Biology subjects

Delneri, D.

Publications and source records attributed to Delneri, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Characterisation of Saccharomyces cerevisiae and Saccharomyces jurei hybrids for oenological applications

The Saccharomyces genus present as a genetically diverse set of microorganisms capable of tolerating a range of environmental stressors, demonstrating high fermentation capacity and producing interesting flavour compounds. Such diversity can be exploited in a single organism by producing interspecies hybrids, overcoming the limitations of a single species. Here, as proof of principle, we exploited a library of F12 interspecies diploid hybrids between Saccharomyces cerevisiae and Saccharomyces jurei (Sc/Sj), to identify new strains harbouring traits of oenological relevance, such as ethanol and glycerol production, superior tolerance to acetic acid, limited production of H2S, and optimal growth on fructose. Moreover, we calculated robustness across strains tested on solid media comparing the trade-off between performance on a single conditions and overall robustness. Progeny from a range of robustness values with favourable H2S production profiles were isolated for further analysis via micro and small-scale fermentations. Micro-scale fermentations in synthetic grape must containing individual wine-associated stressors were performed, and the robustness of the selected strains was confirmed. The wine characteristics of the hybrids were tested in small-scale fermentations in synthetic grape media. We found that both ethanol and glycerol production across our selected progeny matched or exceeding that from the commercial wine strain, and most hybrids produced less acetic acid and more fatty-acids, including higher quantities of associated esters. Overall, we were able to identify suitable Sc/Sj hybrids with interesting aroma profiles to develop further for wine fermentation.

microbiology↗

bioRxiv2026

BRIDGE: A broad-host platform for interkingdom DNA delivery enabling the genetic domestication of phylogenetically diverse yeasts

Efficient DNA delivery remains one of the greatest barriers to engineering non-conventional yeasts, limiting their genetic domestication and exploitation as next-generation microbial cell factories. Here, we present BRIDGE (Bacteria-to-yeast Rapid Interkingdom DNA Gene Exchange), an integrated synthetic biology platform for broad-host interkingdom DNA delivery. BRIDGE is centred on a compact 6-kb Pan/ARS-oriT broad-host BRIDGE vector, enabled by a superconjugative helper plasmid (pSC5). Using BRIDGE, we expanded interkingdom DNA transfer from representatives of four genera accessible using pSC5 alone to ten phylogenetically diverse yeast genera, including Saccharomyces, Maudiozyma, Starmerella, Kazachstania, Yarrowia, Zygosaccharomyces, Lachancea, Kluyveromyces, Pichia and Komagataella. To demonstrate the versatility of BRIDGE, we engineered a 16-kb visual reporter carrying a synthetic five-gene violacein biosynthetic pathway from Chromobacterium violaceum. Individual transcriptional units were first constructed using the YeastFab modular cloning system and subsequently assembled into the complete pathway by single-step in vivo homologous recombination in Saccharomyces cerevisiae, followed by rapid plasmid recovery using the EASY-C platform. The reporter was successfully delivered to all ten yeast genera, demonstrating BRIDGE-mediated transfer of complete multigene synthetic pathways. Robust violacein production was observed across all six Saccharomyces species tested, providing a rapid visual marker for transformant identification, while modest functional pathway expression was also detected in Kazachstania and Kluyveromyces. Successful pathway transfer, albeit without visible pigmentation, was achieved in the remaining genera, indicating that regulatory compatibility, rather than DNA transfer, is the principal determinant of heterologous pathway expression in distantly related yeasts. Collectively, BRIDGE establishes an integrated Design-Build-Recover-Deliver workflow that combines modular in vitro construction of transcriptional units, single-step in vivo assembly of multigene pathways, rapid plasmid recovery using the EASY-C platform and broad-host interkingdom DNA delivery. This versatile framework enables the rapid genetic modification of previously intractable microorganisms, expanding the synthetic biology toolbox for sustainable biomanufacturing and industrial biotechnology.

