Équipe Schacherer - VISEG - GMGM - Génétique moléculaire, génomique, microbiologie - Université de Strasbourg https://gmgm.unistra.fr fr Équipe Schacherer - VISEG - GMGM - Génétique moléculaire, génomique, microbiologie - Université de Strasbourg Thu, 18 Apr 2024 21:12:11 +0200 Thu, 18 Apr 2024 21:12:11 +0200 TYPO3 EXT:news news-16241 Fri, 15 Mar 2024 09:43:39 +0100 New publication in collaboration /en/news/piece-of-news/nouvelle-publication-en-collaboration Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast Lachancea kluyveri.
Sylvain Legrand, Asma Saifudeen, Hélène Bordelet, Julien Vernerey, Arnaud Guille, Amaury Bignaud, Agnès Thierry, Laurent Acquaviva, Maxime Gaudin, Aurore Sanchez, Dominic Johnson, Anne Friedrich, Joseph Schacherer, Matthew J Neale, Valérie Borde, Romain Koszul, Bertrand Llorente.
PNAS. 2024. doi:10.1073/pnas.2312820121

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 mechanism for recombination suppression described here may apply to other species, with the potential to impact sex chromosome evolution.

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Actualités du GMGM Publications de l'Équipe Schacherer
news-16111 Fri, 16 Feb 2024 12:06:18 +0100 New publication of the team /en/news/piece-of-news/nouvelle-publication-de-lequipe Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast.
Andreas Tsouris, Gauthier Brach, Anne Friedrich, Jing Hou, Joseph Schacherer.
Mol Syst Biol. 2024. doi:10.1038/s44320-024-00021-0

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.

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news-16032 Tue, 30 Jan 2024 20:46:48 +0100 New publication in NAR /en/news/piece-of-news/nouvelle-publcation-dans-nar Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast.
Elie M Teyssonniere, Yuichi Shichino, Mari Mito, Anne Friedrich, Shintaro Iwasaki, Joseph Schacherer.
Nucleic Acids Research. 2024. doi:10.1093/nar/gkae030
 

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.

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news-15835 Fri, 19 Jan 2024 15:55:17 +0100 New publication in PLos Genetics /en/news/piece-of-news/nouvelle-publication-dans-plos-genetics-1 Species-wide survey of the expressivity and complexity spectrum of traits in yeast.
Andreas Tsouris, Téo Fournier, Anne Friedrich, Jing Hou, Maitreya J. Dunham, Joseph Schacherer.

Assessing the complexity and expressivity of traits at the species level is an essential first step to better dissect the genotype-phenotype relationship. As trait complexity behaves dynamically, the classic dichotomy between monogenic and complex traits is too simplistic. However, no systematic assessment of this complexity spectrum has been carried out on a population scale to date. In this context, we generated a large diallel hybrid panel composed of 190 unique hybrids coming from 20 natural isolates representative of the S. cerevisiae genetic diversity. For each of these hybrids, a large progeny of 160 individuals was obtained, leading to a total of 30,400 offspring individuals. Their mitotic growth was evaluated on 38 conditions inducing various cellular stresses. We developed a classification algorithm to analyze the phenotypic distributions of offspring and assess the trait complexity. We clearly found that traits are mainly complex at the population level. On average, we found that 91.2% of cross/trait combinations exhibit high complexity, while monogenic and oligogenic cases accounted for only 4.1% and 4.7%, respectively. However, the complexity spectrum is very dynamic, trait specific and tightly related to genetic backgrounds. Overall, our study provided greater insight into trait complexity as well as the underlying genetic basis of its spectrum in a natural population.

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news-15617 Mon, 15 Jan 2024 10:14:40 +0100 New publication in Cell Genomics /en/news/piece-of-news/nouvelle-publication-dans-cell-genomics Non-additive genetic components contribute significantly to population-wide gene expression variation.
Andreas Tsouris, Gauthier Brach, Joseph Schacherer, Jing Hou.

