Joëlle Amselem
A5036260327- Plant Pathogens and Fungal Diseases
- Plant Disease Resistance and Genetics
- Wheat and Barley Genetics and Pathology
- Genomics and Phylogenetic Studies
- Yeasts and Rust Fungi Studies
- Mycorrhizal Fungi and Plant Interactions
- Plant-Microbe Interactions and Immunity
- Fungal Biology and Applications
- Plant Virus Research Studies
- Chromosomal and Genetic Variations
- Fungal Plant Pathogen Control
- Fungal and yeast genetics research
- Plant Pathogens and Resistance
- Powdery Mildew Fungal Diseases
- Plant Molecular Biology Research
- Cultural Insights and Digital Impacts
- Agriculture and Rural Development Research
- Insect symbiosis and bacterial influences
- Plant tissue culture and regeneration
- Mycotoxins in Agriculture and Food
- Plant Gene Expression Analysis
- Forest Insect Ecology and Management
- Plant Taxonomy and Phylogenetics
- Plant Reproductive Biology
- CRISPR and Genetic Engineering
Université Paris-Saclay
2017-2024
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2020-2024
Centre Hospitalier de Versailles
2012-2024
Biologie et Gestion des Risques en Agriculture
2007-2016
Institut National de la Recherche Agronomique
1987-2015
Institució Catalana de Recerca i Estudis Avançats
2015
Département Génétique Animale
2011
Laboratoire de Biologie et Modélisation de la Cellule
1987-2005
Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges environmental persistence. These attributes have made these species models understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite similarities, two differ in mating behaviour ability to produce asexual spores. We sequenced genomes one strain S. strains B. cinerea. The comparative analysis relative another other fungal is...
Powdery mildews are phytopathogens whose growth and reproduction entirely dependent on living plant cells. The molecular basis of this life-style, obligate biotrophy, remains unknown. We present the genome analysis barley powdery mildew, Blumeria graminis f.sp. hordei (Blumeria), as well a comparison with two pathogenic dicotyledonous plants. These genomes display massive retrotransposon proliferation, genome-size expansion, gene losses. missing genes encode enzymes primary secondary...
Rust fungi are some of the most devastating pathogens crop plants. They obligate biotrophs, which extract nutrients only from living plant tissues and cannot grow apart their hosts. Their lifestyle has slowed dissection molecular mechanisms underlying host invasion avoidance or suppression innate immunity. We sequenced 101-Mb genome Melampsora larici - populina , causal agent poplar leaf rust, 89-Mb Puccinia graminis f. sp. tritici wheat barley stem rust. then compared 16,399 predicted...
The genome of the Périgord black truffle Tuber melanosporum Vittad., a gourmet delicacy that grows symbiotically on roots European oak, has been sequenced. This is largest and most complex fungal so far unusually gene-poor, but rich in mobile genetic elements known as transposons. Comparison with sequence Laccaria bicolor, another ectomycorrhizal symbiotic fungus, reveals contrasting gene sets reflecting two different molecular toolkits have evolved independently to fit root symbiont...
Fungi are of primary ecological, biotechnological and economic importance. Many fundamental biological processes that shared by animals fungi studied in due to their experimental tractability. pathogens or mutualists model systems analyse effector genes mechanisms diversification. In this study, we report the genome sequence phytopathogenic ascomycete Leptosphaeria maculans characterize its repertoire protein effectors. The L. has an unusual bipartite structure with alternating distinct...
Oaks are an important part of our natural and cultural heritage. Not only they ubiquitous in most common landscapes1 but have also supplied human societies with invaluable services, including food shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe America3, oaks constitute a critical global renewable resource. The longevity (several hundred years) probably underlies their emblematic historical importance. Such long-lived sessile organisms must persist the face...
Emergence of polyphagous herbivorous insects entails significant adaptation to recognize, detoxify and digest a variety host-plants. Despite its biological practical importance - since eat 20% crops no exhaustive analysis gene repertoires required for adaptations in generalist insect herbivores has previously been performed. The noctuid moth Spodoptera frugiperda ranks as one the world's worst agricultural pests. This is while majority other lepidopteran are specialist. It consists two...
Thomas Wicker and colleagues report the whole-genome sequencing of four wheat powdery mildew (Blumeria graminis forma specialis tritici) isolates from different geographic regions. Their comparative genomic analysis provides insights into evolution mildews, which are obligate biotropic fungal pathogens. Wheat mildew, Blumeria tritici, is a devastating pathogen with poorly understood evolutionary history. Here we draft genome sequence resequencing three additional regions analyses barley...
Zymoseptoria tritici is the causal agent of Septoria blotch, a major pathogen wheat globally and most damaging in Europe. A gene-for-gene (GFG) interaction between Z. cultivars carrying Stb6 resistance gene has been postulated for many years, but genes have not identified. We identified AvrStb6 by combining quantitative trait locus mapping cross two Swiss strains with genome-wide association study using natural population c. 100 from France. functionally validated ectopic transformations....
Nearly 7000 Arabidopsis thaliana ‐expressed sequence tags (ESTs) from 10 cDNA libraries have been sequenced, of which almost 5000 non‐redundant submitted to the EMBL data bank. The quality used is analysed. Similarity searches in international protein banks allowed detection significant similarities a wide range proteins many organisms. Alignment with ESTs rice systematic sequencing project has amino acid motifs are conserved between two organisms, thus identifying genes encoding highly...