synthetic biology↗

bioRxiv2025

SWR1C loss promotes longevity through tRNA-mediated proteostasis

The conserved SWR1C chromatin remodeling complex promotes cellular aging, yet the mechanisms linking its activity to lifespan control remain poorly defined. Although SWR1C shapes chromatin architecture and regulates non-coding RNA expression, how these activities relate to its role in aging remains unclear. Here, we combine genetic and lifespan-epistasis analyses to identify the cellular processes that underlie SWR1C-dependent chronological longevity in Saccharomyces cerevisiae. Loss of subunits specifically required for H2A.Z deposition robustly extends longevity, and this effect is functionally linked to cytosolic translation and proteostasis pathways. Lifespan profiling of ncRNA deletions reveals a substantial fraction of aging phenotypes and prevalent genetic interactions with SWR1, with tRNAs emerging as key determinants of its long-lived phenotype. The expression of specific tRNA genes is dysregulated in swr1{Delta} cells, and interactions with tyrosine-decoding tRNA genes are linked to ER proteotoxic stress, suggesting that altered tRNA pools affect proteostasis during aging. These findings establish tRNAs as central mediators of SWR1C-associated longevity, revealing a fundamental connection between chromatin remodeling, RNA biology, and proteostasis stress responses in lifespan regulation.

cell biology↗

bioRxiv2025

Construction of a reference genome for Starmerella batistae and annotation of Starmerella species reveal a close evolutionary relationship with Schizosaccharomyces pombe and suggest an alternative pathway for sophorolipid production.

The Starmerella clade is known for displaying osmotolerant and acidophilic traits from their association with bees. Several species in this genus can produce sophorolipids, which are commercially produced as biosurfactants. Here, we isolated a yeast contaminant from the laboratory environment, identified as Starmerella batistae, able to thrive under low pH, including high concentrations of lactic acid, and relative high temperatures. We have sequenced and conducted a de novo genome assembly in three chromosomes and a mitochondrial genome for S. batistae (ca 9.3 Mb). Based on this reference genome we functionally annotated 29 different Starmerella species, using the publicly available sequences. Phylogenetic analysis across different yeast clades revealed a close relationship of Starmerella species with Schizosaccharomyces yeasts. Fifteen genes were uniquely shared between Sz. pombe and S. batistae, of which twelve were involved in cell morphology. Interestingly, the shape of S. batistae cells is elongated rather than round, similar to the Sz. pombe. Additionally, we found that all the Starmerella strains capable of producing sophorolipids shared a last common ancestor. Such clustering can help identify other sophorolipid-producing Starmerella yeasts that have not yet been characterised. We did not find the one-to-one orthologs of S. bombicola sophorolipid pathway in any of the Starmerella sp. with the exception of S. kuoi, S. powellii and S. floricola. In S. etchelsii, the antisense and telomeric pair UGTA1/CYP52M1 was found to be structurally conserved although not functionally. These findings support the notion that alternative pathways for the production of sophorolipids have evolved in different Starmerella lineages.

genomics↗

bioRxiv2025

Unveiling the genetic basis of the low pH response in the acidophilic yeast Maudiozyma bulderi as a potential host for biorefinery

Non-conventional yeasts represent a great genetic and phenotypic diversity with potential for industrial strain development in the bio-production of green chemicals. In recent years, mass genome sequencing of non-conventional yeasts has opened avenues to improved understanding of transcriptional networks and phenotypic plasticity and gene function, including the discovery of novel genes. Here, we investigated the expressional and morphological changes at low-pH in three strains of the acidophilic yeast Maudiozyma bulderi (previously Kazachstania bulderi and Saccharomyces bulderi): CBS 8638, CBS 8639 and NRRL Y-27205. The comparison of the transcriptome of cells growing in a bioreactor at pH=5.5 vs pH= 2.5, primarily showed dysregulation of genes involved in cell wall integrity, with NRRL Y-27205 the least acidophilic strain, showing the largest transcriptional response when compared to the other two strains. We identified four uncharacterised genes, unique to M. bulderi, and predicted function as transporters, upregulated at low pH. Microscopy studies showed that M. bulderi cell wall is not damaged in acidic environment, and the membrane lipid composition remains stable at low pH, unlike S. cerevisiae. Overall, our data on transcriptional variability in M. bulderi highlights genes and cellular pathways involved in the acidophilic adaptation of this species and can aid further strain development.