Gene expression variation, an essential step between genotype and phenotype, is collectively controlled by local (cis) and distant (trans) regulatory changes. Nevertheless, how these regulatory elements differentially influence gene expression variation remains unclear. Here, we bridge this gap by analyzing the transcriptomes of a large diallel panel consisting of 323 unique hybrids originating from genetically divergent Saccharomyces cerevisiae isolates. Our analysis across 5,087 transcript abundance traits showed that non-additive components account for 36% of the gene expression variance on average. By comparing allele-specific read counts in parent-hybrid trios, we found that trans-regulatory changes underlie the majority of gene expression variation in the population. Remarkably, most cis-regulatory variations are also exaggerated or attenuated by additional trans effects. Overall, we showed that the transcriptome is globally buffered at the genetic level mainly due to trans-regulatory variation in the population.

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news-14627 Mon, 04 Sep 2023 21:36:14 +0200 New publication in Nature Genetics /en/news/piece-of-news/nouvelle-publication-dans-nature-genetics Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae.
Samuel O’Donnell, Jia-Xing Yue, Omar Abou Saada, Nicolas Agier, Claudia Caradec, Thomas Cokelaer, Matteo De Chiara, Stéphane Delmas, Fabien Dutreux, Téo Fournier, Anne Friedrich, Etienne Kornobis, Jing Li, Zepu Miao, Lorenzo Tattini, Joseph Schacherer, Gianni Liti, Gilles Fischer.

Pangenomes provide access to an accurate representation of the genetic diversity of species, both in terms of sequence polymorphisms and structural variants (SVs). Here we generated the Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising reference-quality genomes for 142 strains representing the species’ phylogenetic and ecological diversity. The ScRAP includes phased haplotype assemblies for several heterozygous diploid and polyploid isolates. We identified circa (ca.) 4,800 nonredundant SVs that provide a broad view of the genomic diversity, including the dynamics of telomere length and transposable elements. We uncovered frequent cases of complex aneuploidies where large chromosomes underwent large deletions and translocations. We found that SVs can impact gene expression near the breakpoints and substantially contribute to gene repertoire evolution. We also discovered that horizontally acquired regions insert at chromosome ends and can generate new telomeres. Overall, the ScRAP demonstrates the benefit of a pangenome in understanding genome evolution at population scale.

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news-14625 Mon, 04 Sep 2023 21:27:14 +0200 New publication in collabration /en/news/piece-of-news/nouvelle-publication-en-collabration Copy number variation alters local and global mutational tolerance.
Grace Avecilla, Pieter Spealman, Julia Matthews, Elodie Caudal, Joseph Schacherer, David Gresham.

Copy number variants (CNVs), duplications and deletions of genomic sequences, 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 acquired adaptive CNVs of variable structures and copy numbers following experimental evolution in glutamine-limited chemostats. Although beneficial in the selective environment, CNVs result in decreased fitness compared with the euploid ancestor in rich media. We used transposon mutagenesis to investigate mutational tolerance and genome-wide genetic interactions in CNV strains. We find that CNVs increase mutational target size, confer increased mutational tolerance in amplified essential genes, and result in novel genetic interactions with unlinked genes. We validated a novel genetic interaction between different CNVs and BMH1 that was common to multiple strains. We also analyzed global gene expression and found that transcriptional dosage compensation does not affect most genes amplified by CNVs, although gene-specific transcriptional dosage compensation does occur for ∼12% of amplified genes. Furthermore, we find that CNV strains do not show previously described transcriptional signatures of aneuploidy. 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.

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news-13674 Mon, 19 Jun 2023 13:37:10 +0200 New publication in G3 /en/news/piece-of-news/nouvelle-publication-dans-g3-1 Impact of the acquired subgenome on the transcriptional landscape in Brettanomyces bruxellensis allopolyploids.
Arthur Jallet, Anne Friedrich, Joseph Schacherer.
G3 Genes|Genomes|Genetics. 2023. doi:10.1093/g3journal/jkad115

Gene expression variation can provide an overview of the changes in regulatory networks that underlie phenotypic diversity. Certain evolutionary trajectories such as polyploidization events can have an impact on the transcriptional landscape. Interestingly, the evolution of the yeast species Brettanomyces bruxellensis has been punctuated by diverse allopolyploidization events leading to the coexistence of a primary diploid genome associated with various haploid acquired genomes. To assess the impact of these events on gene expression, we generated and compared the transcriptomes of a set of 87 B. bruxellensis isolates, selected as being representative of the genomic diversity of this species. Our analysis revealed that acquired subgenomes strongly impact the transcriptional patterns and allow discrimination of allopolyploid populations. In addition, clear transcriptional signatures related to specific populations have been revealed. The transcriptional variations observed are related to some specific biological processes such as transmembrane transport and amino acids metabolism. Moreover, we also found that the acquired subgenome causes the overexpression of some genes involved in the production of flavor-impacting secondary metabolites, especially in isolates of the beer population.

