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PloidYeast

Effects of polyploidization during adaptive evolution in yeasts

Project overview

Project lead: David Peris Navarro, University of Oslo and Institute of Agrochemistry and Food Technology (IATA-CSIC) (Spain)
Partners: Stockholm University (Sweden), I²SysBio at University of Valencia (Spain), Ghent University (Belgium), Lawrence Berkeley National Laboratory (USA)
Funding: Research Council of Norway (RCN) grant no. RCN 324253
Duration: 2021 - 2026
Website: Effects of polyploidization during adaptive evolution in yeasts (PloidYeast) - Department of Biosciences

Munoz, Sara Orellana; Haberkorn, Chloé; Csoboz, Balint; Stelkens, Rike & Peris, David (2026). Mitochondrial inheritance as an important parameter for the rational design of synthetic yeast polyploids. BioRxiv. ISSN 0362-4331. doi: https:/www.biorxiv.org/content/10.64898/2026.09.22.753424v1. Full text in Research Archive
Lü, Dabao Sun; Methlie, Ine-Susanne Hopland; Sønstebø, Jørn Henrik; Andersen, Anneli; Peris, David & Maurice, Sundy Ursula MaryJanne [Show all 8 contributors for this article] (2025). Postglacial History of a Widespread Wood-Decaying Fungus in Europe Suggests Migration out of Multiple Refugia Followed by Admixture. Molecular Ecology. ISSN 0962-1083. 34(22), p. 1–14. doi: 10.1111/mec.70053. Full text in Research Archive Show summary
While postglacial migration patterns have been well-studied in plants and animals in Europe, the same is not true for microorganisms such as fungi, and it remains unclear whether fungi have followed the same postglacial migration trajectories. In this study, we infer the postglacial history of the widespread wood-decay fungus Trichaptum abietinum in Europe. We investigate whether this fungus resided in multiple glacial refugia, as observed in many plants and animals, and how it migrated following the retreat of the ice. Population genomic analyses of T. abietinum suggest at least two glacial refugia in Europe: a southern refugium extending from Portugal to the Caucasus (potentially formed by several earlier distinct refugia), an eastern refugium and a potential third western refugium. Expansion from these refugia followed by migration and secondary contact has led to a complex genomic pattern of what we call the Mediterranean, Boreal, Atlantic and Central European admixed groups. From the southern and potential western refugia there have likely been northwards expansions resulting in the Mediterranean and Atlantic groups, while the Boreal group probably expanded westwards from the eastern refugium. A contact zone is present in Central Europe, where the Mediterranean and Boreal groups are admixing. In these admixed individuals, the second half of their largest scaffold is entirely inherited from the Boreal group, indicating either strong selection or genomic incompatibilities. In Scandinavia, the Atlantic and Boreal groups are in close contact but with limited admixture. Tajima's D and analyses of linkage disequilibrium decay support a recent history of contraction and expansion of this fungus in Europe. We conclude that the postglacial migration patterns in T. abietinum resemble those observed in several plants and animals, suggesting multiple glacial refugia followed by admixture during northward and westward expansions.
Lü, Dabao Sun; Peris, David; Sønstebø, Jørn Henrik; James, Timothy Y.; Rieseberg, Loren H. & Maurice, Sundy [Show all 9 contributors for this article] (2024). Reticulate evolution and rapid development of reproductive barriers upon secondary contact in a forest fungus. Current Biology. ISSN 0960-9822. 34(19), p. 4513–4525. doi: 10.1016/j.cub.2024.08.046. Full text in Research Archive Show summary
Reproductive barriers between sister species of the mushroom-forming fungi tend to be stronger in sympatry, leading to speculation on whether they are being reinforced by selection against hybrids. We have used population genomic analyses together with in vitro crosses of a global sample of the wood decay fungus Trichaptum abietinum to investigate reproductive barriers within this species complex and the processes that have shaped them. Our phylogeographic analyses show that T. abietinum is delimited into six major genetic groups: one in Asia, two in Europe, and three in North America. The groups present in Europe are interfertile and admixed, whereas our crosses show that the North American groups are reproductively isolated. In Asia, a more complex pattern appears, with partial intersterility between subgroups that likely originated independently and more recently than the reproductive barriers in North America. We found pre-mating barriers in T. abietinum to be moderately correlated with genomic divergence, whereas mean growth reduction of the mated hybrids showed a strong correlation with increasing genomic divergence. Genome-wide association analyses identified candidate genes with programmed cell death annotations, which are known to be involved in intersterility in distantly related fungi, although their link here remains unproven. Our demographic modeling and phylogenetic network analyses fit a scenario where reproductive barriers in Trichaptum abietinum could have been reinforced upon secondary contact between groups that diverged in allopatry during the Pleistocene glacial cycles. Our combination of experimental and genomic approaches demonstrates how T. abietinum is a tractable system for studying speciation mechanisms.