genomics↗

bioRxiv2024

Aroma compounds profile is affected by the initial yeast ratio in wort co-fermentations

In recent years, the boom of the craft beer industry refocused the biotech interest from ethanol production to diversification of beer aroma profiles. This study analyses the fermentative phenotype of a collection of non-conventional yeasts and examines their role in creating new flavours, particularly through co-fermentation with industrial Saccharomyces cerevisiae. High-throughput solid and liquid media fitness screening compared the ability of eight Saccharomyces and four non-Saccharomyces yeast strains to grow in wort. We determined the volatile profile of these yeast strains and found that Hanseniaspora vineae displayed a particularly high production of the desirable aroma compounds ethyl acetate and 2-phenethyl acetate. Given that H. vineae on its own was a poor fermenter, we carried out mixed wort co-fermentations with a S. cerevisiae brewing strain at different ratios. The two yeast strains were able to co-exist throughout the experiment, regardless of their initial inoculum, and the increase in the production of the esters observed in the H. vineae monoculture was maintained, alongside with a high ethanol production. Moreover, different inoculum ratios yielded different aroma profiles: the 50/50 S. cerevisiae/H. vineae ratio produced a more balanced profile, while the 10/90 ratio generated stronger floral aromas. Our findings show the potential of using different yeasts and different inoculum combinations to tailor the final aroma, thus offering new possibilities for a broader range of beer flavours and styles. IMPORTANCECraft brewing underwent an unprecedented growth in the last years due to customer demand for more unique and complex beverages. Brewers started to explore innovative fermentation methods using new ingredients, different brewing conditions, and new yeasts to explore a larger flavour landscape. The use of non-Saccharomyces yeasts has emerged as an effective strategy to produce novel distinct flavour profiles, however, knowledge regarding their fermentation performance and volatiles production is still limited, which hinders their industrial application. In this study, we expand on the knowledge of several non-Saccharomyces yeasts in terms of their brewing application and highlight the potential of H. vineae in co-fermentation with S. cerevisiae for producing unique fruity beers with a standard ethanol content. Our findings provide the craft beer industry with a new strategy to produce distinctive fruity beers.

microbiology↗

bioRxiv2024

Exploring adaptation routes to low temperatures in the Saccharomyces genus

The identification of traits that affect adaptation of microbial species to external abiotic factors, such as temperature, is key for our understanding of how biodiversity originates and can be maintained in a constantly changing environment. The Saccharomyces genus, which includes eight species with different thermotolerant profiles, represent an ideal experimental platform to study the impact of adaptive alleles in different genetic backgrounds. Previous studies identified a group of genes important for maintenance of growth at lower temperatures. Here, we carried out a genus-wide functional analysis in all eight Saccharomyces species for six candidate genes. We showed that the cold tolerance trait of S. kudriavzevii and S. eubayanus is likely to be evolved from different routes, involving genes important for the conservation of redox-balance, and for the long-chain fatty acid metabolism, respectively. For several loci, temperature- and species-dependent epistasis was detected, underlying the plasticity and complexity of the genetic interactions. The natural isolates of S. kudriavzevii, S. jurei and S. mikatae had a significantly higher expression of the genes involved in the redox balance compared to S. cerevisiae, raising the question of what proportion of the trait is accounted for solely due to transcriptional strength. To tease apart the role of gene expression from that of allelic variation, for two genes we independently replaced in four yeast species either the promoters or the alleles with those derived from S. kudriavzevii. Our data consistently showed a significant fitness improvement at cold temperatures in the strains carrying the S. kudriavzevii promoter, while growth was lower upon allele swapping. These results suggest that transcriptional strength plays a bigger role in growth maintenance at cold over the allele type and supports a model of adaptation centred on stochastic tuning of the expression network. Author summaryThe decline in biodiversity due to environmental changes influences the stability of ecosystems by altering the geographic distribution of several microbial and fungal species. Temperature is one of the leading factors that drive adaptation and different organisms share the same habitat because of their different thermal profiles. It is therefore important to study the genes that affect the fitness of microorganisms at different temperatures in order to understand both how biodiversity originated and how can be maintained. The Saccharomyces genus, which includes species with different thermotolerant profiles, represent an ideal experimental platform to investigate the impact of adaptive alleles in response to temperature changes. Here, we carried out a functional analysis for putative cold-tolerant genes and showed that this trait is likely to be evolved from different routes in different species, involving the conservation of redox-balance and alteration of membrane fluidity. Furthermore, for several species, genetic interactions display fitness tradeoffs in different environments. Finally, by unravelling the interplay between gene expression, allele variation, genetic background and environment, this study shed light on the intricate nature of transcriptional regulation and its pivotal role in facilitating cold adaptation in Saccharomyces species.