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news-12929 Mon, 16 Jan 2023 11:27:48 +0100 New publication in Genome Biology and Evolution /en/news/piece-of-news/nouvelle-publication-dans-genome-biology-and-evolution Contrasting genomic evolution between domesticated and wild Kluyveromyces lactis yeast populations.
Anne Friedrich, Jean-Sébastien Gounot, Andreas Tsouris, Claudine Bleykasten, Kelle Freel, Claudia Caradec, Joseph Schacherer.
Genome Biology and Evolution. 2023. doi:10.1093/gbe/evad004

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 Kluyveromyces lactis, a yeast species well-known 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 K. lactis isolates and found that the overall genetic diversity of this species is very high (θw = 3.3 × 10−2) compared to other species such as Saccharomyces cerevisiae (θw = 1.6 × 10−2). However, the domesticated dairy population shows a reduced level of diversity (θw = 1 × 10−3), 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.

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news-12925 Fri, 13 Jan 2023 20:01:45 +0100 New publication in PLoS Genetics /en/news/piece-of-news/nouvelle-publication-dans-plos-genetics Lessons from the meiotic recombination landscape of the ZMM deficient budding yeast Lachancea waltii.
Fabien Dutreux, Abhishek Dutta, Emilien Peltier, Sabrina Bibi-Triki, Anne Friedrich, Bertrand Llorente, Joseph Schacherer.
PLoS Genet. 2023. doi:10.1371/journal.pgen.1010592

Meiotic recombination is a driving force for genome evolution, deeply characterized in a few model species, notably in the budding yeast Saccharomyces cerevisiae. Interestingly, Zip2, Zip3, Zip4, Spo16, Msh4, and Msh5, members of the so-called ZMM pathway that implements the interfering meiotic crossover pathway in S. cerevisiae, have been lost in Lachancea yeast species after the divergence of Lachancea kluyveri from the rest of the clade. In this context, after investigating meiosis in L. kluyveri, we determined the meiotic recombination landscape of Lachancea waltii. Attempts to generate diploid strains with fully hybrid genomes invariably resulted in strains with frequent whole-chromosome aneuploidy and multiple extended regions of loss of heterozygosity (LOH), which mechanistic origin is so far unclear. Despite the lack of multiple ZMM pro-crossover factors in L. waltii, numbers of crossovers and noncrossovers per meiosis were higher than in L. kluyveri but lower than in S. cerevisiae, for comparable genome sizes. Similar to L. kluyveri but opposite to S. cerevisiae, L. waltii exhibits an elevated frequency of zero-crossover bivalents. Lengths of gene conversion tracts for both crossovers and non-crossovers in L. waltii were comparable to those observed in S. cerevisiae and shorter than in L. kluyveri despite the lack of Mlh2, a factor limiting conversion tract size in S. cerevisiae. L. waltii recombination hotspots were 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, L. waltii crossover interference was reduced relative to S. cerevisiae, with interference being detected only in the 25 kb distance range. Detection of positive inference only at short distance scales in the absence of multiple ZMM factors required for interference-sensitive crossovers in other systems likely reflects interference between early recombination precursors such as DSBs.

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news-12541 Mon, 10 Oct 2022 08:54:49 +0200 New publication in Molecular Biology and Evolution /en/news/piece-of-news/nouvelle-publication-dans-molecular-biology-and-evolution-1 Loss of heterozygosity spectrum depends on ploidy level in natural yeast populations.
Abhishek Dutta, Fabien Dutreux, Joseph Schacherer.
Molecular Biology and Evolution. 2022. doi:10.1093/molbev/msac214

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 9.3×10−3, 2.2×10−2, and 8.4×10−2 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.

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news-12383 Thu, 08 Sep 2022 10:55:44 +0200 New publication in PNAS /en/news/piece-of-news/nouvelle-publication-dans-pnas Loss-of-function mutation survey revealed that genes with background-dependent fitness are rare and functionally related in yeast.
Elodie Caudal, Anne Friedrich, Arthur Jallet, Marion Garin, Jing Hou, Joseph Schacherer.
Proc Natl Acad Sci U S A. 2022. doi:10.1073/pnas.2204206119

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 with the reference strain S288C. Out of these 632 genes with predicted background-dependent fitness effects, around 2/3 impact multiple backgrounds with a gradient of predicted fitness change 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 genes with background-dependent fitness effects 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.

