Biology subjects

Schacherer, J.

Publications and source records attributed to Schacherer, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2021

Lessons from the meiotic recombination landscape of the ZMM deficient budding yeast Lachancea waltii

Meiotic recombination has been deeply characterized in a few model species only, notably in the budding yeast Saccharomyces cerevisiae. Interestingly, most members of the ZMM pathway that implements meiotic crossover interference in S. cerevisiae have been lost in Lachancea yeast species after the divergence of Lachancea kluyveri from the rest of the clade. This suggests major differences in the control of crossover distribution. After investigating meiosis in L. kluyveri, we determined the meiotic recombination landscape of Lachancea waltii and identified several characteristics that should help understand better the underlying mechanisms. Such characteristics include systematic regions of loss of heterozygosity (LOH) in L. waltii hybrids, compatible with dysregulated Spo11-mediated DNA double strand breaks (DSB) independently of meiosis. They include a higher recombination rate in L. waltii than in L. kluyveri despite the lack of multiple ZMM pro-crossover factors. L. waltii exhibits an elevated frequency of zero-crossover bivalents as L. kluyveri but opposite to S. cerevisiae. L. waltii gene conversion tracts lengths are comparable to those observed in S. cerevisiae and shorter than in L. kluyveri despite the lack of Mlh2, a factor limiting conversion tracts size in S. cerevisiae. L. waltii recombination hotspots are not shared with either S. cerevisiae or L. kluyveri, showing that meiotic recombination hotspots can evolve at a rather limited evolutionary scale within budding yeasts. Finally, in line with the loss of several ZMM genes, we found only residual crossover interference in L. waltii likely coming from the modest interference existing between recombination precursors. Significance statementStudying non-model species is relevant to understand better biological processes by shedding light on their evolutionary variations. Here we chose the non-model budding yeast Lachancea waltii to study meiotic recombination. In sexually reproducing organisms, meiotic recombination shuffles parental genetic combinations notably by crossovers that cluster in hotspots at the population level. We found remarkable variations compared to both the canonical Saccharomyces cerevisiae model and another close relative Lachancea kluyveri. Such variations notably include the loss in L. waltii of a layer of regulation of crossover distribution that is otherwise conserved in budding yeasts and mammals. They also include the lack of conservation of crossover hotspots across the Lachancea species while crossover hotspots are remarkably stable across the Saccharomyces species. Highlights- Extensive LOH events in L. waltii intraspecific hybrids - No conservation of the recombination hotspots across the Lachancea genus - Reduced but not suppressed crossover interference in the absence of the ZMM pathway - Similar gene conversion tract lengths in L. waltii, S. cerevisiae, and L. kluyveri despite the lack of MLH2 in L. waltii

genetics↗

bioRxiv2021

Population-level survey of loss-of-function mutations revealed that background dependent fitness genes are rare and functionally related in yeast

In natural populations, the same mutation can lead to different phenotypic outcomes due to the genetic variation that exists among individuals. Such genetic background effects are commonly observed, including in the context of many human diseases. However, systematic characterization of these effects at the species level is still lacking to date. Here, we sought to comprehensively survey background-dependent traits associated with gene loss-of-function (LoF) mutations in 39 natural isolates of Saccharomyces cerevisiae using a transposon saturation strategy. By analyzing the modeled fitness variability of a total of 4,469 genes, we found that 15% of them, when impacted by a LoF mutation, exhibited a significant gain- or loss-of-fitness phenotype in certain natural isolates compared to the reference strain S288C. Out of these 632 genetic background-dependent fitness genes identified, a total of 2/3 show a continuous variation across the population while 1/3 are specific to a single genetic background. Genes related to mitochondrial function are significantly overrepresented in the set of genes showing a continuous variation and display a potential functional rewiring with other genes involved in transcription and chromatin remodeling as well as in nuclear-cytoplasmic transport. Such rewiring effects are likely modulated by both the genetic background and the environment. While background-specific cases are rare and span diverse cellular processes, they can be functionally related at the individual level. All background-dependent fitness genes tend to have an intermediate connectivity in the global genetic interaction network and have shown relaxed selection pressure at the population level, highlighting their potential evolutionary characteristics.

