Biology subjects

Schacherer, J.

Publications and source records attributed to Schacherer, J..

At least 19 recordsLinked to original sources

bioRxiv2025

Population-scale chemical response revealed by a barcoded yeast collection

Natural genetic variation shapes how microbial populations adapt to environmental and chemical challenges, but scalable approaches to map genotype-phenotype relationships across diverse genetic backgrounds remain limited. Here, we developed a systematically barcoded collection of 520 Saccharomyces cerevisiae natural isolates that captures the ecological, geographical and genetic diversity of the species. Using pooled barcode sequencing, we profiled fitness responses to over 600 bioactive and natural compounds, revealing broader and more polarized bioactivity than the standard yeast gene-deletion collection. Fitness-based clustering defined six major compound groups with reproducible, population-structured sensitivity patterns. Genome-wide association analysis identified significant genetic variants across 107 compounds, linking natural polymorphisms to chemical responses and involving genes in genome maintenance, ribosome biogenesis, vesicular trafficking and stress tolerance. Together, our barcoded natural population provides a scalable framework for chemical-genetic screening, enabling systematic dissection of how genetic diversity shapes microbial fitness and adaptation.

evolutionary biology↗

bioRxiv2025

An empirical long-term competition among natural yeast isolates reveals that short-term fitness largely but not entirely predicts long-term outcomes

The fitness of an organism determines its likelihood of succeeding in short-term competition, but many other factors can influence its long-term success. In this study, we investigate the relative contribution of initial fitness to a strain's long-term success in a naturally diverse population. Specifically, we compete a pool of 282 genetically barcoded S. cerevisiae isolates for up to 720 generations in six distinct environments. We find that the strains that remain at detectable frequency until the end of the competition uniformly come from the initially fittest top 5% of strains, rendering initial fitness a strong predictor of long-term success. However, small fitness differences among the top strains matter little for their long-term evolutionary fate. Indeed, we often see heterogeneity in the competition outcomes across replicates, suggesting that stochastic, large-effect adaptive mutations overwrite small differences in the initial fitness of the highest fitness strains. In addition, our results hint that evolvability differences might result in certain strains consistently over- or underperforming in the competition. We further demonstrate that the "finalists" of our competition accumulate a diverse spectrum of de novo genetic changes: single nucleotide mutations, indels, whole chromosome losses and amplifications, and widespread losses of heterozygosity that occasionally span hundreds of kilobases. Taken together, we show that for a pool of natural strains, high initial fitness is necessary, though not sufficient, to succeed long-term, and that adaptive evolution can drive unexpected outcomes in a long-term competition in a novel environment.

evolutionary biology↗

bioRxiv2025

Graph-based pangenome analysis uncovers structural and functional impacts of allopolyploidization events

The emergence of graph pangenomes has significantly advanced the study of structural variants (SVs) across diverse species. However, the impact of complex polyploidization events, particularly allopolyploidy, on SV landscapes remains poorly explored. Brettanomyces bruxellensis, a yeast species shaped by multiple allopolyploidization events, offers a compelling model due to its well-characterized genomic and phenotypic diversity. Here, we integrated subgenome-resolved assemblies with population-scale genomic and transcriptomic datasets to characterize SVs distribution and their functional impact at the species level. Leveraging a constructed reference graph pangenome, we identified sequences that are unique to each subgenome, and detected 212,177 SVs across 1,060 sequenced isolates. Allopolyploid genomes harbored significantly more SVs (320 on average) than diploid genomes (116 on average), reflecting the extensive impact of hybridization on the genome architecture. A subset of SVs originating from ancestral divergence between subgenomes (hybridization-associated SVs) formed distinct hotspots of structural diversity. Furthermore, functional association analysis revealed that 27.5% of SVs exert local regulatory effects on gene expression. Interestingly, hybridization-associated structural variants disproportionately affect gene expression, with a greater proportion of associated variants and a significantly larger effect size compared to other SVs. Overall, these findings underscore the role of allopolyploidization in driving both structural and functional genomic diversification. Our study also highlights the value of graph-based approaches in dissecting complex genome evolution.