Peris, David; Ubbelohde, Emily J; Kuang, Meihua Christina; Kominek, Jacek; Langdon, Quinn K & Adams, Marie [Show all 23 contributors for this article] (2023). Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces. Nature Communications. 14(1), p. 690–690. doi: 10.1038/s41467-023-36139-2. Full text in Research Archive
Sorribes-Daudén, Raquel; Jordá, Tania; Peris, David; Martínez-Pastor, María Teresa & Puig, Sergi (2022). Adaptation of Saccharomyces Species to High-Iron Conditions. International Journal of Molecular Sciences. ISSN 1661-6596. 23(22). doi: 10.3390/ijms232213965. Full text in Research Archive Show summary
Iron is an indispensable element that participates as an essential cofactor in multiple biological processes. However, when present in excess, iron can engage in redox reactions that generate reactive oxygen species that damage cells at multiple levels. In this report, we characterized the response of budding yeast species from the Saccharomyces genus to elevated environmental iron concentrations. We have observed that S. cerevisiae strains are more resistant to high-iron concentrations than Saccharomyces non-cerevisiae species. Liquid growth assays showed that species evolutionarily closer to S. cerevisiae, such as S. paradoxus, S. jurei, S. mikatae, and S. arboricola, were more resistant to high-iron levels than the more distant species S. eubayanus and S. uvarum. Remarkably, S. kudriavzevii strains were especially iron sensitive. Growth assays in solid media suggested that S. cerevisiae and S. paradoxus were more resistant to the oxidative stress caused by elevated iron concentrations. When comparing iron accumulation and sensitivity, different patterns were observed. As previously described for S. cerevisiae, S. uvarum and particular strains of S. kudriavzevii and S. paradoxus became more sensitive to iron while accumulating more intracellular iron levels. However, no remarkable changes in intracellular iron accumulation were observed for the remainder of species. These results indicate that different mechanisms of response to elevated iron concentrations exist in the different species of the genus Saccharomyces.
Peris, David; Lü, Dabao Sun; Kinneberg, Vilde Bruhn; Methlie, Ine-Susanne Hopland; Dahl, Malin Stapnes & James, Timothy Y. [Show all 8 contributors for this article] (2022). Large-scale fungal strain sequencing unravels the molecular diversity in mating loci maintained by long-term balancing selection. PLoS Genetics. ISSN 1553-7390. 18(3). doi: 10.1371/journal.pgen.1010097. Full text in Research Archive Show summary
Balancing selection, an evolutionary force that retains genetic diversity, has been detected in multiple genes and organisms, such as the sexual mating loci in fungi. However, to quantify the strength of balancing selection and define the mating-related genes require a large number of strains. In tetrapolar basidiomycete fungi, sexual type is determined by two unlinked loci, MATA and MATB. Genes in both loci define mating type identity, control successful mating and completion of the life cycle. These loci are usually highly diverse. Previous studies have speculated, based on culture crosses, that species of the non-model genus Trichaptum (Hymenochaetales, Basidiomycota) possess a tetrapolar mating system, with multiple alleles. Here, we sequenced a hundred and eighty strains of three Trichaptum species. We characterized the chromosomal location of MATA and MATB, the molecular structure of MAT regions and their allelic richness. The sequencing effort was sufficient to molecularly characterize multiple MAT alleles segregating before the speciation event of Trichaptum species. Analyses suggested that long-term balancing selection has generated trans-species polymorphisms. Mating sequences were classified in different allelic classes based on an amino acid identity (AAI) threshold supported by phylogenetics. 17,550 mating types were predicted based on the allelic classes. In vitro crosses allowed us to support the degree of allelic divergence needed for successful mating. Even with the high amount of divergence, key amino acids in functional domains are conserved. We conclude that the genetic diversity of mating loci in Trichaptum is due to long-term balancing selection, with limited recombination and duplication activity. The large number of sequenced strains highlighted the importance of sequencing multiple individuals from different species to detect the mating-related genes, the mechanisms generating diversity and the evolutionary forces maintaining them.

