The Ecology and Evolution of the Baker’s Yeast Saccharomyces cerevisiae

Abstract

The baker’s yeast Saccharomyces cerevisiae has become a powerful model in ecology and evolutionary biology. A global effort on field survey and population genetics and genomics of S. cerevisiae in past decades has shown that the yeast distributes ubiquitously in nature with clearly structured populations. The global genetic diversity of S. cerevisiae is mainly contributed by strains from Far East Asia, and the ancient basal lineages of the species have been found only in China, supporting an ‘out-of-China’ origin hypothesis. The wild and domesticated populations are clearly separated in phylogeny and exhibit hallmark differences in sexuality, heterozygosity, gene copy number variation (CNV), horizontal gene transfer (HGT) and introgression events, and maltose utilization ability. The domesticated strains from different niches generally form distinct lineages and harbor lineage-specific CNVs, HGTs and introgressions, which contribute to their adaptations to specific fermentation environments. However, whether the domesticated lineages originated from a single, or multiple domestication events is still hotly debated and the mechanism causing the diversification of the wild lineages remains to be illuminated. Further worldwide investigations on both wild and domesticated S. cerevisiae, especially in Africa and West Asia, will be helpful for a better understanding of the natural and domestication histories and evolution of S. cerevisiae.

Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae

“…Saccharomyces cerevisiae is a single celled eukaryote that can be stably propagated in either a haploid or diploid state ( Jurica and Stoddard, 1999 ; Duina et al, 2014 ; Bai et al, 2022 ) . Importantly, S. cerevisiae was one of the first eukaryotic species to be genetically modified using transformation methods ( Hinnen et al, 1978 ) and is still a widely used model system for genetic engineering.…”

Domestication of different varieties in the cheese-making fungusGeotrichum candidum

“…However, despite their economic and industrial importance, and their utility as biological models for studying adaptive divergence, the fungi used by humans have yet been little studied. An exception is the budding yeast Saccharomyces cerevisiae used in the production of beer, wine and bread (Bai et al, 2022;Duan et al, 2018;Fay and Benavides, 2005;Gallone et al, 2016;Lahue et al, 2020;Legras et al, 2018;Libkind et al, 2011;Liti et al, 2009;Peter et al, 2018) , and to a lesser extent the filamentous fungus Aspergillus oryzae used to ferment soy and rice products in Asia (Galagan et al, 2005;Gibbons et al, 2012;Machida et al, 2005) and the Penicillium species used for cheese ripening, e.g. P. camemberti for soft cheeses (Ropars et al, 2020), and P. roqueforti for blue cheeses (Cheeseman et al, 2014;Dumas et al, 2020;Ropars et al, 2015).…”

The model system Ectocarpus: Integrating functional genomics into brown algal research

“…In the brown algal community, many laboratories are interested in questions concerning the evolution, diversification and biogeography of brown algal species and populations, and it may not be immediately obvious how a model organism approach might be relevant to these questions. Interestingly, although work on classical model systems in other lineages often initially tended to focus on limited numbers of laboratory strains and to ignore the organisms' ecology and natural variability, it was quickly realised that integrating natural variation into model system research not only provided a means to obtain new insights into gene and genome function but also allowed the tools developed for a model organism to be brought to bear on ecological or population-related questions (Cutter et al 2009, Weigel 2012, Takou et al 2019, Haudry et al 2020, Bai et al 2022. Work on natural populations of Ectocarpus are complicated by the need to analyse field isolates in the laboratory to distinguish Ectocarpus from several similar filamentous Ectocarpales species and to distinguish different species within the genus.…”