genomics↗

bioRxiv2024

Overview of the Saccharomyces cerevisiae population structure through the lens of 3,034 genomes

With the rise of high-throughput sequencing technologies, a holistic view of genetic variation within populations - through population genomics studies - appears feasible, although it remains an ongoing effort. Genetic variation arises from a diverse range of evolutionary forces, with mutation and recombination being key drivers in shaping genomes. Studying genetic variation within a population represents a crucial first step in understanding the relationship between genotype and phenotype and the evolutionary history of species. In this context, the budding yeast Saccharomyces cerevisiae has been at the forefront of population genomic studies. In addition, it has a complex history that involves adaptation to a wide range of wild and human-related ecological niches. Although to date more than three thousand diverse isolates have been sequenced, there is currently a lack of a resource bringing together sequencing data and associated metadata for all sequenced isolates. To perform a comprehensive analysis of the population structure of S. cerevisiae, we collected genome sequencing data from 3,034 natural isolates and processed the data uniformly. We determined ploidy levels, identified single nucleotide polymorphisms (SNPs), small insertion-deletions (InDels), copy number variations (CNVs), and aneuploidies across the population, creating a publicly accessible resource for the yeast research community. Interestingly, we showed that this population captures [~]93% of the species diversity. Using neighbor-joining and Bayesian methods, we redefined the populations, revealing clustering patterns primarily based on ecological origin. This work represents a valuable resource for the community and efforts have been made to make it evolvable and integrable to future yeast population studies.

genomics↗

bioRxiv2024

Mining Yeast Diversity Unveils Novel Targets for Improved Heterologous Laccase Production in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae is a widely utilized host cell for recombinant protein production due to its well studied and annotated genome, its ability to secrete large and post-translationally modified proteins, fast growth and cost-effective culturing. However, recombinant protein yields from S. cerevisiae often fall behind that of other host systems. To address this, we developed a high throughput screen of wild, industrial and laboratory S. cerevisiae isolates to identify strains with a natural propensity for greater recombinant protein production, specifically focussing on laccase multicopper oxidases from the fungi Trametes trogii and Myceliophthora thermophila. Using this method, we identified 20 non-laboratory strains with higher capacity to produce active laccase. Interestingly, lower levels of laccase mRNA were measured in most cases, indicating that the drivers of elevated protein production capacity lie beyond the regulation of recombinant gene expression. We characterized the identified strains using complementary genomic and proteomic approaches to reveal several potential pathways driving the improved expression phenotype. Gene ontology analysis suggests broad changes in cellular metabolism, specifically in genes/proteins involved in carbohydrate catabolism, thiamine biosynthesis, transmembrane transport and vacuolar degradation. Targeted deletions of the hexose transporter HXT11 and the Coat protein complex II interacting paralogs PRM8 and 9, involved in ER to Golgi transport, resulted in significantly improved laccase production from the S288C laboratory strain. Whereas the deletion of the Hsp110 SSE1 gene, guided by our proteomic analysis, also led to higher laccase activity, we did not observe major changes of the protein homeostasis network within the strains with higher laccase activity. This study opens new avenues to leverage the vast diversity of Saccharomyces cerevisiae for recombinant protein production, as well as offers new strategies and insights to enhance recombinant protein yields of current strains.

molecular biology↗

bioRxiv2024

Whole-genome sequencing and phenotyping reveal specific adaptations of Lachancea thermotolerans to the winemaking environment

