, Coton E, Schacherer J, Spano G, Capozzi V, Blaiotta G, Salin F, et al. Brettanomyces bruxellensis population survey reveals a diploid-triploid complex structured according to substrate of isolation and geographical distribution. Sci Rep. 2018;8(1):4136.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hellborg L, Piskur J. Complex nature of the genome in a wine spoilage yeast, Dekkera bruxellensis. Eukaryot Cell. 2009;8(11):1739–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koren S, Phillippy AM. One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly. Curr Opin Microbiol. 2015;23:110–20.
Article
CAS
PubMed
Google Scholar
Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36:338.
Article
CAS
PubMed
PubMed Central
Google Scholar
van der Walt J. Brettanomyces custersianus Nov. spec. Antonie Van Leeuwenhoek. 1961;27:332–6.
Article
PubMed
Google Scholar
Kolfschoten GA, Yarrow D. Brettanomyces naardenensis, a new yeast from soft drinks. Antonie Van Leeuwenhoek. 1970;36(1):458–60.
Article
CAS
PubMed
Google Scholar
Smith MT, van Grinsven AM. Dekkera anomala sp. nov., the teleomorph of Brettanomyces anomalus, recovered from spoiled soft drinks. Antonie Van Leeuwenhoek. 1984;50(2):143–8.
Article
CAS
PubMed
Google Scholar
Boekhout T, Kurtzman CP, O'Donnell K, Smith MT. Phylogeny of the yeast genera Hanseniaspora (anamorph Kloeckera), Dekkera (anamorph Brettanomyces), and Eeniella as inferred from partial 26S ribosomal DNA nucleotide sequences. Int J Syst Bacteriol. 1994;44(4):781–6.
Article
CAS
PubMed
Google Scholar
Cheng J, Guo X, Cai P, Cheng X, Piškur J, Ma Y, Jiang H, Gu Z. Parallel evolution of chromatin structure underlying metabolic adaptation. Mol Biol Evol. 2017;34(11):2870–8.
Article
CAS
PubMed
Google Scholar
Piskur J, Ling Z, Marcet-Houben M, Ishchuk OP, Aerts A, LaButti K, Copeland A, Lindquist E, Barry K, Compagno C, et al. The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties. Int J Food Microbiol. 2012;157(2):202–9.
Article
CAS
PubMed
Google Scholar
Shen X-X, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, et al. Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum. Cell. 2018;175(6):1533–1545.e1520.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tiukova IA, Jiang H, Dainat J, Hoeppner MP, Lantz H, Piskur J, Sandgren M, Nielsen J, Gu Z, Passoth V. Assembly and analysis of the genome sequence of the yeast Brettanomyces naardenensis CBS 7540. Microorganisms. 2019;7(11):489.
Article
PubMed Central
Google Scholar
Roach MJ, Schmidt SA, Borneman AR. Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies. BMC Bioinformatics. 2018;19(1):460.
Article
CAS
PubMed
PubMed Central
Google Scholar
Reuber BE, Karl C, Reimann SA, Mihalik SJ, Dodt G. Cloning and functional expression of a mammalian gene for a Peroxisomal Sarcosine oxidase. J Biol Chem. 1997;272(10):6766–76.
Article
CAS
PubMed
Google Scholar
Wagner MA, Jorns MS. Monomeric Sarcosine oxidase: 2. Kinetic studies with Sarcosine, alternate substrates, and a substrate analogue. Biochemistry. 2000;39(30):8825–9.
Article
CAS
PubMed
Google Scholar
Yoshida N, Akazawa S-I, Katsuragi T, Tani Y. Characterization of two fructosyl-amino acid oxidase homologs of Schizosaccharomyces pombe. J Biosci Bioeng. 2004;97(4):278–80.
Article
CAS
PubMed
Google Scholar
Nishiya Y, Nakano S, Kawamura K. Monomeric sarcosine oxidase acts on both L- and D-substrates. 生物試料分析. 2012;35(5):426–30.