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news-12382 Thu, 08 Sep 2022 10:49:45 +0200 New publication /en/news/piece-of-news/nouvelle-publication Extensive simulations assess the performance of genome-wide association mapping in various Saccharomyces cerevisiae subpopulations.
Jackson Peter, Anne Friedrich, Gianni Liti, Joseph Schacherer.
Philosophical Proceedings of the Royal Society B. 2022. doi:10.1098/rstb.2020.0514

With the advent of high throughput sequencing technologies, genome-wide association studies (GWAS) have become a powerful paradigm for dissecting the genetic origins of the observed phenotypic variation. We recently completely sequenced the genome of 1011 Saccharomyces cerevisiae isolates, laying a strong foundation for GWAS. To assess the feasibility and the limits of this approach, we performed extensive simulations using five selected subpopulations as well as the total set of 1011 genomes. We measured the ability to detect the causal genetic variants involved in Mendelian and more complex traits using a linear mixed model approach. The results showed that population structure is well accounted for and is not the main problem when the sample size is high enough. While the genetic determinant of a Mendelian trait is easily mapped in all studied subpopulations, discrepancies are seen between datasets when performing GWAS on a complex trait in terms of detection, false positive and false negative rate. Finally, we performed GWAS on the different defined subpopulations using a real quantitative trait (resistance to copper sulfate) and showed the feasibility of this approach. The performance of each dataset depends simultaneously on several factors such as sample size, relatedness and population evolutionary history.

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news-12102 Tue, 07 Jun 2022 15:28:00 +0200 Junior chairs in the field of research on mitochondria /en/news/piece-of-news/chaires-juniors-dans-le-domaine-de-recherches-sur-les-mitochondries The Laboratory of Excellence (LabEx) MitoCross announces the call for applications for two junior chairs in the field of research on mitochondria. See details HERE.

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news-11998 Fri, 13 May 2022 09:29:52 +0200 Book chapter /en/news/piece-of-news/chapitre-douvrage RNA interference (RNAi) as a tool for high-resolution phenotypic screening of the pathogenic yeast Candida glabrata. Andreas Tsouris, Joseph Schacherer, Olena P. Ishchuk. Yeast Functional Genomics. 2022. doi:10.1007/978-1-0716-2257-5_18 RNA interference (RNAi) as a tool for high-resolution phenotypic screening of the pathogenic yeast Candida glabrata.
Andreas Tsouris, Joseph Schacherer, Olena P. Ishchuk.
Yeast Functional Genomics. 2022. doi:10.1007/978-1-0716-2257-5_18

After its discovery RNA interference (RNAi) has become a powerful tool to study gene functions in different organisms. RNAi has been applied at genome-wide scale and can be nowadays performed using high-throughput automated systems (robotics). The simplest RNAi process requires the expression of two genes (Dicer and Argonaute) to function. To initiate the silencing, constructs generating either double-strand RNA or antisense RNA are required. Recently, RNAi was reconstituted by expressing Saccharomyces castellii genes in the human pathogenic yeast Candida glabrata and was used to identify new genes related to the virulence of this pathogen. In this chapter, we describe a method to make the C. glabrata pathogenic yeast competent for RNAi and to use RNA silencing as a tool for low- or high-resolution phenotypic screening in this species.

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news-11165 Mon, 02 May 2022 17:05:27 +0200 New publication in Genomics /en/news/piece-of-news/nouvelle-publivation-dans-genomics Towards accurate, contiguous and complete alignment-based polyploid phasing algorithms.
Omar Abou Saada, Anne Friedrich, Joseph Schacherer.
Genomics. 2022. doi:10.1016/j.ygeno.2022.110369