genetics↗

bioRxiv2021

Sex without crossing over in the yeast Saccharomycodes ludwigii

Meiotic recombination is a ubiquitous function of sexual reproduction throughout eukaryotes. Here we report that recombination is extremely suppressed during meiosis in the yeast species Saccharomycodes ludwigii. DNA double-strand break formation, processing and repair are required for normal meiosis but do not lead to crossing over. Although the species has retained an intact meiotic gene repertoire, genetic and population analyses suggest the exceptionally rare occurrence of meiotic crossovers. We propose that Sd. ludwigii has followed a unique evolutionary trajectory that possibly derives fitness benefits from the combination of frequent fertilization within the meiotic tetrad with the absence of meiotic recombination.

genetics↗

bioRxiv2021

Evolution of quantitative trait locus hotspots in yeast species

Dissecting the genetic basis of complex trait remains a real challenge. The budding yeast Saccharomyces cerevisiae has become a model organism for studying quantitative traits, successfully increasing our knowledge in many aspects. However, the exploration of the genotype-phenotype relationship in non-model yeast species could provide a deeper insight into the genetic basis of complex traits. Here, we have studied this relationship in the Lachancea waltii species which diverged from the S. cerevisiae lineage prior to the whole-genome duplication. By performing linkage mapping analyses in this species, we identified 86 quantitative trait loci (QTL) affecting growth fitness in a large number of conditions. The distribution of these loci across the genome has revealed two major QTL hotspots. A first hotspot corresponds to a general fitness QTL, impacting a wide range of conditions. By contrast, the second hotspot highlighted a fitness trade-off with a disadvantageous allele for drug-free conditions which proved to be advantageous in the presence of several drugs. Finally, the comparison of the detected QTL in L. waltii with those which had been previously identified for the same traits in a closely related species, Lachancea kluyveri, clearly revealed the absence of interspecific conservation of these loci. Altogether, our results expand our knowledge on the variation of the QTL landscape across different yeast species.

genetics↗

bioRxiv2021

Species-wide transposable element repertoires retrace the evolutionary history of the Saccharomyces cerevisiae host

Transposable elements (TE) are an important source of genetic variation with a dynamic and content that greatly differ in a wide range of species. The origin of the intraspecific content variation is not always clear and little is known about the precise nature of it. Here, we surveyed the species-wide content of the Ty LTR-retrotransposons in a broad collection of 1,011 Saccharomyces cerevisiae natural isolates to understand what can stand behind the variation of the repertoire, i.e. the type and number of Ty elements. We have compiled an exhaustive catalog of all TE variants present in the S. cerevisiae species by identifying a large set of new variants. The characterization of the TE content in each isolate clearly highlighted that each subpopulation exhibits a unique and specific repertoire, retracing the evolutionary history of the species. Most interestingly, we have shown that ancient interspecific hybridization events had a major impact in the birth of new variants and therefore in the shaping of the TE repertoires. We also investigated the transpositional activity of these elements in a large set of natural isolates, and we found a broad variability related to the level of ploidy as well as the genetic background. Overall, our results pointed out that the evolution of the Ty content is deeply impacted by clade-specific events such as introgressions and therefore follows the population structure. In addition, our study lays the foundation for future investigations to better understand the transpositional regulation and more broadly the TE-host interactions. Authors summaryMobile DNA elements are widely distributed in the genomes of many eukaryotes, but their contents greatly vary between species, populations and even individuals. In fact, little is known about the origin of this variation of transposable element (TE) content across individuals of the same species. Here, we surveyed the Ty LTR-retrotransposon content in a broad collection of 1,011 Saccharomyces cerevisiae yeast natural isolates. We have defined an exhaustive and precise catalog of the TE variants present in the S. cerevisiae species. We found that the TE content follows the evolutionary history of the species because each subpopulation has a unique and specific content. Interestingly, our results highlighted that ancient interspecific hybridization events led to the appearance of new TE variants and therefore had a strong impact on the variation of the TE repertoires in this species. We also investigated the transpositional activity of these elements and found a wide variability related to the genetic background diversity. Altogether, our results have led to a better understanding of the variability of TE content at a species level.

