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763 results for “Saccharomyces”
Saccharomyces cerevisiae protein phosphorylation and translation accuracy
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Evidence for two main domestication trajectories in Saccharomyces cerevisiae linked to distinct bread-making processes
<p>Data and code supporting the manuscript "Evidence for two main domestication trajectories in <em>Saccharomyces cerevisiae</em> linked to distinct bread-making processes" by Bigey et al. (2020)</p>
Increased time sampling in an evolve-and-resequence experiment with outcrossing Saccharomyces cerevisiae reveals multiple paths of adaptive change
<p>"Evolve and resequence" (E&R) studies combine experimental evolution and whole-genome sequencing to interrogate the genetics underlying adaptation. Due to ease of handling, E&R work with asexual organisms like bacteria can employ optimized experimental design, with large experiments and many generations of selection. By contrast, E&R experiments with sexually reproducing organisms are more difficult to implement, and design parameters vary dramatically among studies. Thus, efforts have been made to assess how these differences, such as number of independent replicates, or size of experimental populations, impact inference. We add to this work by investigating the role of time sampling – the number of discrete timepoints sequence data is collected from evolving populations. Using data from an E&R experiment with outcrossing <i>Saccharomyces cerevisiae </i>in which populations were sequenced 17 times over ~540 generations, we address the following questions: (i) do more timepoints improve the ability to identify candidate regions underlying selection? And (ii) does high-resolution sampling provide unique insight into evolutionary processes driving adaptation? We find that while time sampling does not improve the ability to identify candidate regions, high-resolution sampling does provide valuable opportunities to characterize evolutionary dynamics. Increased time sampling reveals three distinct trajectories for adaptive alleles: one consistent with classic population genetic theory (i.e. models assuming constant selection coefficients), and two where trajectories suggest more context-dependent responses (i.e. models involving dynamic selection coefficients). We conclude that while time sampling has limited impact on candidate region identification, sampling 8 or more timepoints has clear benefits for studying complex evolutionary dynamics.</p>
Data from: Population structure and reticulate evolution of Saccharomyces eubayanus and its lager-brewing hybrids
Reticulate evolution can be a major driver of diversification into new niches, especially in disturbed habitats and at the edges of ranges. Industrial fermentation strains of yeast provide a window into these processes, but progress has been hampered by a limited understanding of the natural diversity and distribution of Saccharomyces species and populations. For example, lager beer is brewed with Saccharomyces pastorianus, an alloploid hybrid of S. cerevisiae and S. eubayanus, a species only recently discovered in Patagonia, Argentina. Here we report that genetically diverse strains of S. eubayanus are readily isolated from Patagonia, demonstrating that the species is well established there. Analyses of multi-locus sequence data strongly suggest that there are two diverse and highly differentiated Patagonian populations. S. eubayanus alleles present among hybrid European brewing strains had strikingly low diversity, suggesting they were drawn from a small subpopulation that is closely related to one of the Patagonian populations. For the first time, we also report the rare isolation of S. eubayanus outside of Patagonia, in Wisconsin, USA. In contrast to the clear population differentiation in Patagonia, the North American strains represent a recent and possibly transient admixture of the two Patagonian populations. These complex and varied reticulation events are not adequately captured by conventional phylogenetic methods and required analyses of Bayesian concordance factors and phylogenetic networks to accurately summarize and interpret. These findings show how genetically diverse eukaryotic microbes can produce rare but economically important hybrids with low genetic diversity when they migrate from their natural ecological context.
Variation at an adhesin locus suggests sociality in natural populations of the yeast Saccharomyces cerevisiae
<p>Microbes engage in numerous social behaviors that are critical for survival and reproduction, and that require individuals to act as a collective. Various mechanisms ensure that collectives are composed of related, cooperating cells, thus allowing for the evolution and stability of these traits, and for selection to favor traits beneficial to the collective. Since microbes are difficult to observe directly, sociality in natural populations can instead be investigated using evolutionary genetic signatures, as social loci can be evolutionary hotspots. The budding yeast has been studied for over a century, yet little is known about its social behavior in nature. Flo11 is a highly regulated cell adhesin required for most lab social phenotypes; studies suggest it may function in cell recognition and its heterogenous expression may be adaptive for collectives such as biofilms. We investigated this locus and found positive selection in the areas implicated in cell-cell interaction, suggesting selection for kin discrimination. We also found balancing selection at an upstream activation site, suggesting selection on the level of variegated gene expression. Our results suggest this model yeast is surprisingly social in natural environments and is likely engaging in various forms of sociality. By utilizing genomic data, this research provides a glimpse of otherwise unobservable interactions.</p>
Saccharomyces boulardii in addition to antofloxacin-based bismuth quadruple therapy for Helicobacter pylori eradication
<p><em>Hpylori</em> is a gram-negative bacterium colonized in gastric mucosa. Currently, the infection rate of <em>H. pylori</em> in China is about 50%, which is not only closely related to a variety of digestive system diseases, but also induces a series of immune responses to other systems.</p>
Saccharomyces boulardii in addition to antofloxacin-based bismuth quadruple therapy for Helicobacter pylori eradication
<p><em>Hpylori</em> is a gram-negative bacterium colonized in gastric mucosa. Currently, the infection rate of <em>H. pylori</em> in China is about 50%, which is not only closely related to a variety of digestive system diseases, but also induces a series of immune responses to other systems.</p>
Figs 22–24 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 22–24. Orthogonius pseudocheni Tian & Deuve, 2006. 22. habitus, male; 23–24. aedeagus, lateral view and apical lamella, dorsal view.
