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Hittinger, C.T., Rokas, A., Bai, F.-Y., Boekhout, T., Gonçalves, P., Jeffries, T.W., Kominek, J., Lachance, M.-A., Libkind, D., Rosa, C.A., et al. Genomics and the making of yeast biodiversity. Curr Opin Genet Dev 35 (2015), 100–109.
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Marsit, S., Mena, A., Bigey, F., Sauvage, F.-X., Couloux, A., Guy, J., Legras, J.-L., Barrio, E., Dequin, S., Galeote, V., Evolutionary advantage conferred by an eukaryote-to-eukaryote gene transfer event in wine yeasts. Mol Biol Evol 32 (2015), 1695–1707.
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Ohnuki, S., Okada, H., Friedrich, A., Kanno, Y., Goshima, T., Hasuda, H., Inahashi, M., Okazaki, N., Tamura, H., Nakamura, R., et al. Phenotypic diagnosis of lineage and differentiation during sake yeast breeding. G3 (Bethesda) 7 (2017), 2807–2820.
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1397–1410.e16 Similar in design, timing, and conclusions to another recent study [crf0225], this study compared the genome sequences and phenotypes of more than 100 ale-brewing strains. In ale strains, they found elevated copy numbers of MALtose utilization genes, inactivating mutations in PAD1 and FDC1, and reduced sporulation. They also used fdc1 mutant alleles to reduce 4-vinylguaiacol production by marker-assisted breeding, a crossing technique common in crop and livestock breeding.
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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, 166, 2016 1397–1410.e16 Similar in design, timing, and conclusions to another recent study [crf0225], this study compared the genome sequences and phenotypes of more than 100 ale-brewing strains. In ale strains, they found elevated copy numbers of MALtose utilization genes, inactivating mutations in PAD1 and FDC1, and reduced sporulation. They also used fdc1 mutant alleles to reduce 4-vinylguaiacol production by marker-assisted breeding, a crossing technique common in crop and livestock breeding.
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Similar in design, timing, and conclusions to another recent study [crf0230], this study compared the genome sequences and phenotypes of more than 25 ale-brewing strains. In ale strains, they found elevated copy numbers of MALtose utilization genes and inactivating mutations in PAD1 and FDC1.
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Gonçalves, M., Pontes, A., Almeida, P., Barbosa, R., Serra, M., Libkind, D., Hutzler, M., Gonçalves, P., Sampaio, J.P., Distinct domestication trajectories in top-fermenting beer yeasts and wine yeasts. Curr Biol 26 (2016), 2750–2761 Similar in design, timing, and conclusions to another recent study [crf0230], this study compared the genome sequences and phenotypes of more than 25 ale-brewing strains. In ale strains, they found elevated copy numbers of MALtose utilization genes and inactivating mutations in PAD1 and FDC1.
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Libkind, D., Hittinger, C.T., Valerio, E., Goncalves, C., Dover, J., Johnston, M., Goncalves, P., Sampaio, J.P., Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci U S A 108 (2011), 14539–14544.
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Peris, D., Sylvester, K., Libkind, D., Gonçalves, P., Sampaio, J.P., Alexander, W.G., Hittinger, C.T., Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids. Mol Ecol 23 (2014), 2031–2045.
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This study sequenced and analyzed more than 25 S. eubayanus genomes. They concluded the species was highly diverse in South America but found that a low-diversity lineage distributed across the Holarctic ecozone of the Northern Hemisphere included the closest known relatives of lager-brewing yeasts. Interestingly, different lager strains and different genomic regions had different ancestries.
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Peris, D., Langdon, Q.K., Moriarty, R.V., Sylvester, K., Bontrager, M., Charron, G., Leducq, J.-B., Landry, C.R., Libkind, D., Hittinger, C.T., Complex ancestries of lager-brewing hybrids were shaped by standing variation in the wild yeast Saccharomyces eubayanus. PLoS Genet, 12, 2016, e1006155 This study sequenced and analyzed more than 25 S. eubayanus genomes. They concluded the species was highly diverse in South America but found that a low-diversity lineage distributed across the Holarctic ecozone of the Northern Hemisphere included the closest known relatives of lager-brewing yeasts. Interestingly, different lager strains and different genomic regions had different ancestries.
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•], this study reported the construction, phenotypic analysis, and brewing performance of allodiploid synthetic lager strains (S. cerevisiae × S. eubayanus that are GMO).
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•], this study reported the construction, phenotypic analysis, and brewing performance of allodiploid synthetic lager strains (S. cerevisiae × S. eubayanus that are GMO).
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•], this study reported the construction, phenotypic analysis, and brewing performance of allotriploid synthetic lager strains (S. cerevisiae × S. eubayanus that are non-GMO).
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•], this study reported the construction, phenotypic analysis, and brewing performance of allotriploid synthetic lager strains (S. cerevisiae × S. eubayanus that are non-GMO).
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This study successfully reduced 4-vinylguaiacol production in allotetraploid synthetic lager strains (S. cerevisiae × S. eubayanus) by recovering aneuploid meiotic segregants. Although the S. eubayanus genes have not directly been tested, reduced 4-vinylguaiacol levels correlated with the loss of S. eubayanus chromosome XIII, which contains PAD1 and FDC1.
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Krogerus, K., Seppänen-Laakso, T., Castillo, S., Gibson, B., Inheritance of brewing-relevant phenotypes in constructed Saccharomyces cerevisiae × Saccharomyces eubayanus hybrids. Microb Cell Fact, 16, 2017, 66 This study successfully reduced 4-vinylguaiacol production in allotetraploid synthetic lager strains (S. cerevisiae × S. eubayanus) by recovering aneuploid meiotic segregants. Although the S. eubayanus genes have not directly been tested, reduced 4-vinylguaiacol levels correlated with the loss of S. eubayanus chromosome XIII, which contains PAD1 and FDC1.