genomics↗

bioRxiv2021

Flor yeasts rewire the central carbon metabolism during wine alcoholic fermentation

The identification of natural allelic variations controlling quantitative traits could contribute to decipher metabolic adaptation mechanisms within different populations of the same species. Such variations could result from man-mediated selection pressures and participate to the domestication. In this study, the genetic causes of the phenotypic variability of the central carbon metabolism Saccharomyces cerevisiae were investigated in the context of the enological fermentation. Carbon dioxide and glycerol production as well as malic acid consumption modulate the fermentation yield revealing a high level of genetic complexity. Their genetic determinism was found out by a multi environment QTL mapping approach allowing the identification of 14 quantitative trait loci from which 8 of them were validated down to the gene level by genetic engineering. Most of the validated genes had allelic variations involving flor yeast specific alleles. Those alleles were brought in the offspring by one parental strain that is closely related to the flor yeast genetic group while the second parental strain is part of the wine group. The causative genes identified are functionally linked to quantitative proteomic variations that would explain divergent metabolic features of wine and flor yeasts involving the tricarboxylic acid cycle (TCA), the glyoxylate shunt and the homeostasis of proton and redox cofactors. Overall, this work led to the identification of genetic factors that are hallmarks of adaptive divergence between flor yeast and wine yeast in the wine biotope. These alleles can also be used in the context of yeast selection to improve oenological traits linked to fermentation yield.

genetics↗

bioRxiv2021

High-throughput functional analysis of natural variants in yeast

How natural variation affects phenotype is difficult to determine given our incomplete ability to deduce the functional impact of the polymorphisms detected in a population. Although current computational and experimental tools can predict and measure allele function, there has previously been no assay that does so in a high-throughput manner while also representing haplotypes derived from wild populations. Here, we present such an assay that measures the fitness of hundreds of natural alleles of a given gene without site-directed mutagenesis or DNA synthesis. With a large collection of diverse Saccharomyces cerevisiae natural isolates, we piloted this technique using the gene SUL1, which encodes a high-affinity sulfate permease that, at increased copy number, can improve the fitness of cells grown in sulfate-limited media. We cloned and barcoded all alleles from a collection of over 1000 natural isolates en masse and matched barcodes with their respective variants using PacBio long-read sequencing and a novel error-correction algorithm. We then transformed the reference S288C strain with this library and used barcode sequencing to track growth ability in sulfate limitation of lineages carrying each allele. We show that this approach allows us to measure the fitness conferred by each allele and stratify functional and nonfunctional alleles. Additionally, we pinpoint which polymorphisms in both coding and noncoding regions are detrimental to fitness or are of small effect and result in intermediate phenotypes. Integrating these results with a phylogenetic tree, we observe how often loss-of-function occurs and whether or not there is an evolutionary pattern to our observable phenotypic results. This approach is easily applicable to other genes. Our results complement classic genotype-phenotype mapping strategies and demonstrate a high-throughput approach for understanding the effects of polymorphisms across an entire species which can greatly propel future investigations into quantitative traits.

genetics↗

bioRxiv2021

Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species

Polyploidization events are observed across the tree of life and occurred in many fungi, plant and animal species. Polyploidy is thought to be an important source of speciation and tumorigenesis. However, the origins of polyploid populations are not always clear and little is known about the precise nature and structure of their complex genome. Using a long-read sequencing strategy, we sequenced a large number of isolates from the Brettanomyces bruxellensis yeast species, which is found in anthropized environments (e.g. beer, contaminant of wine, kombucha and ethanol production) and characterized by several polyploid subpopulations. To reconstruct the polyploid genomes, we phased them by using different strategies and we found that each subpopulation had a unique polyploidization history with distinct trajectories. The polyploid genomes contain either genetically closely related (with a genetic divergence < 1%) or diverged copies (> 3%), indicating auto- as well as allopolyploidization events. These latest events have occurred independently with a specific and unique donor in each of the polyploid subpopulations, and exclude the known Brettanomyces sister species as possible donors. Finally, loss of heterozygosity events have shaped the structure of these polyploid genomes and underline their dynamic. Overall, our study highlights the multiplicity of the trajectories leading to polyploid genomes within a same species.

