Alliance, T. & Consortium, G. R. The alliance of genome resources: Building a modern data ecosystem for model organism databases. Genetics 213, 1189–1196 (2019).
Google Scholar
Cubillos, F. A. Exploiting budding yeast natural variation for industrial processes. Curr. Genet. 62, 745–751 (2016).
Google Scholar
Pretorius, I. S. & Boeke, J. D. Yeast 2.0-connecting the dots in the construction of the world’s first functional synthetic eukaryotic genome. FEMS Yeast Res. 18, 1–15 (2018).
Google Scholar
Replogle, K., Hovland, L. & Rivier, D. H. Designer deletion and prototrophic strains derived from Saccharomyces cerevisiae strain W303–1a. Yeast 15, 1141–1149 (1999).
Google Scholar
Carter, Z. & Delneri, D. New generation of loxP-mutated deletion cassettes for the genetic manipulation of yeast natural isolates. Yeast 27, 765–775 (2010).
Google Scholar
Akada, R. et al. PCR-mediated seamless gene deletion and marker recycling in Saccharomyces cerevisiae. Yeast 23, 399–405 (2006).
Google Scholar
Giaever, G. & Nislow, C. The yeast deletion collection: A decade of functional genomics. Genetics 197, 451–465 (2014).
Google Scholar
Cubillos, F. A., Louis, E. J. & Liti, G. Generation of a large set of genetically tractable haploid and diploid Saccharomyces strains. FEMS Yeast Res. 9, 1217–1225 (2009).
Google Scholar
Louvel, H., Gillet-Markowska, A., Liti, G. & Fischer, G. A set of genetically diverged Saccharomyces cerevisiae strains with markerless deletions of multiple auxotrophic genes. Yeast 31, 91–101 (2014).
Google Scholar
Alexander, W. G., Doering, D. T. & Hittinger, C. T. High-efficiency genome editing and allele replacement in prototrophic and wild strains of saccharomyces. Genetics 198, 859–866 (2014).
Google Scholar
Coi, A. L., Legras, J. L., Zara, G., Dequin, S. & Budroni, M. A set of haploid strains available for genetic studies of Saccharomyces cerevisiae flor yeasts. FEMS Yeast Res. 16, 1–9 (2016).
Google Scholar
Shao, S. et al. Enhancing CRISPR/Cas9-mediated homology-directed repair in mammalian cells by expressing Saccharomyces cerevisiae Rad52. Int. J. Biochem. Cell Biol. 92, 43–52 (2017).
Google Scholar
McIlwraith, M. J. & West, S. C. DNA repair synthesis facilitates RAD52-mediated second-end capture during DSB repair. Mol. Cell 29, 510–516 (2008).
Google Scholar
Rainha, J., Rodrigues, J. L. & Rodrigues, L. R. CRISPR-Cas9: A powerful tool to efficiently engineer saccharomyces cerevisiae. Life 11, 1–16 (2021).
Fraczek, M. G., Naseeb, S. & Delneri, D. History of genome editing in yeast. Yeast 35, 361–368 (2018).
Google Scholar
Baganz, F., Hayes, A., Marren, D., Gardner, D. C. & Oliver, S. G. Suitability of replacement markers for functional analysis studies in Saccharomyces cerevisiae. Yeast 13, 1563–1573 (1997).
Google Scholar
Park, Y., Masison, D., Eisenberg, E. & Greene, L. E. Application of the FLP/FRT system for conditional gene deletion in yeast Saccharomyces cerevisiae. Yeast 28, 673–681 (2011).
Google Scholar
Yamanishi, M. & Matsuyama, T. A modified cre-lox genetic switch to dynamically control metabolic flow in Saccharomyces cerevisiae. ACS Synth. Biol. 1, 172–180 (2012).
Google Scholar
Solis-Escalante, D. et al. Efficient simultaneous excision of multiple selectable marker cassettes using I-SceI-induced double-strand DNA breaks in Saccharomyces cerevisiae. FEMS Yeast Res. 14, 741–754 (2014).
Google Scholar
Mans, R. et al. CRISPR/Cas9: A molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae. FEMS Yeast Res. 15, 1–15 (2015).
Google Scholar
Stovicek, V., Holkenbrink, C. & Borodina, I. CRISPR/Cas system for yeast genome engineering: Advances and applications. FEMS Yeast Res. 17, 1–16 (2017).
Google Scholar
Dicarlo, J. E. et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucl. Acids Res. 41, 4336–4343 (2013).
Google Scholar
Vigentini, I., Gebbia, M., Belotti, A., Foschino, R. & Roth, F. P. CRISPR/Cas9 system as a valuable genome editing tool for wine yeasts with application to decrease urea production. Front. Microbiol. 8, 1–11 (2017).
