Domestication reprogrammed the budding yeast life cycle

Chiara, Matteo De; Barré, Benjamin; Persson, Karl; Irizar, Agurtzane; Vischioni, Chiara; Khaiwal, Sakshi; Stenberg, Simon; Amadi, Onyetugo C.; Žun, Gašper; Doberšek, Katja; Taccioli, Cristian; Schacherer, Joseph; Petrovič, Uroš; Warringer, Jonas; Liti, Gianni

doi:10.1038/s41559-022-01671-9

Cited by 50 publications

(66 citation statements)

References 114 publications

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“…2006; De Chiara et al. 2020). The African strain, WA, which is thought to be only partially domesticated (see Methods), had an intermediate fraction of spores.…”

Section: Resultsmentioning

confidence: 99%

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Testing the adaptive value of sporulation in budding yeast using experimental evolution

et al. 2021

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“…2006; De Chiara et al. 2020). The African strain, WA, which is thought to be only partially domesticated (see Methods), had an intermediate fraction of spores.…”

Section: Resultsmentioning

confidence: 99%

“…2006; De Chiara et al. 2020). Changes in the sporulation response could thus be due to selection on genotypic variants of detection of environmental information or due to selection on variants enacting the sporulation program.…”

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confidence: 99%

Testing the adaptive value of sporulation in budding yeast using experimental evolution

et al. 2021

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“…For example, associating mat traits, like the pH environment generated by a strain, with the niche from which it was collected may provide insights into which traits are favored under different ecological circumstances. Furthermore, uncovering natural genetic variants that control mat biofilm formation, as has been done for other complex life‐history traits in yeast (De Chiara et al, 2022), or further investigating the biochemical properties of natural FLO11 variants (Oppler et al, 2019) and the conditions under which they generate the greatest cell‐cell adhesion (Bouyx et al, 2021; Brückner et al, 2020) could provide insight into the molecular basis of how multicellularity is favored in this organism.…”

Section: Discussionmentioning

confidence: 99%

Variation in pH gradients and FLO11 expression in mat biofilms from environmental isolates of the yeast Saccharomyces cerevisiae

et al. 2022

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Saccharomyces cerevisiae produces a multicellular phenotype, known as a mat, on a semi‐solid medium. This biofilm phenotype was first described in the lab strain Σ1278b and has been analyzed mostly in this same background. Yeast cells form a mat by spreading across the medium and adhering to each other and the surface, in part through the variegated expression of the cell adhesion, FLO11. This process creates a characteristic floral pattern and generates pH and glucose gradients outward from the center of the mat. Mats are encapsulated in a liquid which may aid in surface spreading and diffusion. Here, we examine thirteen environmental isolates that vary visually in the phenotype. We predicted that mat properties were universal and increased morphological complexity would be associated with more extreme trait values. Our results showed that pH varied significantly among strains, but was not correlated to mat complexity. Only two isolates generated significant liquid boundaries and neither produced visually complex mats. In five isolates, we tracked the initiation of FLO11 using green fluorescent protein (GFP) under the control of the endogenous promoter. Strains varied in when and how much GFP was detected, with increased signal associated with increased morphological complexity. Generally, the signal was strongest in the center of the mat and absent at the expanding edge. Our results show that traits discovered in one background vary and exist independently of mat complexity in natural isolates. The environment may favor different sets of traits, which could have implications for how this yeast adapts to its many ecological niches.

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“…For example, a strain isolated from Malaysia (UWOPS03‐461.4) has been shown to have severely reshuffled chromosomes (Marie‐Nelly et al, 2014; Yue et al, 2017) resulting in a high level of reproductive isolation with all other strains (Cubillos et al, 2011). Domestication within S. cerevisiae has also been shown to significantly affect spore viability and is driven by aneuploidies and gene function losses (De Chiara et al, 2020).…”

Section: Reproductive Isolation In Saccharomycesmentioning

confidence: 99%

Saccharomyces yeast hybrids on the rise

Bendixsen

Frazão

Stelkens

2021

Yeast

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Saccharomyces hybrid yeasts are receiving increasing attention as a powerful model system to understand adaptation to environmental stress and speciation mechanisms, using experimental evolution and omics techniques. We compiled all genomic resources available from public repositories of the eight recognized Saccharomyces species and their interspecific hybrids. We present the newest numbers on genomes sequenced, assemblies, annotations, and sequencing runs, and an updated species phylogeny using orthogroup inference. While genomic resources are highly skewed towards Saccharomyces cerevisiae, there is a noticeable movement to use wild, recently discovered yeast species in recent years. To illustrate the degree and potential causes of reproductive isolation, we reanalyzed published data on hybrid spore viabilities across the entire genus and tested for the role of genetic, geographic, and ecological divergence within and between species (28 cross types and 371 independent crosses). Hybrid viability generally decreased with parental genetic distance likely due to antirecombination and negative epistasis, but notable exceptions emphasize the importance of strain-specific structural variation and ploidy differences. Surprisingly, the viability of crosses within species varied widely, from near reproductive isolation to near-perfect viability. Geographic and ecological origins of the parents predicted cross viability to an extent, but with certain caveats. Finally, we highlight publication trends in the field and point out areas of special interest, where hybrid yeasts are particularly promising for innovation through research and development, and experimental evolution and fermentation. Take AwayThis article provides (1) a quantitative review of all genomic resources of Saccharomyces yeast species and their hybrids, (2) a compilation of published data on reproductive isolation (spore viabilities) within and between species, (3) highlights and trends in the publication efforts within this field, and (4) areas where yeast hybrids are and will be particularly useful for research and development in the future.

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Domestication reprogrammed the budding yeast life cycle

Cited by 50 publications

References 114 publications

Testing the adaptive value of sporulation in budding yeast using experimental evolution

Testing the adaptive value of sporulation in budding yeast using experimental evolution

Variation in pH gradients and FLO11 expression in mat biofilms from environmental isolates of the yeast Saccharomyces cerevisiae

Saccharomyces yeast hybrids on the rise

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