genomics↗

bioRxiv2020

nPhase: An accurate and contiguous phasing method for polyploids

While genome sequencing and assembly are now routine, we still do not have a full and precise picture of polyploid genomes. Phasing these genomes, i.e. deducing haplotypes from genomic data, remains a challenge. Despite numerous attempts, no existing polyploid phasing method provides accurate and contiguous haplotype predictions. To address this need, we developed nPhase, a ploidy agnostic pipeline and algorithm that leverage the accuracy of short reads and the length of long reads to solve reference alignment-based phasing for samples of unspecified ploidy (https://github.com/nPhasePipeline/nPhase). nPhase was validated on virtually constructed polyploid genomes of the model species Saccharomyces cerevisiae, generated by combining sequencing data of homozygous isolates. nPhase obtained on average >95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover >90% of each chromosome (heterozygosity rate [≥]0.5%). This new phasing method opens the door to explore polyploid genomes through applications such as population genomics and hybrid studies.

genomics↗

bioRxiv2020

Genomic stability and adaptation of beer brewing yeasts during serial repitching in the brewery

Ale brewing yeast are the result of admixture between diverse strains of Saccharomyces cerevisiae, resulting in a heterozygous tetraploid that has since undergone numerous genomic rearrangements. As a result, comparisons between the genomes of modern related ale brewing strains show both extensive aneuploidy and mitotic recombination that has resulted in a loss of intragenomic diversity. Similar patterns of intraspecific admixture and subsequent selection for one haplotype have been seen in many domesticated crops, potentially reflecting a general pattern of domestication syndrome between these systems. We set out to explore the evolution of the ale brewing yeast, to understand both polyploid evolution and the process of domestication in the ecologically relevant environment of the brewery. Utilizing a common brewery practice known as repitching, in which yeasts are reused over multiple beer fermentations, we generated population time courses from multiple breweries utilizing similar strains of ale yeast. Applying whole-genome sequencing to the time courses, we have found that the same structural variations in the form of aneuploidy and mitotic recombination of particular chromosomes reproducibly rise to detectable frequency during adaptation to brewing conditions across multiple related strains in different breweries. Our results demonstrate that domestication of ale strains is an ongoing process and will likely continue to occur as modern brewing practices develop.

evolutionary biology↗

bioRxiv2020

CRISpy-pop: a web tool for designing CRISPR/Cas9-driven genetic modifications in diverse populations

CRISPR/Cas9 is a powerful tool for editing genomes, but design decisions are generally made with respect to a single reference genome. With population genomic data becoming available for an increasing number of model organisms, researchers are interested in manipulating multiple strains and lines. CRISpy-pop is a web application that generates and filters guide RNA sequences for CRISPR/Cas9 genome editing for diverse yeast and bacterial strains. The current implementation designs and predicts the activity of guide RNAs against more than 1000 Saccharomyces cerevisiae genomes, including 167 strains frequently used in bioenergy research. Zymomonas mobilis, an increasingly popular bacterial bioenergy research model, is also supported. CRISpy-pop is available as a web application (https://CRISpy-pop.glbrc.org/) with an intuitive graphical user interface. CRISpy-pop also cross-references the human genome to allow users to avoid the selection of sgRNAs with potential biosafety concerns. Additionally, CRISpy-pop predicts the strain coverage of each guide RNA within the supported strain sets, which aids in functional population genetic studies. Finally, we validate how CRISpy-pop can accurately predict the activity of guide RNAs across strains using population genomic data.

genetics↗

bioRxiv2020

Pervasive phenotypic impact of a large non-recombining introgressed region in yeast