genetics↗

bioRxiv2024

Impact of inter-species hybridisation on antifungal drug response in the Saccharomyces genus.

Antifungal drug resistance across fungal and yeast pathogens presents one of the major concerns for global public health. Understanding the interactions between genetic background and environment is important for the development of new, effective treatments of infections. Allelic variation within populations of Ascomycota as well as hybridisation impacts the phenotype in response to stressful conditions, including to antifungal drugs. We exploited recent advances in multigenerational breeding of Saccharomyces interspecies hybrids to study the impact of hybridisation on antifungal resistance and identify quantitative trait loci (QTL) responsible for the phenotypes observed. A library of Saccharomyces cerevisiae x S. kudriavzevii hybrid offspring was screened in the presence of sub-lethal concentrations of six antifungal drugs and revealed a broad phenotypic diversity across the progeny. QTL analysis was carried out comparing alleles between the pools of high and low fitness offspring, identifying hybrid-specific genetic regions involved in resistance to fluconazole, micafungin and flucytosine. We found both drug specific and pleiotropic regions, and through gene ontology and SIFT analysis we identify potential causal genes, such as BCK2 and DNF1 that were validated via reciprocal hemizygosity analysis. We highlight 41 regions that contain genes not previously associated with resistance phenotypes in the literature. The results of this screening will help identify new pathways contributing to drug resistance, and lead to greater understanding of how allelic variation, hybridisation and evolution affect antifungal drug resistance in yeast and fungi.

genetics↗

bioRxiv2023

Development of a genome scale metabolic model for the lager hybrid yeast S. pastorianus to understand evolution of metabolic pathways in industrial settings.

In silico tools such as genome-scale metabolic models (GSMM) have shown to be powerful for metabolic engineering of microorganisms. Here, we created the iSP_1513 GSMM for the aneuploid hybrid S. pastorianus CBS1513 to allow top-down computational approaches to predict the evolution of metabolic pathways and to aid strain optimisation and media engineering in production processes. The iSP_1513 comprises 4062 reactions, 1808 alleles and 2747 metabolites, and takes into account the functional redundancy in the gene-protein-reaction rule caused by the presence of orthologous genes. Moreover, a universal algorithm to constrain GSMM reactions using transcriptome data was developed as a python library and enabled the integration of temperature as parameter. Essentiality datasets, growth data on various carbohydrates and volatile metabolites secretion were used to validate the model. Overall, the iSP_1513 GSMM represent an important step towards understanding the metabolic capabilities, evolutionary trajectories and adaptation potential of S. pastorianus in different industrial settings.

systems biology↗

bioRxiv2023

High quality de novo genome assembly of non-conventional yeast Kazachstania bulderi a new potential low pH production host for biorefineries.

