Query: Saccharomyces cerevisiae population evolution Europe

title: Population Analysis and Evolution of Saccharomyces cerevisiae Mitogenomes
abstract: The study of mitogenomes allows the unraveling of some paths of yeast evolution that are often not exposed when analyzing the nuclear genome. Although both nuclear and mitochondrial genomes are known to determine phenotypic diversity and fitness, no concordance has yet established between the two, mainly regarding strains' technological uses and/or geographical distribution. In the current work, we proposed a new method to align and analyze yeast mitogenomes, overcoming current difficulties that make it impossible to obtain comparable mitogenomes for a large number of isolates. To this end, 12,016 mitogenomes were considered, and we developed a novel approach consisting of the design of a reference sequence intended to be comparable between all mitogenomes. Subsequently, the population structure of 6646 Saccharomyces cerevisiae mitogenomes was assessed. Results revealed the existence of particular clusters associated with the technological use of the strains, in particular regarding clinical isolates, laboratory strains, and yeasts used for wine associated activities. As far as we know, this is the first time that a positive concordance between nuclear and mitogenomes has been reported for S. cerevisiae, in terms of strains' technological applications. The results obtained highlighted the importance of including the mtDNA genome in evolutionary analysis, in order to clarify the origin and history of yeast species.

title: Population genomics reveals evolution and variation of Saccharomyces cerevisiae in the human and insects gut
abstract: The quest to discover the variety of ecological niches inhabited by Saccharomyces cerevisiae has led to research in areas as diverse as wineries, oak trees and insect guts. The discovery of fungal communities in the human gastrointestinal tract suggested the host's gut as a potential reservoir for yeast adaptation. Here, we report the existence of yeast populations associated with the human gut (HG) that differ from those isolated from other human body sites. Phylogenetic analysis on 12 microsatellite loci and 1715 combined CDSs from whole genome sequencing revealed three subclusters of HG strains with further evidence of clonal colonization within the host's gut. The presence of such subclusters was supported by other genomic features, such as copy number variation, absence/introgressions of CDSs and relative polymorphism frequency. Functional analysis of CDSs specific of the different subclusters suggested possible alterations in cell wall composition and sporulation features. The phenotypic analysis combined with immunological profiling of these strains further showed that sporulation was related with strain specific genomic characteristics in the immune recognition pattern. We conclude that both genetic and environmental factors involved in cell wall remodelling and sporulation are the main drivers of adaptation in S. cerevisiae populations in the human gut.

title: Genome evolution across 1,011 Saccharomyces cerevisiae isolates
abstract: Large scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report the whole genome sequencing and phenotyping of 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture of the genomic variants that shape the species wide phenotypic landscape of this yeast. Genomic analyses support a single 'out of China' origin for this species, followed by several independent domestication events. Although domesticated isolates exhibit high variation in ploidy, aneuploidy and genome content, genome evolution in wild isolates is mainly driven by the accumulation of single nucleotide polymorphisms. A common feature is the extensive loss of heterozygosity, which represents an essential source of inter individual variation in this mainly asexual species. Most of the single nucleotide polymorphisms, including experimentally identified functional polymorphisms, are present at very low frequencies. The largest numbers of variants identified by genome wide association are copy number changes, which have a greater phenotypic effect than do single nucleotide polymorphisms. This resource will guide future population genomics and genotype phenotype studies in this classic model system.Whole genome sequencing of 1,011 natural isolates of the yeast Saccharomyces cerevisiae reveals its evolutionary history, including a single out of China origin and multiple domestication events, and provides a framework for genotype phenotype studies in this model organism.

title: Myriocin induced adaptive laboratory evolution of an industrial strain of Saccharomyces cerevisiae reveals its potential to remodel lipid composition and heat tolerance
abstract: The modification of lipid composition allows cells to adjust membrane biophysical properties in response to changes in environmental temperature. Here, we use adaptive laboratory evolution (ALE) in the presence of myriocin, a sphingolipid (SLs) biosynthesis inhibitor, to remodel the lipid profile of an industrial yeast strain (LH) of Saccharomyces cerevisiae. The approach enabled to obtain a heterogeneous population (LHev) of myriocin tolerant evolved clones characterized by its growth capacity at high temperature. Myriocin exposure also caused tolerance to soraphen A, an inhibitor of the acetyl CoA carboxylase Acc1, the rate limiting enzyme in fatty acid de novo production, supporting a change in lipid metabolism during ALE. In line with this, characterization of two randomly selected clones, LH03 and LH09, showed the presence of lipids with increased saturation degree and reduced acyl length. In addition, the clone LH03, which displays the greater improvement in fitness at 40degC, exhibited higher SL content as compared with the parental strain. Analysis of the LH03 and LH09 genomes revealed a loss of chromosomes affecting genes that have a role in fatty acid synthesis and elongation. The link between ploidy level and growth at high temperature was further supported by the analysis of a fully isogenic set of yeast strains with ploidy between 1N and 4N which showed that the loss of genome content provides heat tolerance. Consistent with this, a thermotolerant evolved population (LH40deg) generated from the parental LH strain by heat driven ALE exhibited a reduction in the chromosome copy number. Thus, our results identify myriocin driven evolution as a powerful approach to investigate the mechanisms of acquired thermotolerance and to generate improved strains.