CAS
Google Scholar
Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C, Zhou J, Oren A, Zhang Y-Z. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol. 2014;196(12):2210–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dunn B, Richter C, Kvitek DJ, Pugh T, Sherlock G. Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome Res. 2012;22(5):908–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gallone B, Steensels J, Prahl T, Soriaga L, Saels V, Herrera-Malaver B, Merlevede A, Roncoroni M, Voordeckers K, Miraglia L, et al. Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts. Cell. 2016;166(6):1397–1410.e1316.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gonçalves M, Pontes A, Almeida P, Barbosa R, Serra M, Libkind D, Hutzler M, Gonçalves P, Sampaio José P. Distinct domestication trajectories in top-fermenting beer yeasts and wine yeasts. Curr Biol. 2016;26(20):2750–61.
Article
CAS
PubMed
Google Scholar
Harris V, Ford CM, Jiranek V, Grbin PR. Survey of enzyme activity responsible for phenolic off-flavour production by Dekkera and Brettanomyces yeast. Appl Microbiol Biotechnol. 2009;81(6):1117–27.
Article
CAS
PubMed
Google Scholar
Ault RG, Newton R. Spoilage Organisms in Brewing. In: Findlay WPK, editor. Modern Brewing Technology. Edited by. London: The Macmillan Press; 1971. p. 164–97.
Google Scholar
Conterno L, Joseph CML, Arvik TJ, Henick-Kling T, Bisson LF. Genetic and physiological characterization of Brettanomyces bruxellensis strains isolated from wines. Am J Enol Vitic. 2006;57(2):139.
CAS
Google Scholar
Woolfit M, Rozpędowska E, Piškur J, Wolfe KH. Genome survey sequencing of the wine spoilage yeast Dekkera (Brettanomyces) bruxellensis. Eukaryot Cell. 2007;6(4):721.
Article
CAS
PubMed
PubMed Central
Google Scholar
Parente DC, Cajueiro DBB, Moreno ICP, Leite FCB, De Barros PW, De Morais Jr MA. On the catabolism of amino acids in the yeast Dekkera bruxellensis and the implications for industrial fermentation processes. Yeast. 2018;35(3):299–309.
Article
CAS
PubMed
Google Scholar
Ough CS, Stashak RM. Further studies on Proline concentration in grapes and wines. Am J Enol Vitic. 1974;25(1):7.
CAS
Google Scholar
Jin H, Ferguson K, Bond M, Kavanagh T, Hawthorne D. Malt nitrogen parameters and yeast fermentation behaviour. In: Proceedings of the convention-institute of brewing asia pacific section, vol. 1996; 1996. p. 44–50.
Google Scholar
Gorinstein S, Zemser M, Vargas-Albores F, Ochoa JL, Paredes-Lopez O, Scheler C, Salnikow J, Martin-Belloso O, Trakhtenberg S. Proteins and amino acids in beers, their contents and relationships with other analytical data. Food Chem. 1999;67(1):71–8.
Article
CAS
Google Scholar
Crauwels S, Van Assche A, de Jonge R, Borneman AR, Verreth C, Troels P, De Samblanx G, Marchal K, Van de Peer Y, Willems KA, et al. Comparative phenomics and targeted use of genomics reveals variation in carbon and nitrogen assimilation among different Brettanomyces bruxellensis strains. Appl Microbiol Biotechnol. 2015;99(21):9123–34.
Article
CAS
PubMed
Google Scholar
Marsit S, Sanchez I, Galeote V, Dequin S. Horizontally acquired oligopeptide transporters favour adaptation of Saccharomyces cerevisiae wine yeast to oenological environment. Environ Microbiol. 2016;18(4):1148–61.
Article
CAS
PubMed
Google Scholar
Camarasa C, Bigey F, Marsit S, Dequin S, Nidelet T, Galeote V, Legras J-L, Sanchez I, Couloux A, Guy J, et al. Adaptation of S. cerevisiae to fermented food environments reveals remarkable genome plasticity and the footprints of domestication. Mol Biol Evol. 2018;35(7):1712–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Feurtey A, Stukenbrock EH. Interspecific gene exchange as a driver of adaptive evolution in Fungi. Annu Rev Microbiol. 2018;72(1):377–98.