Kazachstania bulderi is a yeast species belonging to a ubiquitous group of non-conventional yeasts which has the ability to grow efficiently on glucose and {delta}-gluconolactone at low pH. This unique trait makes K. bulderi an ideal candidate as a new host for low pH fermentation processes for sustainable production of green chemicals such as organic acids. To accelerate strain development with this species, detailed information of its genetics is needed. Here, by employing high accuracy long read sequencing we report a high-quality phased genome assembly for three strains belonging to K. bulderi species, including the type strain. The sequences were assembled into 12 chromosomes with a total length of 14Mb, and the genome was fully annotated at structural and functional levels, including allelic and structural variants, ribosomal array, centromeres and mating type locus. This high-quality reference genome provides an essential resource to advance our fundamental knowledge of biotechno-logically relevant non-conventional yeasts and to support the development of genetic tools for manipulating such strains towards their use as production hosts biotechnological processes.

genomics↗

bioRxiv2022

Volatile aroma compound production is affected by growth rate in S. cerevisiae

The initial growth rate of a yeast strain is a key parameter in the production of fermented beverages. Fast growth is linked with higher fermentative capacity and results in less slow and stuck fermentations unable to reach the expected final gravity. As concentrations of metabolites are in constant state of flux, quantitative data on how growth rate affects the production of aromatic compounds becomes an important factor for brewers. Chemostats allow to set and keep a specific dilution rate throughout the fermentation and are ideal system to study the effect of growth on aroma production. In this study, we run chemostats alongside batch and fed-batch cultures, compared volatile profiles detected at different growth rates, and identified those affected by the different feeding profiles. Specifically, we quantified six abundant aroma compounds produced in anaerobic glucose-limited continuous cultivations of S. cerevisiae at different dilution rates. We found that volatile production was affected by the growth rate in four out of six compounds assayed, with higher alcohols and esters following opposite trends. Batch and fed-batch fermentations were devised to study the extent by which the final concentration of volatile compounds is influenced by glucose availability. When compared to the batch system, fed-batch fermentations, where the yeast growth was artificially limited by a slow constant release of nutrients in the media, resulted in a significant increase in concentration of higher alcohols, mirroring the results obtained in continuous fermentations. This study paves the way to further process development optimization for the production of fermented beverages. ImportanceThe production of fermentation beverages will need to quickly adapt to changes in both the climate and in customer demands, requiring the development of new strains and processes. Breakthroughs in the field are hindered by the limited knowledge on the physiological role of aroma compounds production in yeast. No quantitative data on how growth rate affects aroma profile is available in the literature to guide optimisation of the complex flavours in fermented beverages. In this study, we exploited the chemostat system, alongside with batch and fed-batch cultures to compare volatile profiles at different growth rates. We identified the aromatic compounds affected by the different feeding profiles and nutrient limitations. Moreover, we uncovered the correlation between yeast growth, esters and higher alcohols production. This study showcases the potential of the application of feeding profiles for the manipulation of aroma in the craft beverage industry.

microbiology↗

bioRxiv2022

Telomere to telomere sequence of model Aspergillus fumigatus genomes

The pathogenic fungus Aspergillus fumigatus is a major etiological agent of fungal invasive and chronic diseases affecting tens of millions of individuals worldwide. A high-quality reference genome is a fundamental resource to study its biology, pathogenicity and virulence as well as to discover better and more effective treatments against diseases caused by this fungus. Here, we used PacBio Single Molecule Real-Time (SMRT) and Oxford Nanopore sequencing for de novo genome assembly of two laboratory reference strains of A. fumigatus,CEA10 and A1160. We generated full length chromosome assemblies and a comprehensive telomere to telomere coverage for these two strains including ribosomal repeats and the sequences of centromeres, which we discovered to be composed of long transposon elements.

genomics↗

bioRxiv2022

Analysis of synthetic genetic interactions of non-coding RNAs in Saccharomyces cerevisiae

