A5029927126- Fungal and yeast genetics research
- Fermentation and Sensory Analysis
- Yeasts and Rust Fungi Studies
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Evolution and Genetic Dynamics
- Horticultural and Viticultural Research
- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
- Microbial Metabolic Engineering and Bioproduction
- RNA and protein synthesis mechanisms
- Bioinformatics and Genomic Networks
- Genetics, Aging, and Longevity in Model Organisms
- Plant Reproductive Biology
- Biofuel production and bioconversion
- Genomics and Chromatin Dynamics
- Telomeres, Telomerase, and Senescence
- Wheat and Barley Genetics and Pathology
- Molecular Biology Techniques and Applications
- Mitochondrial Function and Pathology
- DNA Repair Mechanisms
- Cancer Genomics and Diagnostics
- Plant and animal studies
- Plant Disease Resistance and Genetics
- Genetic diversity and population structure
Institut de Recherche sur le Cancer et le Vieillissement de Nice
2016-2025
Inserm
2016-2025
Université Côte d'Azur
2014-2024
Centre National de la Recherche Scientifique
2015-2024
Sorbonne Université
2014-2021
Fondation ARC pour la Recherche sur le Cancer
2019-2021
University of Salzburg
2020
Institut Pasteur
2014
Queen's Medical Centre
2005-2014
Genomics (United Kingdom)
2013-2014
Large-scale population genomic surveys are essential to explore the phenotypic diversity of natural populations. Here we report whole-genome sequencing and phenotyping 1,011 Saccharomyces cerevisiae isolates, which together provide an accurate evolutionary picture variants that shape species-wide landscape this yeast. Genomic analyses support a single ‘out-of-China’ origin for species, followed by several independent domestication events. Although domesticated isolates exhibit high variation...
A fundamental goal in biology is to achieve a mechanistic understanding of how and what extent ecological variation imposes selection for distinct traits favors the fixation specific genetic variants. Key such an detailed mapping natural genomic phenomic space bridging gap that separates these worlds. Here we chart high-resolution map trait one most important model organisms, budding yeast Saccharomyces cerevisiae, its closest wild relatives trace basis timing major phenotype changing events...
Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major subpopulations the partially domesticated yeast Saccharomyces cerevisiae its wild relative paradoxus. These population-level high-quality genomes comprehensive annotation enable...
The question of how genetic variation in a population influences phenotypic and evolution is major importance modern biology.Yet much still unknown about the relative functional different forms genome they are shaped by evolutionary processes.Here we address these questions level sequencing 42 strains from budding yeast Saccharomyces cerevisiae its closest S. paradoxus.We find that content variation, form presence or absence as well copy number material, higher within than paradoxus, despite...
One approach to understanding the genetic basis of traits is study their pattern inheritance among offspring phenotypically different parents. Previously, such analysis has been limited by low mapping resolution, high labor costs, and large sample size requirements for detecting modest effects. Here, we present a novel map trait loci using artificial selection. First, generated populations 10–100 million haploid diploid segregants crossing two budding yeast strains heat tolerance up 12...
Abstract The budding yeast, S accharomyces cerevisiae , is a leading system in genetics, genomics and molecular biology becoming powerful tool to illuminate ecological evolutionary principles. However, little known of the ecology population structure this species nature. Here, we present field survey yeast at an unprecedented scale have performed genetics analysis Chinese wild isolates with different geographical origins. We also included set worldwide that represent maximum genetic...
Abstract Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder (PGGB), pipeline for constructing pangenome without bias exclusion. PGGB uses all-to-all alignments graph in which identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.
Pangenomes provide access to an accurate representation of the genetic diversity species, both in terms sequence polymorphisms and structural variants (SVs). Here we generated Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising reference-quality genomes for 142 strains representing species' phylogenetic ecological diversity. The ScRAP includes phased haplotype assemblies several heterozygous diploid polyploid isolates. We identified circa (ca.) 4,800 nonredundant SVs that a...
Abstract Accessing the natural genetic diversity of species unveils hidden traits, clarifies gene functions and allows generalizability laboratory findings to be assessed. One notable discovery made in isolates Saccharomyces cerevisiae is that aneuploidy—an imbalance chromosome copy numbers—is frequent 1,2 (around 20%), which seems contradict substantial fitness costs transient nature aneuploidy when it engineered 3–5 . Here we generate a proteomic resource merge with genomic 1...
Using the biological species definition, yeasts of genus Saccharomyces sensu stricto comprise six and one natural hybrid. Previous work has shown that reproductive isolation between is due primarily to sequence divergence acted upon by mismatch repair system not major gene differences or chromosomal rearrangements. Sequence through also been cause partial among populations within a species. We have surveyed variation in measured meiotic sterility hybrids. This allows us determine necessary...
Abstract Phenotypic variation arising from populations adapting to different niches has a complex underlying genetic architecture. A major challenge in modern biology is identify the causative variants driving phenotypic variation. Recently, baker’s yeast, Saccharomyces cerevisiae emerged as powerful model for dissecting traits. However, past studies using laboratory strain were unable reveal complete architecture of polygenic Here, we present linkage study 576 recombinant strains obtained...
Abstract Closing gaps in draft genome assemblies can be costly and time-consuming, published genomes are therefore often left ‘unfinished.’ Here we show that genome-wide chromosome conformation capture (3C) data used to overcome these limitations, present a computational approach rooted polymer physics determines the most likely structure using chromosomal contact data. This algorithm—named GRAAL—generates high-quality of which repeated duplicated regions accurately represented offers direct...
In "evolve-and-resequence" (E&R) experiments, whole-genome sequence data from laboratory-evolved populations can potentially uncover mechanisms of adaptive change. E&R experiments with initially isogenic, asexually reproducing microbes have repeatedly shown that beneficial de novo mutations drive adaptation, and these are not shared among independently evolving replicate populations. Recent higher eukaryotes maintain genetic variation via sexual reproduction implicate largely different...
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long reads with average fragment lengths over 10,000 base-pairs maximum reaching 100,000 base- pairs. Compared short reads, the assemblies obtained from long-read platforms have much higher contig continuity genome completeness fragments able to extend paths into problematic or repetitive regions. Many successful assembly applications technology been reported ranging small...
Abstract Background: Oxford Nanopore Technologies Ltd (Oxford, UK) have recently commercialized MinION, a small single-molecule nanopore sequencer, that offers the possibility of sequencing long DNA fragments from genomes in matter seconds. The technology is truly disruptive; it has potential to revolutionize genomic applications due its portability, low cost, and ease use compared with existing reads technologies. MinION sequencer enables rapid eukaryotic genomes, such as yeast genome....
A large fraction of human complex trait heritability is due to a high number variants with small marginal effects and their interactions genotype environment. Such alleles are more easily studied in model organisms, where environment, genetic makeup, allele frequencies can be controlled. Here, we examine the effect natural variation on heritable traits very pool baker's yeast from multiparent 12th generation intercross. We selected four representative founder strains produce Saccharomyces...
Saccharomyces cerevisiae has proved to be an invaluable model in classical and molecular genetics studies. Despite several hundreds of isolates already available, the scientific community relies on use only a handful unrelated strains. The lack sequence information, haploid derivatives genetic markers prevented novel strains from being used. Here, we release set 55 S. paradoxus genetically tractable strains, previously sequenced Genome Resequencing Project. These are stable ura3 auxotrophs...
Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements especially common following interspecific hybridization, and some of these could be expected have strong selective value. To test this expectation we created de novo yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a...