To explore the origin of the diversity observed in natural populations, many studies have investigated the relationship between genotype and phenotype. In yeast species, especially in Saccharomyces cerevisiae, these studies are mainly conducted using recombinant offspring derived from two genetically diverse isolates, allowing to define the phenotypic effect of genetic variants. However, large genomic variants such as interspecies introgressions are usually overlooked even if they are known to modify the genotype-phenotype relationship. To have a better insight into the overall phenotypic impact of introgressions, we took advantage of the presence of a 1-Mb introgressed region, which lacks recombination and contains the mating-type determinant in the Lachancea kluyveri budding yeast. By performing linkage mapping analyses in this species, we identified a total of 89 loci affecting growth fitness in a large number of conditions and 2,187 loci affecting gene expression mostly grouped into two major hotspots, one being the introgressed region carrying the mating-type locus. Because of the absence of recombination, our results highlight the presence of a sexual dimorphism in a budding yeast for the first time. Overall, by describing the phenotype-genotype relationship in the L. kluyveri species, we expanded our knowledge on how genetic characteristics of large introgression events can affect the phenotypic landscape.

genetics↗

bioRxiv2019

Discordant evolution of mitochondrial and nuclear yeast genomes at population level

Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from nuclear genome, potentially uncoupling their evolutionary trajectories. Here, we analysed mitochondrial sequences obtained from the 1,011 Saccharomyces cerevisiae strain collection and identified pronounced differences with their nuclear genome counterparts. In contrast with most fungal species, S. cerevisiae mitochondrial genomes show higher genetic diversity compared to the nuclear genomes. Strikingly, mitochondrial genomes appear to be highly admixed, resulting in a complex interconnected phylogeny with weak grouping of isolates, whereas interspecies introgressions are very rare. Complete genome assemblies revealed that structural rearrangements are nearly absent with rare inversions detected. We tracked introns variation in COX1 and COB to infer gain and loss events throughout the species evolutionary history. Mitochondrial genome copy number is connected with the nuclear genome and linearly scale up with ploidy. We observed rare cases of naturally occurring mitochondrial DNA loss, petite, with a subset of them that do not suffer fitness growth defects. Overall, our results illustrate how differences in the biology of two genomes coexisting in the same cells can lead to discordant evolutionary histories.

genomics↗

bioRxiv2019

High complexity and degree of genetic variation in Brettanomyces bruxellensis population

Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype-phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to explore an uncharacterized yeast species, Brettanomyces bruxellensis, which is a major cause of wine spoilage but also can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions while aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared to S. cerevisiae. The pangenome is composed of 4,923 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.

genomics↗

bioRxiv2019

Extensive impact of low-frequency variants on the phenotypic landscape at population-scale

Genome-wide association studies (GWAS) allows to dissect the genetic basis of complex traits at the population level1. However, despite the extensive number of trait-associated loci found, they often fail to explain a large part of the observed phenotypic variance2-4. One potential source of this discrepancy could be the preponderance of undetected low-frequency genetic variants in natural populations5,6. To increase the allele frequency of those variants and assess their phenotypic effects at the population level, we generated a diallel panel consisting of 3,025 hybrids, derived from pairwise crosses between a subset of natural isolates from a completely sequenced 1,011 Saccharomyces cerevisiae population. We examined each hybrid across a large number of growth traits, resulting in a total of 148,225 cross/trait combinations. Parental versus hybrid regression analysis showed that while most phenotypic variance is explained by additivity, a significant proportion (29%) is governed by non-additive effects. This is confirmed by the fact that a majority of complete dominance is observed in 25% of the traits. By performing GWAS on the diallel panel, we detected 1,723 significantly associated genetic variants, with 16.3% of them being low-frequency variants in the initial population. These variants, which would not be detected using classical GWAS, explain 21% of the phenotypic variance on average. Altogether, our results demonstrate that low-frequency variants should be accounted for as they contribute to a large part of the phenotypic variation observed in a population.

genomics↗

bioRxiv2018

Multiple signaling pathways converge onto the regulation of HAD-like phosphatases to modulate cellular resistance to the metabolic inhibitor 2-deoxyglucose