Non-coding RNAs (ncRNAs) with unknown function have been found to be responsible for fitness changes in yeast. With the help of synthetic genetic array (SGA) methodology, genetic interaction screenings between protein-coding genes have contributed to the understanding of complex genetic pathways in eukaryotes. By extending this approach to the ncRNAs, we created more than 15,000 ncRNA double mutants and scored their epistasis in different environments. More than 90% of ncRNA interactions did not correlate with the epistasis of their neighbouring protein-coding genes, showing that the ncRNA and protein interaction networks are largely independent. In the presence of different stressors, epistatic changes were observed with an overall increase in negative interactions. Such network plasticity supports the notion that these ncRNAs may have environmentally dependent functions and can contribute to phenotypic adaptation. The U3 paralogs, SNR17A and SNR17B, share most interactions in rich media, as expected, however, in stressful conditions, there was an increase of paralog-unique interactions, suggesting that SNR17A and SNR17B may have diverged cellular roles under different environmental pressures and may have neo-functionalised after genome duplication. Further investigation of the interaction networks between SNR17 and protein-coding genes revealed the emergence of paralog-specific interactions under stress conditions. Gene Ontology enrichment analysis suggested a novel potential role of SNR17B in chromatin structural remodelling and DNA topology under osmotic and oxidative stress. Overall, this genome-wide study uncovers the level of epistasis involving ncRNA mutants aiding functional assignment and expanding our fundamental knowledge of these genetic elements.

genetics↗

bioRxiv2021

Aneuploidy influences the gene expression profiles in Saccharomyces pastorianus group I and II strains during fermentation.

The lager yeasts, Saccharomyces pastorianus, are hybrids of Saccharomyces cerevisiae and Saccharomyces eubayanus and are divided into two broad groups, Group I and II. The two groups evolved from at least one common hybridisation event but have subsequently diverged with Group I strains losing many S. cerevisiae chromosomes while the Group II strains retain both sub-genomes. The complex genomes, containing orthologous alleles from the parental chromosomes, pose interesting questions regarding gene regulation and its impact on the fermentation properties of the strains. Superimposed on the presence of orthologous alleles are complexities of gene dosage due to the aneuploid nature of the genomes. We examined the contribution of the S. cerevisiae and S. eubayanus alleles to the gene expression patterns of Group I and II strains during fermentation. We show that the relative expression of S. cerevisiae and S. eubayanus orthologues is positively correlated with gene copy number. Despite the reduced S. cerevisiae content in the Group I strain, S. cerevisiae orthologues contribute to biochemical pathways upregulated during fermentation which may explain the retention of specific chromosomes in the strain. Conversely, S. eubayanus genes are significantly overrepresented in the upregulated gene pool in the Group II strain. Comparison of the transcription profiles of Group I and II strains during fermentation identified both common and unique gene expression patterns, with gene copy number being a dominant contributory factor. Thus, the aneuploid genomes create complex patterns of gene expression during fermentation with gene dosage playing a crucial role both within and between strains.

genetics↗

bioRxiv2021

Quantitative characterisation of low abundant yeast mitochondrial proteins reveals compensation for haplo-insufficiency in different environments

Quantification of low abundant membrane-binding proteins such as transcriptional factors and chaperones has been proved difficult even with the most sophisticated analytical technologies. Here we exploit and optimise the non-invasive Fluorescence Correlation Spectroscopy (FCS) for quantitation of low abundance proteins and as proof of principle we choose two interacting proteins involved in fission of mitochondria in yeast, Fis1p and Mdv1p. In Saccharomyces cerevisiae the recruitment of Fis1p and Mdv1p to mitochondria is essential for the scission of the organelles and the retention of functional mitochondrial structures in the cell. We used FCS in single, GFP-labelled live yeast cells to quantify the protein abundance in homozygote and heterozygote cells, and to investigate the impact of the environments on protein copy number, bound/unbound protein state and mobility kinetics. Both proteins were observed to localise predominantly at mitochondrial structures with the Mdv1p bound state increasing significantly in a strictly respiratory environment. Moreover, a compensatory mechanism which controls Fis1p abundance upon deletion of one allele was observed in Fis1p but not in Mdv1p, suggesting differential regulation of Fis1p and Mdv1p protein expression.

biochemistry↗

bioRxiv2021

Transcriptional network of the industrial hybrid Saccharomyces pastorianus reveals temperature-dependent allele expression bias and preferential orthologous protein assemblies