Jara, M. et al. Mapping genetic variants underlying differences in the central nitrogen metabolism in fermenter yeasts. PLoS ONE 9, e86533 (2014).
Google Scholar
Cubillos, F. A. et al. High-resolution mapping of complex traits with a four-parent advanced intercross yeast population. Genetics 195, 1141–1155 (2013).
Google Scholar
Salinas, F. et al. The genetic basis of natural variation in oenological traits in saccharomyces cerevisiae. PLoS ONE 7, e49640 (2012).
Google Scholar
Cubillos, F. et al. Identification of nitrogen consumption genetic variants in yeast through QTL mapping and bulk segregant RNA-seq analyses. G3 Genes Genom. Gen. 7, 1693–1705 (2017).
Google Scholar
Salinas, F. et al. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. Sci. Rep. 6, 21849 (2016).
Google Scholar
Villarroel, C. A., Bastías, M., Canessa, P. & Cubillos, F. A. Uncovering divergence in gene expression regulation in the adaptation of yeast to nitrogen scarcity. mSystems 6, (2021).
Alsammar, H. & Delneri, D. An update on the diversity, ecology and biogeography of the Saccharomyces genus. FEMS Yeast Res. 20, (2020).
Cubillos, F. A., Gibson, B., Grijalva-Vallejos, N., Krogerus, K. & Nikulin, J. Bioprospecting for brewers: Exploiting natural diversity for naturally diverse beers. Yeast https://doi.org/10.1002/yea.3380 (2019).
Google Scholar
Libkind, D. et al. Into the wild: new yeast genomes from natural environments and new tools for their analysis. FEMS Yeast Res. 20, (2020).
Molinet, J. & Cubillos, F. A. Wild yeast for the future: Exploring the use of wild strains for wine and beer fermentation. Front. Genet. 11, 1–8 (2020).
Google Scholar
Urbina, K. et al. Volatile compound screening using HS-SPME-GC/MS on saccharomyces eubayanus strains under low-temperature pilsner wort fermentation. Microorganisms 8, 1–19 (2020).
Google Scholar
Mardones, W. et al. Molecular profiling of beer wort fermentation diversity across natural Saccharomyces eubayanus isolates. Microb. Biotechnol. https://doi.org/10.1111/1751-7915.13545 (2020).
Google Scholar
Nespolo, R. F. et al. An Out-of-Patagonia migration explains the worldwide diversity and distribution of Saccharomyces eubayanus lineages. PLoS Genet. 16, e1008777 (2020).
Google Scholar
Langdon, Q. K. et al. Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids. PLOS Genet. 16, e1008680 (2020).
Google Scholar
Giannakou, K. et al. Biotechnological exploitation of Saccharomyces jurei and its hybrids in craft beer fermentation uncovers new aroma combinations. Food Microbiol. 100, 103838 (2021).
Google Scholar
Hutzler, M. et al. Unique brewing-relevant properties of a strain of saccharomyces jurei isolated from ash (Fraxinus excelsior). Front. Microbiol. 12, 1–14 (2021).
Google Scholar
Magalhães, F., Calton, A., Heiniö, R. L. & Gibson, B. Frozen-dough baking potential of psychrotolerant Saccharomyces species and derived hybrids. Food Microbiol. 94, (2021).
Libkind, D. et al. Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc. Natl. Acad. Sci. 108, 14539–14544 (2011).
Google Scholar
Lin, C. L. et al. Packing a punch: understanding how flavours are produced in lager fermentations. FEMS Yeast Res. 21, 1–14 (2021).
Google Scholar
Bonatto, D. The diversity of commercially available ale and lager yeast strains and the impact of brewer ’ s preferential yeast choice on the fermentative beer profiles. Food Res. Int. 141, 110125 (2021).
Google Scholar
Bing, J., Han, P. J., Liu, W. Q., Wang, Q. M. & Bai, F. Y. Evidence for a far east asian origin of lager beer yeast. Curr. Biol. 24, R380–R381 (2014).
Google Scholar
Peris, D. et al. Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids. Mol. Ecol. 23, 2031–2045 (2014).
Google Scholar
Gayevskiy, V. & Goddard, M. R. Saccharomyces eubayanus and Saccharomyces arboricola reside in North Island native New Zealand forests. Environ. Microbiol. 18, 1137–1147 (2016).
Google Scholar
Eizaguirre, J. I. et al. Phylogeography of the wild Lager-brewing ancestor (Saccharomyces eubayanus) in Patagonia. Environ. Microbiol. 20, 3732–3743 (2018).
Google Scholar
Villarreal, P. et al. Identification of new ethanol-tolerant yeast strains with fermentation potential from central Patagonia. Yeast https://doi.org/10.1002/yea.3662 (2021).
Google Scholar
Gibson, B. et al. New yeasts-new brews: Modern approaches to brewing yeast design and development. FEMS Yeast Res. 17, 1–13 (2017).
