A5071399944- Plant Pathogens and Fungal Diseases
- Mycotoxins in Agriculture and Food
- Plant Virus Research Studies
- Banana Cultivation and Research
- Plant Disease Resistance and Genetics
- Plant-Microbe Interactions and Immunity
- Fungal and yeast genetics research
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Plant Pathogenic Bacteria Studies
- Genetics, Bioinformatics, and Biomedical Research
- Cocoa and Sweet Potato Agronomy
- Wheat and Barley Genetics and Pathology
- Phytoplasmas and Hemiptera pathogens
- Bacteriophages and microbial interactions
- Mycorrhizal Fungi and Plant Interactions
- Chromosomal and Genetic Variations
- RNA and protein synthesis mechanisms
- Plant and Fungal Interactions Research
- Yeasts and Rust Fungi Studies
- Scientific Computing and Data Management
- Plant Pathogens and Resistance
- CRISPR and Genetic Engineering
- Evolution and Genetic Dynamics
- GABA and Rice Research
Centre de Coopération Internationale en Recherche Agronomique pour le Développement
2014-2024
Université de Montpellier
2017-2024
Centre Occitanie-Montpellier
2020-2024
Institut de Recherche pour le Développement
2018-2024
Institut Agro Montpellier
2017-2024
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2020-2024
Plant Health Institute de Montpellier
2020-2024
L'Institut Agro
2020-2024
Centre de Résonance Magnétique des Systèmes Biologiques
2021-2023
Agropolis International
2014-2023
In February 2016, a new fungal disease was spotted in wheat fields across eight districts Bangladesh. The epidemic spread to an estimated 15,000 hectares, about 16 % of the cultivated area Bangladesh, with yield losses reaching up 100 %. Within weeks onset epidemic, we performed transcriptome sequencing symptomatic leaf samples collected directly from Bangladeshi fields. Reinoculation seedlings strains isolated infected grains showed blast symptoms on leaves but not rice. Our phylogenomic...
Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence the structure biodiversity also informs international regulatory decisions.
The evolution of reproductive division labour and social life in insects has lead to the emergence several life-history traits adaptations typical larger organisms: insect colonies can reach masses kilograms, they start reproducing only when are years old, live for decades. These features monopolization reproduction by one or few individuals a colony should affect molecular reducing effective population size. We tested this prediction analysing genome-wide patterns coding sequence...
ABSTRACT The rice blast fungus Magnaporthe oryzae (syn., Pyricularia ) is both a threat to global food security and model for plant pathology. Molecular pathologists need an accurate understanding of the origins line descent M. populations in order identify genetic functional bases pathogen adaptation guide development more effective control strategies. We used whole-genome sequence analysis samples from different times places infer details about makeup collection isolates. Analyses...
Many species of fungal plant pathogens coexist as multiple lineages on the same host, but factors underlying origin and maintenance population structure remain largely unknown. The rice blast fungus Pyricularia oryzae is a widespread model pathogen displaying subdivision. However, most studies natural variation in P . have been limited genomic or geographic resolution, host adaptation only factor that has investigated extensively contributor to In an effort complement previous studies, we...
Plant pathogens secrete proteins called effectors that target host cellular processes to promote disease. Recently, structural genomics has identified several families of fungal share a similar three-dimensional structure despite remarkably variable amino-acid sequences and surface properties. To explore the selective forces underlie sequence variability structurally-analogous effectors, we focused on MAX family are major determinants virulence in rice blast fungus Pyricularia oryzae . Using...
The whole genome sequence of Coffea canephora, the perennial diploid species known as Robusta, has been recently released. In context C. canephora sequencing project and to support post-genomics efforts, we developed Coffee Genome Hub (http://coffee-genome.org/), an integrative information system that allows centralized access genomics genetics data analysis tools facilitate translational applied research in coffee. We provide complete along with gene structure, product information,...
Abstract Traditional agrosystems, where humans, crops and microbes have coevolved over long periods, can serve as models to understand the ecoevolutionary determinants of disease dynamics help engineering durably resistant agrosystems. Here, we investigated genetic phenotypic relationship between rice ( Oryza sativa ) landraces their blast pathogen Pyricularia oryzae in traditional Yuanyang terraces flooded paddies China, been grown bred centuries without significant outbreaks. Analyses...
Multipartite viruses have a segmented genome, with each segment encapsidated separately. In all multipartite virus species for which the question has been addressed, distinct segments reproducibly accumulate at specific and host-dependent relative frequency, defined as 'genome formula'. Here, we test hypothesis that genome organization facilitates regulation of gene expression via changes formula thus copy number variations. first experiment, faba bean necrotic stunt (FBNSV), whose is...
Rapid and repeatable polymorphism analyses have become a necessity with the current amount of genomic data that can be collected in many organisms. Traditionally, such are conducted using variety tools combination, often requiring numerous format translation manipulation. Here, we present massively updated version our previous software package egglib, intended to alleviate costly error-prone tinkering data. egglib has been streamlined into python thoroughly optimized accommodate modern-day...