Phasing, and in particular polyploid phasing, have been challenging problems held back by the limited read length of high-throughput short read sequencing methods which can't overcome the distance between heterozygous sites and labor high cost of alternative methods such as the physical separation of chromosomes for example. Recently developed single molecule long-read sequencing methods provide much longer reads which overcome this previous limitation. Here we review the alignment-based methods of polyploid phasing that rely on four main strategies: population inference methods, which leverage the genetic information of several individuals to phase a sample; objective function minimization methods, which minimize a function such as the Minimum Error Correction (MEC); graph partitioning methods, which represent the read data as a graph and split it into k haplotype subgraphs; cluster building methods, which iteratively grow clusters of similar reads into a final set of clusters that represent the haplotypes. We discuss the advantages and limitations of these methods and the metrics used to assess their performance, proposing that accuracy and contiguity are the most meaningful metrics. Finally, we propose the field of alignment-based polyploid phasing would greatly benefit from the use of a well-designed benchmarking dataset with appropriate evaluation metrics. We consider that there are still significant improvements which can be achieved to obtain more accurate and contiguous polyploid phasing results which reflect the complexity of polyploid genome architectures.

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news-10978 Thu, 31 Mar 2022 20:52:54 +0200 New publication in Molecular Ecology /en/news/piece-of-news/nouvelle-publication-dans-molecular-ecology Brettanomyces bruxellensis: overview of the genetic and phenotypic diversity of an anthropized yeast.
Jules Harrouard, Chris Eberlein, Patricia Ballestra, Marguerite Dols-Lafargue, Isabelle Masneuf-Pomarede, Cécile Miot-Sertier, Joseph Schacherer, Warren Albertin.
Molecular Ecology. 2022. doi: 10.1111/mec.16439

Human-associated microorganisms are ideal models to study the impact of environmental changes on species evolution and adaptation because of their small genome, short generation time, and their colonization of contrasting and ever-changing ecological niches. The yeast Brettanomyces bruxellensis is a good example of organism facing anthropogenic-driven selective pressures. It is associated with fermentation processes in which it can be considered either as a spoiler (e.g. winemaking, bioethanol production) or as a beneficial microorganism (e.g. production of specific beers, kombucha). Besides its industrial interests, noteworthy parallels and dichotomies with Saccharomyces cerevisiae propelled B. bruxellensis as a valuable complementary yeast model. In this review, we emphasize that the broad genetic and phenotypic diversity of this species is only beginning to be uncovered. Population genomic studies have revealed the co-existence of auto- and allotriploidization events with different evolutionary outcomes. The different diploid, autotriploid and allotriploid subpopulations are associated with specific fermented processes, suggesting independent adaptation events to anthropized environments. Phenotypically, B. bruxellensis is renowned for its ability to metabolize a wide variety of carbon and nitrogen sources, which may explain its ability to colonize already fermented environments showing lownutrient contents. Several traits of interest could be related to adaptation to human activities (e.g. nitrate metabolization in bioethanol production, resistance to sulphite treatments in winemaking). However, phenotypic traits are insufficiently studied in view of the great genomic diversity of the species. Future work will have to take into account strains of varied substrates, geographical origins as well as displaying different ploidy levels to improve our understanding of an anthropized yeast’s phenotypic landscape.

 

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news-10812 Sun, 06 Mar 2022 16:39:28 +0100 New publication in Nature Ecology & Evolution /en/news/piece-of-news/nouvelle-publication-dans-nature-ecology-evolution Domestication reprogrammed the budding yeast life cycle. Domestication reprogrammed the budding yeast life cycle.
Matteo De Chiara, Benjamin P Barré, Karl Persson, Agurtzane Irizar, Chiara Vischioni, Sakshi Khaiwal, Simon Stenberg, Onyetugo Chioma Amadi, Gašper Žun , Katja Doberšek, Cristian Taccioli, Joseph Schacherer, Uroš Petrovič, Jonas Warringer, Gianni Liti.

Domestication of plants and animals is the foundation for feeding the world human population but can profoundly alter the biology of the domesticated species. Here we investigated the effect of domestication on one of our prime model organisms, the yeast Saccharomyces cerevisiae, at a species-wide level. We tracked the capacity for sexual and asexual reproduction and the chronological life span across a global collection of 1,011 genome-sequenced yeast isolates and found a remarkable dichotomy between domesticated and wild strains. Domestication had systematically enhanced fermentative and reduced respiratory asexual growth, altered the tolerance to many stresses and abolished or impaired the sexual life cycle. The chronological life span remained largely unaffected by domestication and was instead dictated by clade-specific evolution. We traced the genetic origins of the yeast domestication syndrome using genome-wide association analysis and genetic engineering and disclosed causative effects of aneuploidy, gene presence/absence variations, copy number variations and single-nucleotide polymorphisms. Overall, we propose domestication to be the most dramatic event in budding yeast evolution, raising questions about how much domestication has distorted our understanding of the natural biology of this key model species.

