Research Lab

Yeast Genomics


Lab Members

Research Interests

We use yeasts to study basic and applied aspects of the evolution of genomes and of the emergence key metabolic features. More specifically, we address questions related to the role of horizontal gene transfer in the evolution of metabolism, or to the distribution, ecology and phenotypes of wild and domesticated.


To do so we combine the awesome power of whole-genome sequencing with in-depth physiological and ecological studies. Our work includes computational and experimental methods and integrates
genomics, evolutionary genetics, ecology, microbial diversity and physiology. To learn more on what we do check here.

Research Highlights
Harnessing the power of yeast genomics to understand yeast evolution and to foster innovation in fermentation

Taxonomy and systematics of yeasts can now be illuminated in great detail by comparative genomics. We revisited all the synonyms of the most relevant microbe in biotechnology, Saccharomyces cerevisiae, to clarify their relation to known populations and industrially important variants. We also greatly expanded the available genomes of fructophilic yeasts belonging to the genera Starmerella and Wickerhamiella and re-assessed in detail the impact of loss and re-acquisition of alcoholic fermentation and other traits acquired through horizontal gene transfer by this yeast lineage.


Given the applied relevance of our work, we partnered with national craft brewers to develop novel beverages and with an international company to explore innovative used of yeast diversity for fermentation.


highlight 2020


Representative Projects

  • “Exploring unique metabolic traits of biotechnological interest in fructophilic yeasts”, FCT-MCTES, Total funding: €238,347, Unit funding: €182,997, Paula Gonçalves (PI)
  • “Advancing wine yeast genomics – exploring the evolutionary dimensions of domestication and the emergence of virulence”, FCT-MCTES, Total funding: € 239,997, Unit funding: €210,550, José Paulo Sampaio (PI).
  • “Contract Research Microbiology”, Victor Guedes SA, Total and Unit funding: €20,000, José Paulo Sampaio and Paula Gonçalves (PIs).
  • “Contract Research Microbiology”, Fermentis Lasaffre for Beverages, Total and Unit funding: €10,000, José Paulo Sampaio (PI).

Selected Publications

Koufopanou, V; Lomas, S; Pronina, O; Almeida, P; Sampaio, JP; Mousseau, T; Liti, G; Burt, A. 2020. Population Size, Sex and Purifying Selection: Comparative Genomics of Two Sister Taxa of the Wild Yeast Saccharomyces paradoxus. Genome Biology and Evolution, 12, DOI: 10.1093/gbe/evaa141
Libkind, D; Cadez, N; Opulente, DA; Langdon, QK; Rosa, CA; Sampaio, JP; Goncalves, P; Hittinger, CT; Lachance, MA. 2020. Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences. FEMS YEAST RESEARCH, 20, DOI: 10.1093/femsyr/foaa042
David-Palma, M; Libkind, D; Brito, PH; Silva, M; Bellora, N; Coelho, MA; Heitman, J; Goncalves, P; Sampaio, JP. 2020. The Untapped Australasian Diversity of Astaxanthin-Producing Yeasts with Biotechnological Potential-Phaffia australis sp. nov. and Phaffia tasmanica sp. nov.. Innovative Technologies for Food Preservation - Inactivation of Spoilage and Pathogenic Microorganisms, 8, DOI: 10.3390/microorganisms8111651
Pontes, A; Hutzler, M; Brito, PH; Sampaio, JP. 2020. Revisiting the Taxonomic Synonyms and Populations ofSaccharomyces cerevisiae-Phylogeny, Phenotypes, Ecology and Domestication. Innovative Technologies for Food Preservation - Inactivation of Spoilage and Pathogenic Microorganisms, 8, DOI: 10.3390/microorganisms8060903
Pontes, A; Ruethi, J; Frey, B; Aires, A; Thomas, A; Overy, D; Halti, B; Kerr, R; Sampaio, JP. 2020. Cryolevonia gen. nov. and Cryolevonia schafbergensis sp. nov., a cryophilic yeast from ancient permafrost and melted sea ice. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 70, DOI: 10.1099/ijsem.0.004040