Google Scholar
Baker, E. C. P. et al. Mitochondrial DNA and temperature tolerance in lager yeasts. Sci. Adv. 5, 1–8 (2019).
Brouwers, N. et al. Himalayan saccharomyces eubayanus genome sequences reveal genetic markers explaining heterotic maltotriose consumption by saccharomyces pastorianus hybrids. Appl. Environ. Microbiol. 85, 1–22 (2019).
Google Scholar
Baker, E. C. P. & Hittinger, C. T. Evolution of a novel chimeric maltotriose transporter in Saccharomyces eubayanus from parent proteins unable to perform this function. PLoS Genet. 15, e1007786 (2019).
Google Scholar
Karademir Andersson, A., Oredsson, S. & Cohn, M. Development of stable haploid strains and molecular genetic tools for Naumovozyma castellii (Saccharomyces castellii). Yeast 33, 633–646 (2016).
Google Scholar
Fleiss, A. et al. Reshuffling yeast chromosomes with CRISPR/Cas9. PLOS Genet. 15, e1008332 (2019).
Google Scholar
Brickwedde, A. et al. Structural, physiological and regulatory analysis of maltose transporter genes in Saccharomyces eubayanus CBS 12357T. Front. Microbiol. 9, 1–18 (2018).
Google Scholar
Mertens, S. et al. Reducing phenolic off-flavors through CRISPR-based gene editing of the FDC1 gene in Saccharomyces cerevisiae x Saccharomyces eubayanus hybrid lager beer yeasts. PLoS ONE 14, e0209124 (2019).
Google Scholar
Jakočinas, T. et al. Multiplex metabolic pathway engineering using CRISPR/Cas9 in Saccharomyces cerevisiae. Metab. Eng. 28, 213–222 (2015).
Google Scholar
Brouwers, N. et al. In vivo recombination of Saccharomyces eubayanus maltose-transporter genes yields a chimeric transporter that enables maltotriose fermentation. PLoS Genet. 15, 1–30 (2019).
Google Scholar
Gallone, B. et al. Origins, evolution, domestication and diversity of Saccharomyces beer yeasts. Curr. Opin. Biotechnol. 49, 148–155 (2018).
Google Scholar
Gerke, J., Lorenz, K. & Cohen, B. Genetic interactions between transcription factors cause natural variation in yeast. Science (80-) 323, 498–501 (2009).
Google Scholar
Zörgö, E. et al. Ancient evolutionary trade-offs between yeast ploidy states. PLoS Genet. 9, (2013).
Hebly, M. et al. S. cerevisiae × S. eubayanus interspecific hybrid, the best of both worlds and beyond. FEMS Yeast Res. 15, 1–14 (2015).
Google Scholar
Blattner, G., Cavazza, A., Thrasher, A. J. & Turchiano, G. Gene editing and genotoxicity: Targeting the off-targets. Front. Genome Ed. 2, 1–10 (2020).
Google Scholar
Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016).
Google Scholar
Chin, Y. W., Shin, S. C., Han, S., Jang, H. W. & Kim, H. J. CRISPR/Cas9-mediated Inactivation of arginase in a yeast strain isolated from Nuruk and its impact on the whole genome. J. Biotechnol. 341, 163–167 (2021).
Google Scholar
Gorter De Vries, A. R. et al. Allele-specific genome editing using CRISPR-Cas9 is associated with loss of heterozygosity in diploid yeast. Nucl. Acids Res. 47, 1362–1372 (2019).
Google Scholar
Brion, C. et al. Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts. PLoS Genet. 13, 1–21 (2017).
Google Scholar
Martini, E. et al. Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways. PLoS Genet. 7, (2011).
Simchen, G., Mansour, O., Morciano, L., Zenvirth, D. & Arbel-Eden, A. Mutagenicity in haploid yeast meiosis resulting from repair of DSBs by the sister chromatid. Curr. Genet. 67, 799–806 (2021).
Google Scholar
Onetto, C. A., Borneman, A. R. & Schmidt, S. A. Strain-specific responses by saccharomyces cerevisiae to competition by non-saccharomyces yeasts. Fermentation 7, (2021).
Lang, G. I., Murray, A. W. & Botstein, D. The cost of gene expression underlies a fitness trade-off in yeast. Proc. Natl. Acad. Sci. U. S. A. 106, 5755–5760 (2009).
Google Scholar
Steensels, J., Meersman, E., Snoek, T., Saels, V. & Verstrepen, K. J. Large-scale selection and breeding to generate industrial yeasts with superior aroma production. Appl. Environ. Microbiol. 80, 6965–6975 (2014).
Google Scholar
Stelkens, R. B., Brockhurst, M. A., Hurst, G. D. D. & Greig, D. Hybridization facilitates evolutionary rescue. Evol. Appl. 7, 1209–1217 (2014).
