Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Salazar, Alex N.; Vries, Arthur R. Gorter de; Broek, Marcel van den; Brouwers, Nick; Cortés, Pilar de la Torre; Kuijpers, Niels G. A.; Daran, Jean‐Marc; Abeel, Thomas

doi:10.1186/s12864-019-6263-3

Cited by 42 publications

(43 citation statements)

References 102 publications

(168 reference statements)

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“…The cell line IMS0711 gained one copy of chimeric SeCHRVII-ScCHRVII, while IMS0712 and IMS0714 has lost one copy of SeCHRX-ScCHRX and ScCHRIX, respectively. The fourth sequenced isolate IMS0710 showed a chromosome complement identical to that of CBS 1483 (Salazar et al, 2019). Overall, the non-electroporated single cell lines have an average of 76.8 ± 0.8 chromosomes which represent an average loss of 0.2 chromosome relative to CBS 1483 whose genome comprise 77 chromosomes (Figure 3).…”

Section: Genetic Instability Of Cbs 1483 and Mutagenic Effect Of Elecmentioning

confidence: 98%

“…More than 3 Gb of data per strain representing a minimum of 50-fold coverage of the aneuploid genome of the S. pastorianus were generated. Sequence reads of each strain were mapped onto S. pastorianus CBS 1483 sequence [genome PRJNA522669, (Salazar et al, 2019)] using the Burrows-Wheeler Alignment tool (BWA) and further processed using SAMtools Durbin, 2009, 2010). Single-nucleotide variations and indels were determined using Pilon (Walker et al, 2014) based on the BWA.bam output file.…”

Section: Genomic Dna Extraction Whole Genome Sequencing and Analysismentioning

confidence: 99%

“…However, current assembly algorithms reduce genome assemblies to consensus sequences. Information about sequence variation between different chromosome haplotypes is not captured by consensus assemblies (Salazar et al, 2019). In spite the awareness of this pitfall, analysis of sequence variation of IMS0687, IMS0703, and IMS0716 relative to the CBS 1483 consensus sequence was performed (Figure 3).…”

Section: Chemical Induction Of Chromosome Missegregation As a Strain mentioning

confidence: 99%

“…The lager brewing yeast Saccharomyces pastorianus is an interspecific hybrid of Saccharomyces cerevisiae and the cold-tolerant Saccharomyces eubayanus (Libkind et al, 2011;Salazar et al, 2019). Chromosomes from both parental species are present in the genome of S. pastorianus in varying number of copies, making the genome alloploid and aneuploid (Dunn and Sherlock, 2008).…”

Section: Introductionmentioning

confidence: 99%

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Improving Industrially Relevant Phenotypic Traits by Engineering Chromosome Copy Number in Saccharomyces pastorianus

et al. 2020

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The lager-brewing yeast Saccharomyces pastorianus is a hybrid between S. cerevisiae and S. eubayanus with an exceptional degree of aneuploidy. While chromosome copy number variation (CCNV) is present in many industrial Saccharomyces strains and has been linked to various industrially-relevant traits, its impact on the brewing performance of S. pastorianus remains elusive. Here we attempt to delete single copies of chromosomes which are relevant for the production of off-flavor compound diacetyl by centromere silencing. However, the engineered strains display CNV of multiple nontargeted chromosomes. We attribute this unintended CCNV to inherent instability and to a mutagenic effect of electroporation and of centromere-silencing. Regardless, the resulting strains displayed large phenotypic diversity. By growing centromere-silenced cells in repeated sequential batches in medium containing 10% ethanol, mutants with increased ethanol tolerance were obtained. By using CCNV mutagenesis by exposure to the mitotic inhibitor MBC, selection in the same setup yielded even more tolerant mutants that would not classify as genetically modified organisms. These results show that CCNV of alloaneuploid S. pastorianus genomes is highly unstable, and that CCNV mutagenesis can generate broad diversity. Coupled to effective selection or screening, CCNV mutagenesis presents a potent tool for strain improvement.