Plants have powerful defense mechanisms and extensive immune receptor repertoires, yet crop monocultures are prone to epidemic diseases. Rice (Oryza sativa) is susceptible many diseases, such as rice blast caused by Magnaporthe oryzae. Varietal resistance of relies on intracellular nucleotide binding, leucine-rich repeat (NLR) receptors that recognize specific pathogen molecules trigger responses. In the Yuanyang terraces in southwest China, landraces rarely show severe losses disease...
The explosion of NGS (Next Generation Sequencing) sequence data requires a huge effort in Bioinformatics methods and analyses. creation dedicated, robust reliable pipelines able to handle dozens samples from raw FASTQ relevant biological is time-consuming task all projects relying on NGS. To address this, we created generic modular toolbox for developing such pipelines. TOGGLE (TOolbox Generic nGs anaLysEs) suite tools design that manage large sets softwares utilities. Moreover, offers an...
In February 2016, a new fungal disease was spotted in wheat fields across eight districts Bangladesh. The epidemic spread to an estimated 15,741 hectares, about 16% of cultivated area Bangladesh, with yield losses reaching up 100%. Within weeks the onset epidemic, we performed transcriptome sequencing symptomatic leaf samples collected directly from Bangladeshi fields. Population genomics analyses revealed that outbreak caused by wheat-infecting South American lineage blast fungus...
ABSTRACT The advent of NGS has intensified the need for robust pipelines to perform high-performance automated analyses. required softwares depend on sequencing method used produce raw data (e.g. Whole genome sequencing, Genotyping By Sequencing, RNASeq) as well kind analyses carry (GWAS, population structure, differential expression). These tools have be generic and scalable, should meet biologists needs. Here, we present new version TOGGLe ( To olbox G eneric N S Ana l ys e s), a simple...
Blast disease is a notorious fungal leading to dramatic yield losses on major food crops such as rice and wheat. The causal agent, Pyricularia oryzae, encompasses different lineages, each having host range. Host shifts are suspected have occurred in this species from Setaria spp. Lolium emergence of blast maize Iran was observed for the first time north country 2012. We later identified two additional regions Iran: Gilan 2013 Golestan 2016. Epidemics weed barnyard grass (Echinochloa spp.)...
The South Green Web portal (http://www.southgreen.fr/) provides access to a large panel of public databases, analytical workflows and bioinformatics resources dedicated the genomics tropical Mediterranean crops. contains currently about 20 information systems tools targets broad range crops such as Banana, Cacao, Cassava, Coconut, Coffee, Grape, Rice Sugarcane.
In recent years, Brown spot disease of rice (BSR) has been observed on leaves and seeds in all rice-growing areas Burkina Faso. Bipolaris oryzae Exserohilum rostratum are the main fungal species isolated from BSR infected tissues they frequently same field. However, we lacking information genetic diversity population structure these fungi The mode reproduction is also unknown. isolates B. (n=61) E. (n=151), collected major Faso, was estimated using genotyping-by-sequencing (GBS). mean values...
Rice blast, caused by the filamentous ascomycete Pyricularia oryzae, is one of most devastating diseases rice. Four genetic clusters were previously identified, and three have a large geographic distribution. Asia center diversity origin migrations to other continents, sexual reproduction persisted only in South China–Laos–North Thailand region, which was identified as putative all P. oryzae populations on Despite importance rice blast disease, little known about population structure...
ABSTRACT Plant pathogens secrete proteins called effectors that target host cellular processes to promote disease. Recently, structural genomics has identified several families of fungal share a similar three-dimensional structure despite remarkably variable amino-acid sequences and surface properties. To explore the selective forces underlie sequence variability structurally-analogous effectors, we focused on MAX family are major determinants virulence in rice blast fungus Pyricularia...
Using long reads provides higher contiguity and better genome assemblies. However, producing such high quality sequences from raw requires to chain a growing set of tools, determining the best workflow is complex task.
Plant pathogens can adapt to quantitative resistance, eroding its effectiveness. The aim of this work was reveal the genomic basis adaptation such a resistance in populations fungus Pseudocercospora fijiensis, major devastating pathogen banana, by studying convergent on different cultivars. Samples from P. fijiensis showing local pattern new banana hybrids with were compared, based genome scan approach, samples traditional and more susceptible cultivars Cuba Dominican Republic. Whole-genome...
Abstract The rice blast fungus Magnaporthe oryzae (syn. Pyricularia ) is both a threat to global food security and model for plant pathology. Molecular pathologists need an accurate understanding of the origins line descent M. populations, identify genetic functional bases pathogen adaptation, guide development more effective control strategies. We used whole-genome sequence analysis samples from different times places infer details about makeup collection isolates. Analyses population...