Adaptation to the environment plays an essential role in yeast evolution as a consequence of selective pressures. Lachancea thermotolerans, a yeast related to the fermentative process and one of the current trends in wine technology research, has undergone an anthropization process that has led to a strong differentiation both from a genomic and phenomic perspective. Using whole-genome sequencing, we have investigated the genomic diversity of 145 L. thermotolerans strains, identifying six well-defined groups primarily delineated by their ecological origin and exhibiting high levels of genetic diversity. Anthropized strains showed lower genetic diversity due to the purifying selection imposed by the winemaking environment. Strong evidence of anthropization and adaptation to the wine environment through modification of gene content was also found. Differences in genes involved in the assimilation of alternative carbon and nitrogen sources, such as the MAL1 and DAL5 genes, which confer greater fitness in the winemaking environment, were observed. Additionally, we found that phenotypic traits considered domestication hallmarks are present in anthropized strains. Among these, increased fitness in the presence of ethanol and sulphites, assimilation of non-fermentable carbon sources such as glycerol, and lower levels of residual fructose under fermentative conditions highlight. We hypothesize that lactic acid production by wine-related strains is an anthropization signature consequence of the adaption of early Crabtree-positive yeasts to the fermentative environment. Overall, the results of this work provide valuable insight into the anthropization process in L. thermotolerans and demonstrate how fermentation environments give rise to similar adaptations in different yeast species.

microbiology↗

bioRxiv2024

Recurrent loss of crossover interference punctuates the recombination landscape across yeast species

Meiotic recombination is essential for the accurate chromosome segregation and the generation of genetic diversity through crossover and gene conversion events. Although this process has been studied extensively in a few selected model species, understanding how its properties vary across species remains limited. In this context, we first characterized the meiotic recombination landscape and properties of the Kluyveromyces lactis budding yeast. We then conducted a comprehensive analysis of 28,897 recombination events spanning 567 meioses in five budding yeast species including Saccharomyces cerevisiae, Saccharomyces paradoxus, Lachancea kluyveri, Lachancea waltii and K. lactis. We observed variations in the recombination landscapes and properties across these species. The Saccharomyces yeasts displayed higher recombination rates compared to the non-Saccharomyces yeasts. In addition, bona fide crossover interference and associated crossover homeostasis were found in the Saccharomyces species only. The evolutionarily conserved ZMM pathway, essential for generating interference-dependent crossovers, has undergone multiple losses throughout evolution, suggesting variations in the regulation of crossover formation. Finally, recombination hotspots, although highly conserved within the Saccharomyces yeasts are not conserved beyond the Saccharomyces genus. Overall, these results highlight great variability and evolution in the recombination landscape between species.

genomics↗

bioRxiv2023

Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast

Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse set of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extent and signature of the post-transcriptional buffering.

systems biology↗

bioRxiv2023

Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast

Gene expression varies between individuals and corresponds to a key step linking genotypes to phenotypes. However, our knowledge regarding the species-wide genetic control of protein abundance, including its dependency on transcript levels, is very limited. Here, we have determined quantitative proteomes of a large population of 942 diverse natural Saccharomyces cerevisiae yeast isolates. We found that mRNA and protein abundances are weakly correlated at the population gene level. While the protein co-expression network recapitulates major biological functions, differential expression patterns reveal proteomic signatures related to specific populations. Comprehensive genetic association analyses highlight that genetic variants associated with variation in protein (pQTL) and transcript (eQTL) levels poorly overlap (3.6%). Our results demonstrate that transcriptome and proteome are governed by distinct genetic bases, likely explained by protein turnover. It also highlights the importance of integrating these different levels of gene expression to better understand the genotype-phenotype relationship. HighlightsO_LIAt the level of individual genes, the abundance of transcripts and proteins is weakly correlated within a species ({rho} = 0.165). C_LIO_LIWhile the proteome is not imprinted by population structure, co-expression patterns recapitulate the cellular functional landscape C_LIO_LIWild populations exhibit a higher abundance of respiration-related proteins compared to domesticated populations C_LIO_LILoci that influence protein abundance differ from those that impact transcript levels, likely because of protein turnover C_LI

systems biology↗

bioRxiv2023

Absence of chromosome axis proteins recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri