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Section: Genetic Instability Of Cbs 1483 and Mutagenic Effect Of Elecmentioning

confidence: 98%

Section: Genomic Dna Extraction Whole Genome Sequencing and Analysismentioning

confidence: 99%

Section: Chemical Induction Of Chromosome Missegregation As a Strain mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Improving Industrially Relevant Phenotypic Traits by Engineering Chromosome Copy Number in Saccharomyces pastorianus

et al. 2020

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“…Even if lager strains are the powerhouse of the modern brewing industry, their phenotypic potential is limited due to their containing genetic material from only two or three individual yeast lineages [ 17 , 25 , 26 ]. Therefore, the brewing industry looks toward novel brewing starters to meet the consumer demand for product diversification [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

Hybridization of Saccharomyces cerevisiae Sourdough Strains with Cryotolerant Saccharomyces bayanus NBRC1948 as a Strategy to Increase Diversity of Strains Available for Lager Beer Fermentation

et al. 2021

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The search for novel brewing strains from non-brewing environments represents an emerging trend to increase genetic and phenotypic diversities in brewing yeast culture collections. Another valuable tool is hybridization, where beneficial traits of individual strains are combined in a single organism. This has been used successfully to create de novo hybrids from parental brewing strains by mimicking natural Saccharomycescerevisiae ale × Saccharomyceseubayanus lager yeast hybrids. Here, we integrated both these approaches to create synthetic hybrids for lager fermentation using parental strains from niches other than beer. Using a phenotype-centered strategy, S. cerevisiae sourdough strains and the S. eubayanus × Saccharomyces uvarum strain NBRC1948 (also referred to as Saccharomyces bayanus) were chosen for their brewing aptitudes. We demonstrated that, in contrast to S. cerevisiae × S. uvarum crosses, hybridization yield was positively affected by time of exposure to starvation, but not by staggered mating. In laboratory-scale fermentation trials at 20 °C, one triple S. cerevisiae × S. eubayanus × S. uvarum hybrid showed a heterotic phenotype compared with the parents. In 2 L wort fermentation trials at 12 °C, this hybrid inherited the ability to consume efficiently maltotriose from NBRC1948 and, like the sourdough S. cerevisiae parent, produced appreciable levels of the positive aroma compounds 3-methylbutyl acetate (banana/pear), ethyl acetate (general fruit aroma) and ethyl hexanoate (green apple, aniseed, and cherry aroma). Based on these evidences, the phenotype-centered approach appears promising for designing de novo lager beer hybrids and may help to diversify aroma profiles in lager beer.

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Enhanced flavour profiles through radicicol induced genomic variation in the lager yeasts, Saccharomyces pastorianus

Garcia‐Caro

Thompson

Zhang

et al. 2022

Yeast

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The yeasts, Saccharomyces pastorianus, are hybrids of Saccharomyces cerevisiae and Saccharomyces eubayanus and have acquired traits from the combined parental genomes such as ability to ferment a range of sugars at low temperatures and to produce aromatic flavour compounds, allowing for the production of lager beers with crisp, clean flavours. The polyploid strains are sterile and have reached an evolutionary bottleneck for genetic variation. Here we describe an accelerated evolution approach to obtain lager yeasts with enhanced flavour profiles. As the relative expression of orthologous alleles is a significant contributor to the transcriptome during fermentation, we aimed to induce genetic variation by altering the S. cerevisiae to S. eubayanus chromosome ratio. Aneuploidy was induced through the temporary inhibition of the cell's stress response and strains with increased production of aromatic amino acids via the Shikimate pathway were selected by resistance to amino acid analogues. Genomic changes such as gross chromosomal rearrangements, chromosome loss and chromosome gain were detected in the characterised mutants, as were single‐nucleotide polymorphisms in ARO4, encoding for DAHP synthase, the catalytic enzyme in the first step of the Shikimate pathway. Transcriptome analysis confirmed the upregulation of genes encoding enzymes in the Ehrlich pathway and the concomitant increase in the production of higher alcohols and esters such as 2‐phenylethanol, 2‐phenylethyl acetate, tryptophol, and tyrosol. We propose that the polyploid nature of S. pastorianus genomes is an advantageous trait supporting opportunities for genetic alteration in otherwise sterile strains.

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Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization

Cited by 42 publications

References 102 publications

Improving Industrially Relevant Phenotypic Traits by Engineering Chromosome Copy Number in Saccharomyces pastorianus

Improving Industrially Relevant Phenotypic Traits by Engineering Chromosome Copy Number in Saccharomyces pastorianus

Hybridization of Saccharomyces cerevisiae Sourdough Strains with Cryotolerant Saccharomyces bayanus NBRC1948 as a Strategy to Increase Diversity of Strains Available for Lager Beer Fermentation

Enhanced flavour profiles through radicicol induced genomic variation in the lager yeasts, Saccharomyces pastorianus

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