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Peris, D., Moriarty, R.V., Alexander, W.G., Baker, E., Sylvester, K., Sardi, M., Langdon, Q.K., Libkind, D., Wang, Q.-M., Bai, F.-Y., et al. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels, 10, 2017, 78.
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Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces
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Alexander, W.G., Peris, D., Pfannenstiel, B.T., Opulente, D.A., Kuang, M., Hittinger, C.T., Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces. Fungal Genet Biol 89 (2016), 10–17.
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Brettanomyces yeasts — from spoilage organisms to valuable contributors to industrial fermentations
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Parallel evolution of the make-accumulate-consume strategy in Saccharomyces and Dekkera yeasts
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Rozpedowska, E., Hellborg, L., Ishchuk, O.P., Orhan, F., Galafassi, S., Merico, A., Woolfit, M., Compagno, C., Piskur, J., Parallel evolution of the make-accumulate-consume strategy in Saccharomyces and Dekkera yeasts. Nat Commun, 2, 2011, 302.
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Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C
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This metagenomic study used the new Hi-C sequencing approach to assemble draft genome sequences from a sour beer community. Inhabitants were consistent with previous small-scale culture-based methods, and interestingly, a novel interspecies hybrid of Pichia was detected.
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Heil, C.S., Burton, J.N., Liachko, I., Friedrich, A., Hanson, N.A., Morris, C.L., Schacherer, J., Shendure, J., Thomas, J.H., Dunham, M.J., Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C. Yeast, 2017, 10.1002/yea.3280 This metagenomic study used the new Hi-C sequencing approach to assemble draft genome sequences from a sour beer community. Inhabitants were consistent with previous small-scale culture-based methods, and interestingly, a novel interspecies hybrid of Pichia was detected.
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Yeast
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Heil, C.S.1
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Lachancea thermotolerans as an alternative yeast for the production of beer
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In perhaps the first explicit attempt to replace a complex LAB-yeast community with a monoculture, Lachancea thermotolerans, a yeast that both produces lactic acid and ferments maltose, was shown to make sour beer.
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Domizio, P., House, J.F., Joseph, C.M.L., Bisson, L.F., Bamforth, C.W., Lachancea thermotolerans as an alternative yeast for the production of beer. J Inst Brew 122 (2016), 599–604 In perhaps the first explicit attempt to replace a complex LAB-yeast community with a monoculture, Lachancea thermotolerans, a yeast that both produces lactic acid and ferments maltose, was shown to make sour beer.
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Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources
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Marsh, A.J., O'Sullivan, O., Hill, C., Ross, R.P., Cotter, P.D., Sequencing-based analysis of the bacterial and fungal composition of kefir grains and milks from multiple sources. PLoS ONE, 8, 2013, e69371.
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Facility-specific “house” microbiome drives microbial landscapes of artisan cheesemaking plants
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Bokulich, N.A., Mills, D.A., Facility-specific “house” microbiome drives microbial landscapes of artisan cheesemaking plants. Appl Environ Microbiol 79 (2013), 5214–5223.
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Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity
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This landmark study used modern environmental sequencing techniques to explore the bacterial and fungal communities present in three types of cheese rind: washed (e.g. gruyere), bloomy (e.g. brie), and natural (e.g. clothbound cheddars). They found that communities varied by rind type, over time, by environment (especially moisture), and in response to direct manipulation of community composition.
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Wolfe, B.E., Button, J.E., Santarelli, M., Dutton, R.J., Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158 (2014), 422–433 This landmark study used modern environmental sequencing techniques to explore the bacterial and fungal communities present in three types of cheese rind: washed (e.g. gruyere), bloomy (e.g. brie), and natural (e.g. clothbound cheddars). They found that communities varied by rind type, over time, by environment (especially moisture), and in response to direct manipulation of community composition.
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The sourdough microflora: biodiversity and metabolic interactions
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Monitoring of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis
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Tanaka, Y., Watanabe, J., Mogi, Y., Monitoring of the microbial communities involved in the soy sauce manufacturing process by PCR-denaturing gradient gel electrophoresis. Food Microbiol 31 (2012), 100–106.
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Independent origins of yeast associated with coffee and cacao fermentation
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This study showed that genetically diverse strains of S. cerevisiae can be isolated from unroasted coffee and cacao beans. Using RAD-Seq, a technique that sequences a portion of the genome near restriction sites, they showed that strains vary by substrate and geography and also uncovered several admixture events.
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Ludlow, C.L., Cromie, G.A., Garmendia-Torres, C., Sirr, A., Hays, M., Field, C., Jeffery, E.W., Fay, J.C., Dudley, A.M., Independent origins of yeast associated with coffee and cacao fermentation. Curr Biol 26 (2016), 965–971 This study showed that genetically diverse strains of S. cerevisiae can be isolated from unroasted coffee and cacao beans. Using RAD-Seq, a technique that sequences a portion of the genome near restriction sites, they showed that strains vary by substrate and geography and also uncovered several admixture events.
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Shen, X.-X., Zhou, X., Kominek, J., Kurtzman, C.P., Hittinger, C.T., Rokas, A., Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3 (Bethesda) 6 (2016), 3927–3939.
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Gene-edited CRISPR mushroom escapes US regulation
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Waltz, E., Gene-edited CRISPR mushroom escapes US regulation. Nature, 532, 2016, 293.
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