title: Yeast population dynamics during spontaneous fermentation of icewine and selection of indigenous Saccharomyces cerevisiae strains for the winemaking in Qilian, China.
abstract: Icewine produced in China is getting popular, but only limited knowledge is available on the yeast population that occurs during fermentation and also on the selection of indigenous Saccharomyces cerevisiae strains for its production. In this work, we first investigated yeast species and the evolution of yeast population in spontaneous fermentations of icewine produced in the Qilian region of China and then analyzed the biodiversity and important enological properties of S. cerevisiae isolates.  Seven species of five genera including Saccharomyces cerevisiae, Saccharomyces uvarum, Torulaspora delbrueckii, Hanseniaspora uvarum, Lachancea thermotolerans, Metschnikowia aff. Fructicola and Hanseniaspora osmophila were identified by the colony morphology on Wallerstein Laboratory Nutrient medium and sequence analysis of the 26S rRNA gene D1/D2 domain. S.cerevisiae, H. uvarum and L. thermotolerans were the dominant species, representing almost 87% of the total yeast isolates. Microvinification with seven preselected S. cerevisiae strains were performed on Vidal. All selected strains could complete fermentations, and the enochemical parameters were within the acceptable ranges of the wine industry. W5B3 produced higher amounts of ethyl hexanoate and ethyl octanoate than other strains. R3A10 was a low volatile acid producer and the corresponding icewine presented the highest values on some odorants including b damascenone, 1 octen 3 ol, ethyl 2 methylbutyrate, and isoamyl alcohol. Vidal icewines fermented with R3A10, R3A16 and W5B3 were well accepted by the judges because of superior sensory quality.  Three indigenous strains (R3A10, R3A16 and W5B3) could be used as starters and could potentially improve the regional character of the icewine in Qilian. This article is protected by copyright. All rights reserved.

title: Enhanced mutation through exposure to EMS affects the evolution of ethanol tolerance in Saccharomyces cerevisiae
abstract: Ethanol is a multifunctional compound that has many uses and can be made naturally by sugar fermenting yeast such as Saccharomyces cerevisiae. However, ethanol is toxic to yeast, so in this study we aimed to improve yeast ethanol tolerance, which could result in greater efficiencies in the process of alcohol production. This research explores the effectiveness of artificially inducing population level variation through the application of ethyl methanesulfonate (EMS) on increasing the ethanol tolerance in S. cerevisiae. After several rounds of selection and increasing ethanol concentrations, ranging from 9 27% the two treatment populations (AS Artificial Selection only; and EMS Exposure to EMS and Artificial Selection) were compared to the initial parental population. The parental strain was tolerant to ethanol concentrations of 13% while the AS treatment was tolerant to slightly higher levels, 16% Both of these treatments were well below the EMS treatment which expressed a tolerance of 27% To test differences between strains, the parental strain, selection strain, and the EMS exposed strain were separately plated on ten 27% ethanol plates and ten 0% ethanol plates, and growth was checked after 24 hours. The EMS exposed strain was the only strain that grew at 27% ethanol; all strains grew at 0% ethanol. These results show that EMS, artificial selection, and ethanol as a stressor might be effective in producing strains of S. cerevisiae that are able to produce greater amounts of ethanol before toxicity sets in.

title: Rapid Colorimetric Detection of Genome Evolution in SCRaMbLEd Synthetic Saccharomyces cerevisiae Strains
abstract: Genome scale engineering and custom synthetic genomes are reshaping the next generation of industrial yeast strains. The Cre recombinase mediated chromosomal rearrangement mechanism of designer synthetic Saccharomyces cerevisiae chromosomes, known as SCRaMbLE, is a powerful tool which allows rapid genome evolution upon command. This system is able to generate millions of novel genomes with potential valuable phenotypes, but the excessive loss of essential genes often results in poor growth or even the death of cells with useful phenotypes. In this study we expanded the versatility of SCRaMbLE to industrial strains, and evaluated different control measures to optimize genomic rearrangement, whilst limiting cell death. To achieve this, we have developed RED (rapid evolution detection) a simple colorimetric plate assay procedure to rapidly quantify the degree of genomic rearrangements within a post SCRaMbLE yeast population. RED enabled semi synthetic strains were mated with the haploid progeny of industrial yeast strains to produce stress tolerant heterozygous diploid strains. Analysis of these heterozygous strains with the RED assay, genome sequencing and custom bioinformatics scripts demonstrated a correlation between RED assay frequencies and physical genomic rearrangements. Here we show that RED is a fast and effective method to evaluate the optimal SCRaMbLE induction times of different Cre recombinase expression systems for the development of industrial strains.