Meiotic recombination shows broad variations across species and along chromosomes, and is often suppressed at and around genomic regions determining sexual compatibility such as mating type loci in fungi. Here we show that the absence of Spo11-DSBs and meiotic recombination on Lakl0C-left, the chromosome arm containing the sex locus of the Lachancea kluyveri budding yeast, results from the absence of recruitment of the two chromosome axis proteins Red1 and Hop1, essential for proper Spo11-DSBs formation. Furthermore, cytological observation of spread pachytene meiotic chromosomes reveals that Lakl0C-left does not undergo synapsis. However, we show that the behavior of Lakl0C-left is independent of its particularly early replication timing and is not accompanied by any peculiar chromosome structure as detectable by Hi-C in this yet poorly studied yeast. Finally, we observed an accumulation of heterozygous mutations on Lakl0C-left and a sexual dimorphism of the haploid meiotic offspring, supporting a direct effect of this absence of meiotic recombination on L. kluyveri genome evolution and fitness. Because suppression of meiotic recombination on sex chromosomes is widely observed across eukaryotes, the novel mechanism for recombination suppression described here may apply to other species, with the potential to impact sex chromosome evolution.

genetics↗

bioRxiv2023

Non-additive genetic components contribute significantly to population-wide gene expression variation

Gene expression variation, an essential step between genomic variation and phenotypic landscape, is collectively controlled by local (cis) and distant (trans) regulatory changes. Nevertheless, how these regulatory elements differentially influence the heritability of expression traits remains unclear. Here, we bridge this gap by analyzing the transcriptomes of a large diallel panel consisting of 323 unique hybrids originated from genetically divergent yeast isolates. We estimated the broad- and narrow-sense heritability across 5,087 transcript abundance traits and showed that non-additive components account for 36% of the phenotypic variance on average. By comparing allelic expression ratios in the hybrid and the corresponding parental pair, we identified regulatory changes in 25% of all cases, with a majority acting in trans. We further showed that trans-regulation could underlie coordinated expression variation across highly connected genes, resulting in significantly higher non-additive variance and most likely in some of the missing heritability of gene expression traits. HighlightsO_LIDiallel panel for dissecting genetic components underlying gene expression variation C_LIO_LINon-additive components account for 36% of gene expression trait heritability C_LIO_LIMost cis- regulatory variation is buffered by additional trans-acting variants C_LIO_LIGenes under trans- regulation show high non-additive variance and functional coherence C_LI

genetics↗

bioRxiv2023

Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast

Unraveling the genetic sources of gene expression variation is essential to better understand the origins of phenotypic diversity in natural populations. Genome-wide association studies identified thousands of variants involved in gene expression variation, however, variants detected only explain part of the heritability. In fact, variants such as low-frequency and structural variants (SVs) are poorly captured in association studies. To assess the impact of these variants on gene expression variation, we explored a half-diallel panel composed of 323 hybrids originated from pairwise crosses of 26 natural Saccharomyces cerevisiae isolates. Using short- and long-read sequencing strategies, we established an exhaustive catalog of single nucleotide polymorphisms (SNPs) and SVs for this panel. Combining this dataset with the transcriptomes of all hybrids, we comprehensively mapped SNPs and SVs associated with gene expression variation. While SVs impact gene expression variation, SNPs exhibit a higher effect size with an overrepresentation of low-frequency variants compared to common ones. These results reinforce the importance of dissecting the heritability of complex traits with a comprehensive catalog of genetic variants at the population level.

genomics↗

bioRxiv2023

Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast

Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at a species-level. Here, we generated and analyzed the pan-transcriptome of [~]1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of the transcriptome divergence. Global gene expression patterns combined with population structure show that the heritable expression variation mainly lies within subpopulation-specific signatures, for which the accessory genes are overrepresented. Genome-wide association analyses consistently highlight that the accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.