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news-10810 Sun, 06 Mar 2022 14:53:01 +0100 New publication in Current Biology /en/news/piece-of-news/new-publication-in-current-biology Phased polyploid genomes provide deeper insight into the multiple origins of domesticated Saccharomyces cerevisiae beer yeasts. Phased polyploid genomes provide deeper insight into the multiple origins of domesticated Saccharomyces cerevisiae beer yeasts.
Omar Abou Saada, Andreas Tsouris, Chris Large, Anne Friedrich, Maitreya J Dunham, Joseph Schacherer.

 

Yeasts, and in particular Saccharomyces cerevisiae, have been used for brewing beer for thousands of years. Population genomic surveys highlighted that beer yeasts are polyphyletic, with the emergence of different domesticated subpopulations characterized by high genetic diversity and ploidy level. However, the different origins of these subpopulations are still unclear as reconstruction of polyploid genomes is required. To gain better insight into the differential evolutionary trajectories, we sequenced the genomes of 35 Saccharomyces cerevisiae isolates coming from different beer-brewing clades, using a long-read sequencing strategy. By phasing the genomes and using a windowed approach, we identified three main beer subpopulations based on allelic content (European dominant, Asian dominant, and African beer). They were derived from different admixtures between populations and are characterized by distinctive genomic patterns. By comparing the fully phased genes, the most diverse in our dataset are enriched for functions relevant to the brewing environment such as carbon metabolism, oxidoreduction, and cell wall organization activity. Finally, independent domestication, evolution, and adaptation events across subpopulations were also highlighted by investigating specific genes previously linked to the brewing process. Altogether, our analysis based on phased polyploid genomes has led to new insight into the contrasting evolutionary history of beer isolates.

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Actualités du GMGM Publications du GMGM Actualités de l'Équipe Schacherer
news-10818 Wed, 01 Dec 2021 17:32:00 +0100 New publication in Genome Research /en/news/piece-of-news/nouvelle-publication-dans-genome-research Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species. Different trajectories of polyploidization shape the genomic landscape of the Brettanomyces bruxellensis yeast species.
Chris Eberlein, Omar Abou Saada, Anne Friedrich, Warren Albertin, Joseph Schacherer.
Genome Res. 2021. doi: 10.1101/gr.275380.121

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Publications du GMGM Actualités de l'Équipe Schacherer
news-10820 Tue, 02 Nov 2021 17:37:00 +0100 New publication in G3 /en/news/piece-of-news/nouvelle-publication-dans-g3 Evolution of quantitative trait locus hotspots in yeast species. Evolution of quantitative trait locus hotspots in yeast species.
Emilien Peltier, Sabrina Bibi-Triki, Fabien Dutreux, Claudia Caradec, Anne Friedrich, Bertrand Llorente, Joseph Schacherer.
G3 (Bethesda). 2021. doi: 10.1093/g3journal/jkab242

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Publications du GMGM Actualités de l'Équipe Schacherer
news-10814 Mon, 01 Nov 2021 17:14:00 +0100 New publication in eLife /en/news/piece-of-news/nouvelle-publication-dans-elife Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds. Loss of heterozygosity results in rapid but variable genome homogenization across yeast genetic backgrounds.
Abhishek Dutta, Fabien Dutreux, Joseph Schacherer.

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Publications du GMGM Actualités de l'Équipe Schacherer
news-10822 Sat, 16 Oct 2021 17:47:00 +0200 New publication in Molecular Biology and Evolution /en/news/piece-of-news/nouvelle-publication-dans-molecular-biology-and-evolution Species-wide transposable element repertoires retrace the evolutionary history of the Saccharomyces cerevisiae host. Species-wide transposable element repertoires retrace the evolutionary history of the Saccharomyces cerevisiae host.
Claudine Bleykasten-Grosshans, Roméo Fabrizio, Anne Friedrich, Joseph Schacherer. 