Figs 19–21 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 19–21. Orthogonius macrophthalmus Tian & Deuve, 2013. 19. habitus, male; 20–21. aedeagus, lateral view and apical lamella, dorsal view.
Figs 16–18. Orthogonius angustus Chaudoir, 1871. 16 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 16–18. Orthogonius angustus Chaudoir, 1871. 16. habitus, male; 17–18. aedeagus, lateral view and apical lamella, dorsal view.
Figs 10–12. Orthogonius picipennis Chaudoir, 1871. 10 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 10–12. Orthogonius picipennis Chaudoir, 1871. 10. habitus, holotype, male; 11–12. aedeagus, lateral view and apical lamella, dorsal view.
Figs 6–9 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 6–9. Adeagus of Orthogonius punctum sp. nov., lateral view and dorsal view for apical lamella. 6–7. paratype, from NongNai, S. Vietnam; 8–9. paratype, male, from Khao Lak, S. Thailand.
Figs 4–5 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 4–5. Habitus of Orthogonius punctum sp. nov. 4. paratype, male, from NongNai, S. Vietnam; 5. paratype, male, from Khao Lak, S. Thailand.
Figs 1–3 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 1–3. Orthogonius pectinatus sp. nov. 1. habitus, holotype, male; 2–3. aedeagus, lateral view and apical lamella, dorsal view.
Figs 13–15 in Stepwise and cooperative assembly of a cytokinetic core complex in budding yeast Saccharomyces cerevisiae
Figs 13–15. Orthogonius nigripes Tian & Deuve, 2000. 13. habitus, male; 14–15. aedeagus, lateral view and apical lamella, dorsal view.
Data from: Persistence of resident and transplanted genotypes of the undomesticated yeast, Saccharomyces paradoxus in forest soil
One might expect yeasts in soil to be highly dispersed via water or insects, forming ephemeral, genetically heterogeneous populations subject to competition and environmental stochasticity. Here, we report persistence of genotypes of the yeast Saccharomyces paradoxus in space and time. Within 1 km2 in a mixed hardwood forest on scales from centimeters to tens of meters, we detect persistence over 3 years of native genotypes, identified by SNPs genome-wide, of the wild yeast, Saccharomyces paradoxus around Quercus rubra and Q. alba. Yeasts were recovered by enrichment in ethanol-containing medium, which measures only presence or absence, not abundance. Additional transplantation experiments employed strains marked with spontaneous defects in the URA3 gene, which also confer resistance to 5-Fluoroorotic acid (5FOA). Plating soil suspensions from transplant sites on 5FOA medium permitted one-step quantification of yeast colony-forming units, with no interference from other unmarked yeasts or microorganisms. After an initial steep decrease in abundance, the yeast densities fluctuated over time, increasing in association with rainfall and decreasing in association with drought. After 18 months, the transplanted yeasts remain in place on the nine sites. In vitro transplantation experiments into non-sterile soil in petri dishes showed similar patterns of persistence and response to moisture and drought. To determine whether S. cerevisiae, not previously recovered from soils regionally, can persist in our cold-climate sites, we transplanted marked S. cerevisiae alone and in mixture with S. paradoxus in fall, 2017. Five months on, S. cerevisiae persist to the same extent as S. paradoxus.
SMRT sequencing data on four hypersuppressive Saccharomyces cereviciae mitochondrial DNAs
<p>Hypersuppressive mitochondrial DNAs are thought to be linear tandem repeats of the base unit of specific ORI regions on the mitochondrial genome. Here we confirm the linear tandem repeats using SMRT sequencing technology on four hypersuppressive clones. Mitochondrial DNA from four <em>Saccharomyces cervisiae</em> hypersuppressive mutants and a wild-type control was enriched and sequenced using SMRT sequencing technology.</p>
Supporting Information: High-throughput Saccharomyces cerevisiae cultivation method for credentialing-based untargeted metabolomics
<p>F1: Physiological Constraints: Growth rate, glucose uptake, and intracellular 13C succinate concentration</p> <p>F2: PAVE input and adduct list</p> <p>F3: Credentialing results, HILIC data</p> <p>F4: Credentialing results, RP lipids data</p> <p>F5: HILIC Level 2A annotation with MS-DIAL and manual mass shift quality control</p> <p>F6: R script for the MetFrag/PCLite-based annotation</p> <p>F7: HILIC annotation with MetFrag/PCLite</p> <p>F8: RP-lipids annotation with MS-DIAL</p> <p>F9: Level 1 compounds identification</p> <p>F10: InChKey-based YMDB and HMDB recovery analysis </p> <p>F11: InChKey-based comparison with PAVE publication</p> <p>F12: Statistic Results</p> <p>F13: Supernatant measurements</p>
Genome sequences for 2031 Saccharomyces cerevisiae genome assemblies
<p>Genome sequences for 2031 Saccharomyces cerevisiae genome assemblies</p>
Detailed information for 2032 Saccharomyces cerevisiae genome assemblies
<p>Detailed information for 2032 Saccharomyces cerevisiae genome assemblies</p>
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