genomics↗

bioRxiv2022

Copy number variants alter local and global mutational tolerance

Copy number variants (CNVs), duplications and deletions of genomic content, contribute to evolutionary adaptation, but can also confer deleterious effects, and cause disease. Whereas the effects of amplifying individual genes or whole chromosomes (i.e., aneuploidy) have been studied extensively, much less is known about the genetic and functional effects of CNVs of differing sizes and structures. Here, we investigated Saccharomyces cerevisiae (yeast) strains that have CNVs of variable structures but with multiple copies of the gene GAP1. Although beneficial in glutamine-limited chemostats, CNVs result in decreased fitness compared with the euploid ancestor in rich media. We used transposon mutagenesis to investigate mutational tolerance and genetic interactions with CNVs. We find that CNVs confer novel mutational tolerance in amplified essential genes and novel genetic interactions. We validated a novel genetic interaction with BMH1. CNV strains have increased mutational tolerance in genes related to translation, and reduced mutational tolerance in genes related to mitochondrial function. We performed RNAseq and found that transcriptional dosage compensation does not affect the majority of genes amplified by CNVs. Furthermore, we do not find that CNV strains exhibit previously described transcriptional signatures of aneuploidy. Instead, CNV strains exhibit downregulation of genes involved in cellular respiration, nucleoside biosynthetic processes, and small molecule metabolism, and upregulation of genes involved in transposition, nucleic acid metabolic processes, and siderophore transport. Our study reveals the extent to which local and global mutational tolerance is modified by CNVs with implications for genome evolution and CNV associated diseases, such as cancer.

genetics↗

bioRxiv2022

142 telomere-to-telomere assemblies reveal the genome structural landscape in Saccharomyces cerevisiae

As population genomics is transitioning from single reference genomes to pangenomes, major improvements in terms of genome contiguity, phylogenetic sampling, haplotype phasing and structural variant (SV) calling are required. Here, we generated the Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising 142 reference-quality genomes from strains of various geographic and ecological origins that faithfully represent the genomic diversity and complexity of the species. The ca. 4,800 non-redundant SVs we identified impact the expression of genes near the breakpoints and contribute to gene repertoire evolution through disruptions, duplications, fusions and horizontal transfers. We discovered frequent cases of complex aneuploidies, preferentially involving large chromosomes that underwent large SVs. We also characterized the evolutionary dynamics of complex genomic regions that classically remain unassembled in short read-based projects, including the 5 Ty families and the 32 individual telomeres. Overall, the ScRAP represents a crucial step towards establishing a high-quality, unified and complete S. cerevisiae pangenome.

genomics↗

bioRxiv2022

Contrasting genomic evolution between domesticated and wild Kluyveromyces lactis yeast populations

The process of domestication has variable consequences on genome evolution leading to different phenotypic signatures. Access to the complete genome sequences of a large number of individuals makes it possible to explore the different facets of this domestication process. Here, we sought to explore the genome evolution of the Kluyveromyces lactis yeast species, a well-known species for its involvement in dairy processes but also present in natural environments. Using a combination of short and long-read sequencing strategies, we investigated the genomic variability of 41 Kluyveromyces lactis isolates and found that the overall genetic diversity of this species is very high ({pi} = 2.9 x 10-2) compared to other species such as Saccharomyces cerevisiae ({pi} = 3 x 10-3). However, the domesticated dairy population shows a reduced level of diversity ({pi} = 7 x 10-4), probably due to a domestication bottleneck. In addition, this entire population is characterized by the introgression of the LAC4 and LAC12 genes, responsible for lactose fermentation and coming from the closely related species, Kluyveromyces marxianus, as previously described. Our results also highlighted that the LAC4/LAC12 gene cluster was acquired through multiple and independent introgression events. Finally, we also identified several genes that could play a role in adaptation to dairy environments through copy number variation. These genes are involved in sugar consumption, flocculation and drug resistance, and may play a role in dairy processes. Overall, our study illustrates contrasting genomic evolution and sheds new light on the impact of domestication processes on it.