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Publications du GMGM Actualités de l'Équipe Schacherer
news-10816 Tue, 05 Oct 2021 17:28:00 +0200 New publication in Genome Biology /en/news/piece-of-news/nouvelle-publication-dans-genome-biology Sex without crossing over in the yeast Saccharomycodes ludwigii. Sex without crossing over in the yeast Saccharomycodes ludwigii.
Ioannis A. Papaioannou, Fabien A. Dutreux, France A. Peltier, Hiromi Maekawa, Nicolas Delhomme, Amit Bardhan, Anne Friedrich, Joseph Schacherer, Michael Knop.
Genome Biol. 2021. doi: 10.1186/s13059-021-02521-w

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Publications du GMGM Actualités de l'Équipe Schacherer
news-9601 Thu, 29 Apr 2021 11:31:00 +0200 New publication in Genome Biology /en/news/piece-of-news/nphase-an-accurate-and-contiguous-phasing-method-for-polyploids nPhase: an accurate and contiguous phasing method for polyploids nPhase: an accurate and contiguous phasing method for polyploids
Omar Abou Saada, Andreas Tsouris, Chris Eberlein, Anne Friedrich, Joseph Schacherer

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Actualités de l'Équipe Schacherer
news-9582 Mon, 11 May 2020 22:17:00 +0200 New publication in BMC Biology /en/news/piece-of-news/new-publication-of-the-intraspecific-variation-and-genome-evolution-team-in-bmc-biology Discordant evolution of mitochondrial and nuclear yeast genomes at population level. Discordant evolution of mitochondrial and nuclear yeast genomes at population level.

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Publications du GMGM Actualités de l'Équipe Schacherer
news-9581 Mon, 04 May 2020 22:17:00 +0200 Equipe Variation intra-spécifique et évolution des génomes /en/news/piece-of-news/equipe-variation-intra-specifique-et-evolution-des-genomes-1-1 Nouvelle publication de l'équipe: Pervasive phenotypic impact of a large non-recombining introgressed region in yeast. Nouvelle publication de l'équipe: Pervasive phenotypic impact of a large non-recombining introgressed region in yeast.

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Actualités de l'Équipe Schacherer
news-9579 Tue, 21 Apr 2020 08:33:00 +0200 Equipe Variation intra-spécifique et évolution des génomes /en/news/piece-of-news/equipe-variation-intra-specifique-et-evolution-des-genomes-1-2 Nouvelle publication de l'équipe : High complexity and degree of genetic variation in Brettanomyces bruxellensis population. Nouvelle publication de l'équipe : High complexity and degree of genetic variation in Brettanomyces bruxellensis population.

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Actualités de l'Équipe Schacherer
news-9571 Mon, 28 Oct 2019 19:40:00 +0100 Un nouvel article de l’équipe Variation intra-spécifique et évolution des génomes dans la revue eLife /en/news/piece-of-news/un-nouvel-article-de-lequipe-variation-intra-specifique-et-evolution-des-genomes-dans-la-revue-elife Extensive impact of low-frequency variants on the phenotypic landscape at population-scale. Extensive impact of low-frequency variants on the phenotypic landscape at population-scale.

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Actualités de l'Équipe Schacherer
news-9570 Wed, 04 Sep 2019 21:17:00 +0200 Trois publications en collaboration avec l'équipe Variation intra-spécifique et évolution des génomes /en/news/piece-of-news/trois-publications-en-collaboration-avec-lequipe-variation-intra-specifique-et-evolution-des-genomes The induction of HAD-like phosphatases by multiple signaling pathways confers resistance to the metabolic inhibitor 2-deoxyglucose. Science Signaling 2019, doi: 10.1126/scisignal.aaw8000 Reshuffling yeast chromosomes with CRISPR/Cas9.  PLoS Genet. 2019, doi: 10.1371/journal.pgen.1008332 RNAi as a tool to study virulence in the pathogenic yeast Candida glabrata. Front Microbiol. 2019, doi: 10.3389/fmicb.2019.01679 The induction of HAD-like phosphatases by multiple signaling pathways confers resistance to the metabolic inhibitor 2-deoxyglucose.
Science Signaling 2019, doi: 10.1126/scisignal.aaw8000

Reshuffling yeast chromosomes with CRISPR/Cas9
PLoS Genet. 2019, doi: 10.1371/journal.pgen.1008332

RNAi as a tool to study virulence in the pathogenic yeast Candida glabrata.
Front Microbiol. 2019, doi: 10.3389/fmicb.2019.01679

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Actualités de l'Équipe Schacherer