Article
CAS
PubMed
Google Scholar
Hall C, Brachat S, Dietrich FS. Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell. 2005;4(6):1102.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lin Z, Li W-H. Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts. Mol Biol Evol. 2010;28(1):131–42.
Article
CAS
PubMed
PubMed Central
Google Scholar
Monerawela C, James TC, Bond U, Wolfe KH. Loss of lager specific genes and subtelomeric regions define two different Saccharomyces cerevisiae lineages for Saccharomyces pastorianus Group I and II strains. FEMS Yeast Res. 2015;15(2):fou008.
Steenwyk J, Rokas A. Extensive Copy Number Variation in Fermentation-Related Genes Among Saccharomyces cerevisiae Wine Strains. G3. 2017;7(5):1475.
Article
CAS
PubMed
PubMed Central
Google Scholar
Yue J-X, Li J, Aigrain L, Hallin J, Persson K, Oliver K, Bergström A, Coupland P, Warringer J, Lagomarsino MC, et al. Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nat Genet. 2017;49(6):913–24.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chevreux B, Wetter T, Suhai S. Genome sequence assembly using trace signals and additional sequence information. In: Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, vol. 1999; 1999. p. 45–56.
Google Scholar
Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol. 2012;30(7):693–700.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 2017;27(5):722–36.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics (Oxford, England). 2018;34(18):3094–100.
Article
CAS
Google Scholar
Loman NJ, Quick J, Simpson JT. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods. 2015;12:733.
Article
CAS
PubMed
Google Scholar
Li H: Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:13033997v1 2013.
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, Cuomo CA, Zeng Q, Wortman J, Young SK, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9(11):e112963.
Article
CAS
PubMed
PubMed Central
Google Scholar
Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics (Oxford, England). 2009;25(17):2283–5.
Edge P, Bafna V, Bansal V. HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies. Genome Res. 2017;27(5):801–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Patterson M, Marschall T, Pisanti N, van Iersel L, Stougie L, Klau GW, Schönhuth A. WhatsHap: weighted haplotype assembly for future-generation sequencing reads. J Comput Biol. 2015;22(6):498–509.
Article
CAS
PubMed
Google Scholar
Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL. Versatile and open software for comparing large genomes. Genome Biol. 2004;5(2):R12.
Article
PubMed
PubMed Central
Google Scholar
Gurevich A, Tesler G, Vyahhi N, Saveliev V. QUAST: quality assessment tool for genome assemblies. Bioinformatics (Oxford, England). 2013;29(8):1072–5.
Article
CAS
Google Scholar
Kriventseva EV, Zdobnov EM, Simão FA, Ioannidis P, Waterhouse RM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics (Oxford, England). 2015;31(19):3210–2.
Article
CAS
Google Scholar
Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006;34(Web Server issue):W435–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and Metagenome sequences. J Mol Biol. 2016;428(4):726–31.
Article
CAS
PubMed
Google Scholar
Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, et al. InterProScan 5: genome-scale protein function classification. Bioinformatics (Oxford, England). 2014;30(9):1236–40.
Article
CAS
Google Scholar
Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16(1):157.
Article
CAS
PubMed
PubMed Central
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Suyama M, Torrents D, Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 2006;34(Web Server issue):W609–12.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32(1):268–74.
Article
CAS
PubMed
Google Scholar
Krzywinski M, Schein J, Birol İ, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19(9):1639–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Heymans K, Kuiper M, Maere S. BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics (Oxford, England). 2005;21(16):3448–9.
Article
CAS
Google Scholar
Gouy M, Gascuel O, Guindon S. SeaView version 4: a multiplatform graphical user Interface for sequence alignment and phylogenetic tree building. Mol Biol Evol. 2009;27(2):221–4.
Article
CAS
PubMed
Google Scholar
Pruitt KD, Tatusova T, Klimke W, Maglott DR. NCBI reference sequences: current status, policy and new initiatives. Nucleic Acids Res. 2009;37(Database issue):D32–6.
Article
CAS
PubMed
Google Scholar
Alexander WG, Wisecaver JH, Rokas A, Hittinger CT. Horizontally acquired genes in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. Proc Natl Acad Sci U S A. 2016;113(15):4116–21.
Article
CAS
PubMed
PubMed Central
Google Scholar