genomics↗

bioRxiv2022

Loss of heterozygosity spectrum varies with ploidy levels in natural yeast populations

The appearance of genomic variations such as loss of heterozygosity (LOH) has a significant impact on phenotypic diversity observed in a population. Recent large-scale yeast population genomic surveys have shown a high frequency of these events in natural isolates and more particularly in polyploids. However, the frequency, extent, and spectrum of LOH in polyploid organisms have never been explored and is poorly characterized to date. Here, we accumulated 5,163 LOH events over 1,875 generations in 76 mutation accumulation (MA) lines comprising nine natural heterozygous diploid, triploid, and tetraploid natural S. cerevisiae isolates from different ecological and geographical origins. We found that the rate and spectrum of LOH are variable across ploidy levels. Of the total accumulated LOH events, 8.5%, 21%, and 70.5% of them were found in diploid, triploid, and tetraploid MA lines, respectively. Our results clearly shows that the frequency of generated LOH events increases with ploidy level. In fact, the cumulative LOH rates were estimated to be 9.3 x 10-3, 2.2 x 10-2, and 8.4 x 10-2 events per division for diploids, triploids, and tetraploids, respectively. In addition, a clear bias towards the accumulation of interstitial and short LOH tracts is observed in triploids and tetraploids compared to diploids. The variation of the frequency and spectrum of LOH events across ploidy level could be related to the genomic instability, characterizing higher ploidy isolates. Highlights- Yeast isolates with a high ploidy level (e.g., 3n and 4n) accumulate a larger number of LOH events compared to diploids. - The type of events and the LOH spectrum are both variable according to the ploidy levels. - A clear bias towards the accumulation of short LOH tracts is observed in polyploids compared to diploids. - The variation in LOH spectrum is most likely related to genomic instability present in higher ploidy strains.

genomics↗

bioRxiv2022

The natural diversity of the yeast proteome reveals chromosome-wide dosage compensation in aneuploids

Aneuploidy, an imbalance in chromosome copy numbers, causes genetic disorders, and drives cancer progression, drug tolerance, and antimicrobial resistance. While aneuploidy can confer stress resistance, it is not well understood how cells overcome the fitness burden caused by aberrant chromosomal copy numbers. Studies using both systematically generated 1-5 and natural aneuploid yeasts 6-8 triggered an intense debate about the role of dosage compensation, concluding that aneuploidy is transmitted to the transcriptome and proteome without significant buffering at the chromosome-wide level, and is, at least in lab strains, associated with significant fitness costs. Conversely, systematic sequencing and phenotyping of large collections of natural isolates revealed that aneuploidy is frequent and has few - if any - fitness costs in nature 9. To address these discrepant findings at the proteomic level, we developed a platform that yields highly precise proteomic measurements across large numbers of genetically diverse samples, and applied it to natural isolates collected as part of the 1011 genomes project 9. For 613 of the isolates, we were able to match the proteomes to their corresponding transcriptomes and genomes, subsequently quantifying the effect of aneuploidy on gene expression by comparing 95 aneuploid with 518 euploid strains. We find, as in previous studies, that aneuploid gene dosage is not buffered chromosome-wide at the transcriptome level. Importantly, in the proteome, we detect an attenuation of aneuploidy by about 25% below the aneuploid gene dosage in natural yeast isolates. Furthermore, this chromosome-wide dosage compensation is associated with the ubiquitin-proteasome system (UPS), which is expressed at higher levels and has increased activity across natural aneuploid strains. Thus, through systematic exploration of the species-wide diversity of the yeast proteome, we shed light on a long-standing debate about the biology of aneuploids, revealing that aneuploidy tolerance is mediated through chromosome-wide dosage compensation at the proteome level.

systems biology↗