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View article: Dynamics of genome evolution in the era of pangenome analysis
Dynamics of genome evolution in the era of pangenome analysis Open
The advent of long-read sequencing and telomere-to-telomere (T2T) assemblies has transformed studies of eukaryotic genomic variation. Pangenomes now leverage these advances to generate comprehensive catalogs of structural variants (SVs) an…
View article: From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes
From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes Open
Unravelling the genetic basis of the remarkable phenotypic diversity observed in natural populations remains a central challenge in biology1-4. Despite major advances5-19, no species has yet been characterized with a …
View article: A genetic screen reveals a key role for Reg1 in 2-deoxyglucose sensing and yeast AMPK inhibition
A genetic screen reveals a key role for Reg1 in 2-deoxyglucose sensing and yeast AMPK inhibition Open
The yeast Saccharomyces cerevisiae thrives in sugar-rich environments by rapidly consuming glucose and favoring alcoholic fermentation. This strategy is tightly regulated by the glucose repression pathway, which prevents the expression of …
View article: Graph-based pangenome analysis uncovers structural and functional impacts of allopolyploidization events
Graph-based pangenome analysis uncovers structural and functional impacts of allopolyploidization events Open
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 poorl…
View article: Whole-genome sequencing of 1,060 Brettanomyces bruxellensis isolates reveals significant phenotypic impact of acquired subgenomes in allopolyploids
Whole-genome sequencing of 1,060 Brettanomyces bruxellensis isolates reveals significant phenotypic impact of acquired subgenomes in allopolyploids Open
Genomic architecture changes can significantly influence genome evolution and phenotypic variation within a species. Polyploidization events are thought to be one of the important catalysts for adaptation, speciation and tumorigenesis. How…
View article: A genetic screen reveals a key role for Reg1 in 2-deoxyglucose sensing and yeast AMPK inhibition
A genetic screen reveals a key role for Reg1 in 2-deoxyglucose sensing and yeast AMPK inhibition Open
The yeast Saccharomyces cerevisiae thrives in sugar-rich environments by rapidly consuming glucose and favoring alcoholic fermentation. This metabolic strategy is tightly regulated by glucose signaling pathways, particularly the glucose re…
View article: Immunomodulatory and cardio-protective effects of differentially originated multipotent mesenchymal stroma cells during polymicrobial sepsis in mice
Immunomodulatory and cardio-protective effects of differentially originated multipotent mesenchymal stroma cells during polymicrobial sepsis in mice Open
View article: Comprehensive survey of kombucha microbial communities of diverse origins and fermentation practices
Comprehensive survey of kombucha microbial communities of diverse origins and fermentation practices Open
Kombucha is a unique, naturally fermented sweetened tea produced for thousands of years, relying on a symbiotic microbiota in a floating biofilm, used for successive fermentations. The microbial communities consist of yeast and bacteria sp…
View article: The Systemic Administration of Multipotent Mesenchymal Stroma Cells Alters the Inflammatory Response in the Lung During Murine Polymicrobial Sepsis
The Systemic Administration of Multipotent Mesenchymal Stroma Cells Alters the Inflammatory Response in the Lung During Murine Polymicrobial Sepsis Open
View article: Overview of the <i>Saccharomyces cerevisiae</i> population structure through the lens of 3,034 genomes
Overview of the <i>Saccharomyces cerevisiae</i> population structure through the lens of 3,034 genomes Open
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 …
View article: Multiple independent losses of crossover interference during yeast evolutionary history
Multiple independent losses of crossover interference during yeast evolutionary history Open
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 spe…
View article: Whole-genome sequencing and phenotyping reveal specific adaptations of<i>Lachancea thermotolerans</i>to the winemaking environment
Whole-genome sequencing and phenotyping reveal specific adaptations of<i>Lachancea thermotolerans</i>to the winemaking environment Open
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 resea…
View article: Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast
Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast Open
View article: Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast
Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast Open
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…
View article: Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast <i>Lachancea kluyveri</i>
Absence of chromosome axis protein recruitment prevents meiotic recombination chromosome-wide in the budding yeast <i>Lachancea kluyveri</i> Open
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 S…
View article: Recurrent loss of crossover interference punctuates the recombination landscape across yeast species
Recurrent loss of crossover interference punctuates the recombination landscape across yeast species Open
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 spe…
View article: Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast
Diallel panel reveals a significant impact of low-frequency genetic variants on gene expression variation in yeast Open
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 exp…
View article: Data and code for Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast
Data and code for Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast Open
<p>This repository contains the codes to perform the analysis and the figure for the "Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast" paper. </p>…
View article: Species-wide survey of the expressivity and complexity spectrum of traits in yeast
Species-wide survey of the expressivity and complexity spectrum of traits in yeast Open
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…
View article: Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast Open
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 tra…
View article: Data and code for Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast
Data and code for Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast Open
This repository contains the codes to perform the analysis and the figure for the "Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast" paper. The analysis were perf…
View article: Data and codes for the "Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast" paper
Data and codes for the "Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast" paper Open
This repository contains the codes used to analyse the RNA-seq and Ribo-seq data pulbished in the "Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast". The main analysis were perfor…
View article: Data and codes for the "Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast" paper
Data and codes for the "Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast" paper Open
<p>This repository contains the codes used to analyse the RNA-seq and Ribo-seq data pulbished in the "Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast".</p>\n<p>…
View article: Data and code for Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast
Data and code for Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast Open
This repository contains the codes to perform the analysis and the figure for the "Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast" paper. The analysis were perfo…
View article: Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast
Translation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast Open
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 tra…
View article: Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast
Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast Open
Summary 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 transcrip…
View article: Absence of chromosome axis proteins recruitment prevents meiotic recombination chromosome-wide in the budding yeast<i>Lachancea kluyveri</i>
Absence of chromosome axis proteins recruitment prevents meiotic recombination chromosome-wide in the budding yeast<i>Lachancea kluyveri</i> Open
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 S…
View article: ScRAPv20230731: Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
ScRAPv20230731: Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae Open
Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) v20230731 > The haplotype-resolved and/or collapsed T2T genome assemblies for 142 S. cerevisiae strains isolated from diverse geographical and eco…
View article: Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae Open
View article: ScRAPv20230731: Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae
ScRAPv20230731: Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae Open
Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) v20230731 > The haplotype-resolved and/or collapsed T2T genome assemblies for 142 S. cerevisiae strains isolated from diverse geographical and eco…