title: Rapid Colorimetric Detection of Genome Evolution in SCRaMbLEd Synthetic Saccharomyces cerevisiae Strains
abstract: Genome scale engineering and custom synthetic genomes are reshaping the next generation of industrial yeast strains. The Cre recombinase mediated chromosomal rearrangement mechanism of designer synthetic Saccharomyces cerevisiae chromosomes, known as SCRaMbLE, is a powerful tool which allows rapid genome evolution upon command. This system is able to generate millions of novel genomes with potential valuable phenotypes, but the excessive loss of essential genes often results in poor growth or even the death of cells with useful phenotypes. In this study we expanded the versatility of SCRaMbLE to industrial strains, and evaluated different control measures to optimize genomic rearrangement, whilst limiting cell death. To achieve this, we have developed RED (rapid evolution detection) a simple colorimetric plate assay procedure to rapidly quantify the degree of genomic rearrangements within a post SCRaMbLE yeast population. RED enabled semi synthetic strains were mated with the haploid progeny of industrial yeast strains to produce stress tolerant heterozygous diploid strains. Analysis of these heterozygous strains with the RED assay, genome sequencing and custom bioinformatics scripts demonstrated a correlation between RED assay frequencies and physical genomic rearrangements. Here we show that RED is a fast and effective method to evaluate the optimal SCRaMbLE induction times of different Cre recombinase expression systems for the development of industrial strains.

title: Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae
abstract: Understanding how phenotypes evolve requires disentangling the effects of mutation generating new variation from the effects of selection filtering it. Evolutionary models frequently assume that mutation introduces phenotypic variation symmetrically around the population mean, yet few studies have tested this assumption by deeply sampling the distributions of mutational effects for particular traits. Here, we examine distributions of mutational effects for gene expression in the budding yeast Saccharomyces cerevisiae by measuring the effects of thousands of point mutations introduced randomly throughout the genome. We find that the distributions of mutational effects differ for the 10 genes surveyed and violate the assumption of normality. For example, all ten distributions of mutational effects included more mutations with large effects than expected for normally distributed phenotypes. In addition, some genes also showed asymmetries in their distribution of mutational effects, with new mutations more likely to increase than decrease the gene's expression or vice versa. Neutral models of regulatory evolution that take these empirically determined distributions into account suggest that neutral processes may explain more expression variation within natural populations than currently appreciated. Significance statement New mutations tend to arise randomly throughout the genome, but their phenotypic effects are often not random. This disconnect results from interactions among genes that define the genotype phenotype map. The structure of this map is poorly known and different for each trait, making it challenging to predict the distribution of mutational effects for specific phenotypes. Empirical measures of the distribution of mutational effects are thus necessary to understand how traits can change in the absence of natural selection. In this work, we define such distributions for expression of ten genes in S. cerevisiae and show that they predict greater neutral expression divergence than commonly used models of phenotypic evolution.

title: Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae
abstract: New mutations tend to arise randomly throughout the genome, but their phenotypic effects are often not random. This disconnect results from interactions among genes that define the genotype phenotype map. The structure of this map is poorly known and different for each trait, making it challenging to predict the distribution of mutational effects for specific phenotypes. Empirical measures of the distribution of mutational effects are thus necessary to understand how traits can change in the absence of natural selection. In this work, we define such distributions for expression of 10 genes in Saccharomyces cerevisiae and show that they predict greater neutral expression divergence than commonly used models of phenotypic evolution. Understanding how phenotypes evolve requires disentangling the effects of mutation generating new variation from the effects of selection filtering it. Tests for selection frequently assume that mutation introduces phenotypic variation symmetrically around the population mean, yet few studies have tested this assumption by deeply sampling the distributions of mutational effects for particular traits. Here, we examine distributions of mutational effects for gene expression in the budding yeast Saccharomyces cerevisiae by measuring the effects of thousands of point mutations introduced randomly throughout the genome. We find that the distributions of mutational effects differ for the 10 genes surveyed and are inconsistent with normality. For example, all 10 distributions of mutational effects included more mutations with large effects than expected for normally distributed phenotypes. In addition, some genes also showed asymmetries in their distribution of mutational effects, with new mutations more likely to increase than decrease the gene's expression or vice versa. Neutral models of regulatory evolution that take these empirically determined distributions into account suggest that neutral processes may explain more expression variation within natural populations than currently appreciated.