Cancer cells display an altered metabolism with an increased glycolysis and glucose uptake. Anti-cancer strategies targeting glycolysis through metabolic inhibitors have been considered. Particularly, the glucose analogue 2-deoxyglucose (2DG) is imported into cells and phosphorylated into 2DG-6-phosphate, a toxic by-product that inhibits glycolysis. Recent data suggest that 2DG has additional effects in the cell, and resistance to 2DG has also been observed. Using yeast as a model, we engaged an unbiased, mass-spectrometry-based approach to probe the cellular effects of 2DG on the proteome and study resistance mechanisms. This revealed that two 2DG-6-phosphate phosphatases, Dog1 and Dog2, are induced upon exposure to 2DG and participate in 2DG detoxication. 2DG induces Dog2 by upregulating several signaling pathways, such as the MAPK (Hog1/p38)-based stress-responsive pathway, the Unfolded Protein Response (UPR) triggered by 2DG-induced ER stress, and the MAPK (Slt2)-based Cell Wall Integrity pathway. Thus, 2DG-induced interference with cellular signaling rewires the expression of these endogenous phosphatases to promote 2DG resistance. Consequently, loss of the UPR or CWI pathways leads to hypersensitivity to 2DG. In contrast, DOG2 is transcriptionally repressed by glucose availability in a Snf1/AMPK-dependent manner, and mutants impaired in this pathway are 2DG-resistant. The characterization and genome resequencing of spontaneous 2DG-resistant mutants revealed that DOG2 overexpression is a common strategy to achieve 2DG resistance. The human Dog2 orthologue, HDHD1, also displays 2DG-6-phosphate phosphatase activity in vitro, and its overexpression confers 2DG resistance in HeLa cells, which has important implications for potential future chemotherapies involving 2DG.

genetics↗

bioRxiv2017

High-quality de novo genome assembly of the Dekkera bruxellensis UMY321 yeast isolate using Nanopore MinION sequencing

Genetic variation in natural populations represents the raw material for phenotypic diversity. Species-wide characterization of genetic variants is crucial to have a deeper insight into the genotype-phenotype relationship. With the advent of new sequencing strategies and more recently the release of long-read sequencing platforms, it is now possible to explore the genetic diversity of any non-model organisms, representing a fundamental resource for biological research. In the frame of population genomic surveys, a first step is evidently to obtain the complete sequence and high quality assembly of a reference genome. Here, we completely sequenced and assembled a reference genome of the non-conventional Dekkera bruxellensis yeast. While this species is a major cause of wine spoilage, it paradoxically contributes to the specific flavor profile of some Belgium beers. In addition, an extreme karyotype variability is observed across natural isolates, highlighting that D. bruxellensis genome is very dynamic. The whole genome of the D. bruxellensis UMY321 isolate was sequenced using a combination of Nanopore long-read and Illumina short-read sequencing data. We generated the most complete and contiguous de novo assembly of D. bruxellensis to date and obtained a first glimpse into the genomic variability within this species by comparing the sequences of several isolates. This genome sequence is therefore of high value for population genomic surveys and represents a reference to study genome dynamic in this yeast species.

genomics↗

bioRxiv2017

Identification of a novel interspecific hybrid yeast from a metagenomic open fermentation sample using Hi-C

Interspecific hybridization is a common mechanism enabling genetic diversification and adaptation; however, the detection of hybrid species has been quite difficult. The identification of microbial hybrids is made even more complicated, as most environmental microbes are resistant to culturing and must be studied in their native mixed communities. We have previously adapted the chromosome conformation capture method Hi-C to the assembly of genomes from mixed populations. Here, we show the methods application in assembling genomes directly from an uncultured, mixed population from a spontaneously inoculated beer sample. Our assembly method has enabled us to de-convolute 4 bacterial and 4 yeast genomes from this sample, including a putative yeast hybrid. Downstream isolation and analysis of this hybrid confirmed its genome to consist of Pichia membranifaciens and that of another related, but undescribed yeast. Our work shows that Hi-C-based metagenomic methods can overcome the limitation of traditional sequencing methods in studying complex mixtures of genomes.

genomics↗