Google Scholar
Agarbati, A., Canonico, L., Comitini, F. & Ciani, M. Reduction of sulfur compounds through genetic improvement of native saccharomyces cerevisiae useful for organic and sulfite-free wine. Foods 9, (2020).
Kessi-Pérez, E. et al. Generation of a non-transgenic genetically improved yeast strain for wine production from nitrogen-deficient musts. Microorganisms 8, 1194 (2020).
Google Scholar
Eberlein, C. et al. Hybridization is a recurrent evolutionary stimulus in wild yeast speciation. Nat. Commun. 10, (2019).
Bernardes, J. P., Stelkens, R. B. & Greig, D. Heterosis in hybrids within and between yeast species. J. Evol. Biol. 30, 538–548 (2017).
Google Scholar
Banderas, A., Koltai, M., Anders, A. & Sourjik, V. Sensory input attenuation allows predictive sexual response in yeast. Nat. Commun. 7, 1–9 (2016).
Google Scholar
Toyomura, K. & Hisatomi, T. Postzygotic reproductive isolation among three Saccharomyces yeast species. Yeast 38, 326–335 (2021).
Google Scholar
Selmecki, A. M. et al. Polyploidy can drive rapid adaptation in yeast. Nature 519, 349–351 (2015).
Google Scholar
Gerstein, A. C., Cleathero, L. A., Mandegar, M. A. & Otto, S. P. Haploids adapt faster than diploids across a range of environments. J. Evol. Biol. 24, 531–540 (2011).
Google Scholar
Gerstein, A. C. & Otto, S. P. Cryptic fitness advantage: Diploids invade haploid populations despite lacking any apparent advantage as measured by standard fitness assays. PLoS One 6, (2011).
Bessho, K., Iwasa, Y. & Day, T. The evolutionary advantage of haploid versus diploid microbes in nutrient-poor environments. J. Theor. Biol. 383, 116–129 (2015).
Google Scholar
Mable, B. K. Ploidy evolution in the yeast Saccharomyces cerevisiae: A test of the nutrient limitation hypothesis. J. Evol. Biol. 14, 157–170 (2001).
Google Scholar
Horwitz, A. A. et al. Efficient multiplexed integration of synergistic alleles and metabolic pathways in yeasts via CRISPR-Cas. Cell Syst. 1, 88–96 (2015).
Google Scholar
Gietz, R. D. & Schiestl, R. H. Quick and easy yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protoc. 2, 35–37 (2007).
Google Scholar
Chen, S., Zhou, Y., Chen, Y. & Gu, J. Fastp: An ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Google Scholar
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589–595 (2010).
Google Scholar
Garrison, E. & Marth, G. Haplotype-based variant detection from short-read sequencing. arXiv 1–9 (2012).
Robinson, J. T. et al. Integrative genome viewer. Nat. Biotechnol. 29, 24–26 (2011).
Google Scholar
Li, H. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).
Google Scholar
Shafin, K. et al. Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nat. Methods 18, 1322–1332 (2021).
Google Scholar
Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).
Google Scholar
Marçais, G., Deblasio, D. & Kingsford, C. Asymptotically optimal minimizers schemes. Bioinformatics 34, i13–i22 (2018).
Google Scholar
O’Donnell, S. & Fischer, G. MUM&Co: Accurate detection of all SV types through whole-genome alignment. Bioinformatics 36, 3242–3243 (2020).
Google Scholar
Hall, B. G., Acar, H., Nandipati, A. & Barlow, M. Growth rates made easy. Mol. Biol. Evol. 31, 232–238 (2014).
Google Scholar
White, C. & Zainasheff, J. Yeast: The practical guide to beer fermentation. (Brewers Publications, 2010).
Nissen, T. L., Schulze, U., Nielsen, J. & Villadsen, J. Flux distributions in anaerobic, glucose-limited continuous cultures of saccharomyces cerevisiae. Microbiology 143, 203–218 (1997).
Google Scholar
Krogerus, K., Holmström, S. & Gibson, B. Enhanced wort fermentation with de novo lager hybrids. Appl. Environ. Microbiol. 84, 1–20 (2018).
Google Scholar
Steensels, J. et al. Improving industrial yeast strains: Exploiting natural and artificial diversity. FEMS Microbiol. Rev. 38, 947–995 (2014).
Google Scholar
Zörgö, E. et al. Life history shapes trait heredity by accumulation of loss-of-function alleles in yeast. Mol. Biol. Evol. 29, 1781–1789 (2012).
Google Scholar
Mardones, W. et al. Rapid selection response to ethanol in Saccharomyces eubayanus emulates the domestication process under brewing conditions. Microb. Biotechnol. 2, 1–18 (2021).