Saccharomyces pastorianus is an industrial natural yeast evolved from different hybridisation events between the mesophilic S. cerevisiae and the cold-tolerant S. eubayanus. This complex aneuploid hybrid carries multiple copies of the parental alleles alongside specific hybrid genes and encodes for multiple protein isoforms which impart novel phenotypes, such as the strong ability to ferment at low temperature. These characteristics lead to agonistic or antagonistic competition for substrates and a plethora of biochemical activities, resulting in a unique cellular metabolism. Here, we investigated the transcriptional signature of the different orthologous alleles in S. pastorianus during temperature shifts. We identified temperature-dependent media-independent genes and showed that 35% have their regulation dependent on extracellular leucine uptake, suggesting an interplay between leucine metabolism and temperature response. The analysis of the expression of ortholog parental alleles unveiled that the majority of the genes express preferentially one parental allele over the other, and that S. eubayanus-like alleles are significantly over-represented among the genes involved in cold acclimatisation. The presence of functionally redundant parental alleles may impact on the nature of protein complexes established in the hybrid, where both parental alleles are competing. Our expression data indicate that the majority of the protein complexes in the hybrid are likely to be either exclusively chimeric or uni-specific, and that the redundancy is discouraged, a scenario which fits well with the stoichiometric balance-hypothesis. This study offers the first overview of the transcriptional pattern of S. pastorianus and provide a rationalisation for its unique industrial traits at expression level.

genomics↗

bioRxiv2021

Restoring fertility in yeast hybrids: breeding and quantitative genetics of beneficial traits

Hybrids species can harbour a combination of beneficial traits from each parent and may exhibit hybrid vigour, more readily adapting to new harsher environments. Inter-species hybrids are also sterile and therefore an evolutionary dead-end unless fertility is restored, usually via auto-polyploidisation events. In the Saccharomyces genus, hybrids are readily found in nature and in industrial settings, where they have adapted to severe fermentative conditions. Due to their hybrid sterility, the development of new commercial yeast strains has so far been primarily conducted via selection methods rather than breeding. In this study, we overcame infertility by creating tetraploid intermediates of Saccharomyces inter-species hybrids, to allow continuous multigenerational breeding. We incorporated nuclear and mitochondrial genetic diversity within each parental species, allowing for quantitative genetic analysis of traits exhibited by the hybrids, and for nuclear-mitochondrial interactions to be assessed. Using pooled F12 generation segregants of different hybrids with extreme phenotype distributions, we identified QTLs for tolerance to high and low temperatures, high sugar concentration, high ethanol concentration, and acetic acid levels. We identified QTLs that are species specific, that are shared between species, as well as hybrid specific, where the variants do not exhibit phenotypic differences in the original parental species. Moreover, we could distinguish between mitochondria-type dependent and independent traits. This study tackles the complexity of the genetic interactions and traits in hybrid species, bringing hybrids into the realm of full genetic analysis of diploid species, and paves the road for the biotechnological exploitation of yeast biodiversity.

genetics↗

bioRxiv2021

Biotechnological exploitation of Saccharomyces jurei and its hybrids in craft beer fermentation uncovers new aroma combinations.

Hybridization is an important evolutionary mechanism to bring about novel phenotypes and may produce new hybrids with advantageous combinations of traits of industrial importance. Within the Saccharomyces group, Saccharomyces jurei is a newly discovered species and its biotechnological potential has not yet been fully explored. This yeast was found to be able to grow well in synthetic wort and at low temperatures, qualities necessary in good candidates for fermentated bevarages. Here, we analysed its fermentation and aroma profile and created novel non-GMO hybrids between S. jurei and S. cerevisiae ale yeasts to develop new starter strains with interesting flavours for the craft beer industry. Pilot beer fermentations with specific hybrids showed a good fermentation performance, similar to the ale parent strain, while presenting a better sugar attenuation and a more complex flavour profile. This study exploits the genetic diversity of yeasts and show how inter-specific hybridisation and clone selection can be effectively used in brewing to create new products and to eliminate or increase specific traits.

microbiology↗