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Munoz, Sara Orellana; Haberkorn, Chloé; Csoboz, Balint; Stelkens, Rike & Peris, David (2026). Mitochondrial–nuclear interactions shape hybrid physiology in Saccharomyces. Full text in Research Archive
Sorribes-Daudén, Raquel; Vanacloig-Pedrós, Elena; Aguilar-Díaz, Alejandro; Martínez-Pastor, María Teresa; Peris, David & Puig, Sergi (2026). Unravelling adaptive mechanisms of copper tolerance in yeasts of enological interest. Full text in Research Archive
Araque, Luis; Schweizer, Gabriel; Morard, Miguel; Aguilar-Díaz, Alejandro; Pérez-Adrián, Ana María & Bonet-Aparici, María [Show all 13 contributors for this article] (2026). Defining species boundaries in eukaryotic microorganisms: a persistent puzzle. Full text in Research Archive
Schweizer, Gabriel; Morard, Miguel; Araque, Luis; Aguilar-Díaz, Alejandro; Pérez-Adrián, Ana María & García-Ríos, Estéfani [Show all 7 contributors for this article] (2026). Can we define microbial species? Insights from the Saccharomyces genus. Full text in Research Archive
Aguilar-Díaz, Alejandro; Sorribes-Daudén, Raquel; Vanacloig-Pedrós, Elena; Martínez-Pastor, María Teresa; Puig, Sergi & Peris, David (2025). Tracking genomic adaptation to copper stress in yeast using an integrated bioinformatics pipeline. Full text in Research Archive
Peris, David; Munoz, Sara Orellana; Csoboz, Balint; Sorribes-Daudén, Raquel; Vanacloig-Pedrós, Elena & Aguilar-Díaz, Alejandro [Show all 11 contributors for this article] (2025). FunGIALab: Connecting Fungal Diversity, Evolution, and Biotechnological Applications. Full text in Research Archive
Aguilar, Alejandro; Dauden, Raquel Sorribes; Pedros, Elena Vancloig; Pastor, Maria Teresa Martínez; Puig, Sergi & Peris, David (2025). Harnessing synthetic allopolyploids: unveiling adaptive mechanisms in Saccharomyces yeasts for industrial innovation. Full text in Research Archive
Bonet, María; Araque, Luis; Malo, María López; Peris, David & Ríos, Estéfani García (2025). Generation of inter-specific Saccharomyces hybrids and their phenotypic characterization. Full text in Research Archive
Peris, David (2024). Introduction to fungal biodiversity and industrial applications. Full text in Research Archive
Peris, David (2024). Genomic characterization of yeast polyploids. Full text in Research Archive
Peris, David (2024). Levaduras y vino y otras aplicaciones. Full text in Research Archive
Peris, David (2024). Hongos y aplicaciones industriales. Full text in Research Archive
Peris, David (2024). Introduction to High Computing Performance (HPC). Full text in Research Archive
Peris, David (2024). Characterization of yeast polyploids and their applications. Full text in Research Archive
Peris, David (2024). Fungal Genomics and Industrial Applications Lab. Full text in Research Archive
Peris, David (2024). RCN PloidYeast and Symposium Introduction. Full text in Research Archive
Peris, David (2024). Domestication of yeast polyploids. Full text in Research Archive
Orellana-Muñoz, Sara; Estéfani, García-Ríos; Sorribes-Daudén, Raquel; Vanacloig, Elena; Martínez-Pastor, María Teresa & Puig, Sergi [Show all 7 contributors for this article] (2024). Effects of gene-flow in the evolution of Saccharomyces yeasts. Full text in Research Archive
Orellana-Muñoz, Sara; Borg, Nora; Nygård, Elise; Kauserud, Håvard; Skrede, Inger & Peris, David (2023). Yeast bioprospecting and genomics for a food circular bioeconomy. Full text in Research Archive
Peris, David (2023). Biodiversitat de fongs i les seues aplicacions industrials. Full text in Research Archive
Orellana-Muñoz, Sara; Ramírez-Aroca, Lainy; Querol, Amparo & Peris, David (2023). Polyploidization: can we predict its evolutionary pathway? Full text in Research Archive
Peris, David (2023). Biodiversitat de fongs i les seues aplicacions industrials. Full text in Research Archive
Orellana-Muñoz, Sara; Stelkens, Rike; Kauserud, Håvard; Skrede, Inger & Peris, David (2023). Generating a large collection of Saccharomyces polyploids to study their adaptation to food-related industrial conditions. Full text in Research Archive
Peris, David (2023). Biodiversitat de fongs i les seues aplicacions industrials. Full text in Research Archive
Peris, David (2023). Wild yeasts and their domestication for brewing applications. Full text in Research Archive
Orellana-Muñoz, Sara; Hittinger, Chris Todd; Querol, Amparo; Puig, Sergi & Peris, David (2023). Caracterización de linajes de levadura y su potencial fenotípico para su uso en la industria de los alimentos. Full text in Research Archive
Peris, David; Ubbelohde, Emily J; Wrobel, Russell L & Hittinger, Chris Todd (2022). Saccharomyces, a yeast genus model for understanding “well-established” metabolic pathways. Full text in Research Archive
Orellana-Muñoz, Sara; Stelkens, Rike; Kauserud, Håvard; Skrede, Inger & Peris, David (2022). A high-throughput pipeline for studying the effects of polyploidization during adaptive evolution in yeasts. Full text in Research Archive
Peris, David (2022). Distintas levaduras para distintas cervezas. Full text in Research Archive
Peris, David; Paredes, Rosneyvic González; Borrás, Luis Araque & Andrews, Josefa Oyarzún (2026). Recuperación de la capacidad de esporulación mediante el desarrollo de nuevas cepas lanzadera. University of Valencia. Full text in Research Archive
Peris, David & Cirer, Tania Gimena (2025). Screening de levaduras del género Saccharomyces en subproductos agroalimentarios. University of Valencia. Full text in Research Archive
Pozuelo, Laura Varon; Peris, David & Aguilar, Alejandro (2025). Annotation and phylogenetic analysis of Saccharomyces genes related with carbon sources of brewing interest. University of Valencia. Full text in Research Archive
Peris, David; Estéfani, García-Ríos & María, Bonet-Aparici (2024). Generación de híbridos interespecíficos de Saccharomyces y su caracterización fenotípica. University of Valencia. Full text in Research Archive