Abstract The 1.5 Gbp/2C genome of pedunculate oak ( Quercus robur ) has been sequenced. A strategy was established for dealing with the challenges imposed by sequencing such a large, complex and highly heterozygous whole‐genome shotgun WGS approach, without use costly time‐consuming methods, as fosmid or BAC clone‐based hierarchical methods. combined short long reads. Over 49 million reads provided Roche 454 GS ‐ FLX technology were assembled into contigs shorter Illumina sequence from...
The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions genome sequence were highly fragmented, causing errors in prediction protein-coding genes preventing analysis repetitive sequences architecture. Here, we re-sequenced using single-molecule real-time (SMRT) sequencing technology and, combination with optical map data, this provided a gapless assembly all twelve chromosomes except for...
As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started genome assembly and annotation. The guidelines given are broadly applicable, intended be stable over time, cover all aspects from start finish general annotation project. Intrinsic properties genomes discussed, as is importance using high quality DNA. Different sequencing technologies generally applicable workflows for also detailed. We structural functional...
Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how fungus Magnaporthe oryzae adapts different plants, we sequenced eight M. isolates differing specificity (rice, foxtail millet, wheat, goosegrass), one grisea isolate specific crabgrass. Analysis genomes revealed small variation genome sizes (39–43 Mb) gene content (12,283–14,781 genes) between isolates. The whole set genes comprised 14,966 shared families, 63% which...
Transposable Elements (TEs) are key components that shape the organization and evolution of genomes. Fungi have developed defense mechanisms against TE invasion such as RIP (Repeat-Induced Point mutation), MIP (Methylation Induced Premeiotically) Quelling (RNA interference). inactivates repeated sequences by promoting Cytosine to Thymine mutations, whereas only methylates TEs at C residues. Both require specific cytosine DNA Methyltransferases (RID1/Masc1) Dnmt1 superfamily.We annotated from...
As members of the plant microbiota, arbuscular mycorrhizal fungi (AMF, Glomeromycotina) symbiotically colonize roots. AMF also possess their own hosting some uncultivable endobacteria. Ongoing research has revealed genetics underlying responses to colonization by AMF, but fungal side relationship remains in dark. Here, we sequenced genome Gigaspora margarita, a member Gigasporaceae an early diverging group Glomeromycotina. In contrast other G. margarita may host distinct endobacterial...
Zymoseptoria tritici is the fungal pathogen responsible for Septoria blotch on wheat. Disease outcome in this pathosystem partly determined by isolate-specific resistance, where wheat resistance genes recognize specific factors triggering an immune response. Despite large number of known genes, molecular determinants involved such cultivar-specific remain largely unknown. We identified avirulence factor AvrStb9 using association mapping and functional validation approaches. Pathotyping...
Abstract Knowledge of genetic determinism and evolutionary dynamics mediating host-pathogen interactions is essential to manage fungal plant diseases. Studies on the architecture pathogenicity often focus large-effect effector genes triggering strong, qualitative resistance. It not clear how this translates predominately quantitative interactions. Here, we use Zymoseptoria tritici -wheat model elucidate mechanisms host adaptation. With a multi-host genome-wide association study, identify 19...
In this era of whole genome sequencing, reliable annotations (identification functional regions) are the cornerstones for many subsequent analyses. Not only is careful annotation important studying gene and family content a its host, but also wide-scale transcriptome proteome analyses attempting to describe certain biological process or get global picture cells behavior. Although number sequenced genomes increasing thanks application new technologies, genome-wide will critically depend on...
The genus Microbotryum includes plant pathogenic fungi afflicting a wide variety of hosts with anther smut disease. lychnidis-dioicae infects Silene latifolia and replaces host pollen fungal spores, exhibiting biotrophy necrosis associated altering development. We determined the haploid genome sequence for M. analyzed whole transcriptome data from infections other stages lifecycle, revealing inventory expression level genes that facilitate growth. Compared to related fungi, an expanded...
Thanks to their ability move around and replicate within genomes, transposable elements (TEs) are perhaps the most important contributors genome plasticity evolution. Their detection annotation considered essential in any sequencing project. The number of fully sequenced genomes is rapidly increasing with improvements high-throughput technologies. A automated de novo process for TEs therefore required cope deluge sequence data. However, all procedures error-prone, an procedure TE...
Abstract Endogenous viruses form an important proportion of eukaryote genomes and a source novel functions. How large DNA integrated into genome evolve when they confer benefit to their host, however, remains unknown. Bracoviruses are essential for the parasitism success parasitoid wasps, whose ~103 million years ago. Here we show, from assembly wasp at chromosomal scale, that bracovirus genes colonized all ten chromosomes Cotesia congregata . Most clusters involved in particle production or...
Summary Large numbers of genes are being discovered on a daily basis for variety organisms including Arabidopsis thaliana. To obtain more functional information these genes, efficient expression monitoring methods need to be developed. In this report we studied the steady‐state mRNA levels over 800 in parallel using high‐density arrays partially sequenced cDNA. The technology is simple and robust reliably permits detection down twofold variation levels. limit lies below 0.01% total...
Abstract The evolutionary history of the characters underlying adaptation microorganisms to food and biotechnological uses is poorly understood. We undertook comparative genomics investigate relationships dairy yeast Geotrichum candidum within Saccharomycotina. Surprisingly, a remarkable proportion genes showed discordant phylogenies, clustering with filamentous fungus subphylum (Pezizomycotina), rather than (Saccharomycotina), Ascomycota. These appear not be result Horizontal Gene Transfer...