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Research group

David Peris Navarro, Researcher, project leader, University of Oslo
Sara Orellana Munoz, Postdoctoral fellow, University of Oslo
Balint Csoboz, Postdoctoral fellow, University of Oslo

Gabriel Schweizer, Bioinformatic freelancer, IDL (LinkedIn)
Alejandro Aguilar, PhD fellow, IATA-CSIC
Luis Araque, PhD fellow, IATA-CSIC
Ana M. Pérez, Technician, IATA-CSIC

About the project

Imagine a world where your favorite foods — from bread to beer, cheese to wine — are not just delicious, but also better for the planet. This might sound like science fiction, but PloidYeast is working on a tiny hero that could make it a reality: yeast.

Humans love food, and we are producing more of it than ever. But the way we make food is putting a big strain on the Earth. Climate change, destroyed habitats, and other human activities threaten our ability to keep feeding everyone sustainably. The United Nations has set ambitious goals to change this, and yeast could be a surprising solution.

Harnessing polyploidization

Yeast is more than just the magic that makes dough rise. It is a tiny factory that can transform plants into all sorts of tasty products. But the yeast we use now has limitations. That is where "Frankenyeast" comes in - a new breed of yeast designed to make food production more sustainable. Scientists have discovered that some yeast can increase their entire genome, a trick called polyploidization. It is like a built-in superpower that helps them adapt to tough conditions. By harnessing this power, scientists can create yeast that thrives in the demanding world of industrial food production.

Super-powered hybrids to achieve UN sustainability goals

PloidYeast’s team will mix and match eight different yeast species to create new, super-powered hybrids. Then, they will challenge these yeasts to survive and thrive under four industrially-relevant conditions. Using cutting-edge genetic engineering and data analysis, they will select the strongest yeast population and explore their new traits. Yeasts that can turn food-waste into value-added compounds, reducing waste. Yeasts that can work efficiently with minimal resources, shrinking the environmental footprint of food production. This could be a game-changer for achieving the UN’s sustainability goals.

A food future that is better for people and planet

Creating the “Frankenyeasts” was not easy. The PloidYeast team faced challenges like yeasts’ stress responses that slowed down progress. But with a multidisciplinary approach they overcame some of these hurdles and generated a new collection of 32 unique strains, 168 autotetraploids and 14 autotetraploids from 8 species. There are still a few challenges in the “Frankenyeast” pipeline that need to be solved, but that is a chapter for another story. Yeasts might seem insignificant, but they have the potential to be a mighty ally in the fight for food sustainability. By tapping into yeasts’ natural powers and giving them a genetic boost, PloidYeast can help create a food future that is better for both people and the planet.

Multidisciplinary approach

Polyploidization is a recurrent evolutionary phenomenon that generates diversity and facilitates adaptation. However, the effects of polyploidization are not well understood. PloidYeast applies a multidisciplinary approach combining microbiology, molecular and genetic engineering methods, bioinformatics and mathematical modelling to generate a new generation of industrial strains with application in the food production chain and advance in our understanding of adaptation by polyploidization.