A5090468427- Plant Virus Research Studies
- Plant and Fungal Interactions Research
- Plant Disease Resistance and Genetics
- Probiotics and Fermented Foods
- Gut microbiota and health
- Genomics and Phylogenetic Studies
- Wheat and Barley Genetics and Pathology
- Microbial Community Ecology and Physiology
- Plant-Microbe Interactions and Immunity
- Plant Pathogenic Bacteria Studies
- Bacteriophages and microbial interactions
- Agriculture and Rural Development Research
- Insect-Plant Interactions and Control
- Mycotoxins in Agriculture and Food
- Microbial infections and disease research
- Milk Quality and Mastitis in Dairy Cows
- Plant Parasitism and Resistance
- Chromosomal and Genetic Variations
- Plant Pathogens and Fungal Diseases
- Fermentation and Sensory Analysis
- Aquaculture disease management and microbiota
- Listeria monocytogenes in Food Safety
- Cocoa and Sweet Potato Agronomy
- Plant tissue culture and regeneration
- Microbial Metabolites in Food Biotechnology
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2014-2025
VetAgro Sup
2021-2024
Université Clermont Auvergne
2012-2024
Biologie du Fruit et Pathologie
2013-2023
Université de Bordeaux
2015-2022
Unité Mixte de Recherche sur les Fromages
2020
Bavarian State Research Center for Agriculture
2018-2020
Génétique, Diversité, Écophysiologie des Céréales
2012-2015
University of Bari Aldo Moro
2015
Interactions Sol Plante Atmosphère
2015
We produced a reference sequence of the 1-gigabase chromosome 3B hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% transposable elements. The distribution structural functional features along revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- intrachromosomal gene duplication activities that are...
Transitions between saline and fresh waters have been shown to be infrequent for microorganisms. Based on host-specific interactions, the presence of specific clades among hosts suggests existence freshwater-specific viral clades. Yet, little is known about composition diversity temperate freshwater communities, even if lakes marine harbor distinct particular sub-families, this distinction remains demonstrated a community scale. To help identify characteristics potential specificities such...
The 17 Gb bread wheat genome has massively expanded through the proliferation of transposable elements (TEs) and two recent rounds polyploidization. assembly a 774 Mb reference sequence chromosome 3B provided us with opportunity to explore impact TEs on complex structure evolution at resolution scale not reached so far.We develop an automated workflow, CLARI-TE, for TE modeling in genomes. We delineate precisely 56,488 intact 196,391 fragmented along pseudomolecule, accounting 85% sequence,...
In support of the international effort to obtain a reference sequence bread wheat genome and provide plant communities dealing with large complex genomes versatile, easy-to-use online automated tool for annotation, we have developed TriAnnot pipeline. Its modular architecture allows annotation masking transposable elements, structural, functional protein-coding genes an evidence-based quality indexing, identification conserved non-coding sequences molecular markers. The pipeline is...
<ns4:p>Bioinformatic tools for marker gene sequencing data analysis are continuously and rapidly evolving, thus integrating most recent techniques is challenging. We present an R package of 16S ITS amplicons based sequencing. This workflow on several functions performs automatic treatments from fastq sequence files to diversity differential with statistical validation. The main purpose this automate bioinformatic analysis, ensure reproducibility between projects, be flexible enough quickly...
Metagenomic studies have indicated that the diversity of plant viruses was until recently far underestimated. As important components ecosystems, there is a need to explore and richness associated with populations understand drivers shaping their in space time. Two viral sequence enrichment approaches, double-stranded RNA (dsRNA) virion-associated nucleic acids (VANA), been used compared here for description virome complex pools representative most prevalent species unmanaged cultivated...
Abstract Type VI secretion systems (T6SS), recently described in hypervirulent K. pneumoniae (hvKp) strains , are involved bacterial warfare but their role classical clinical (cKp) has been little investigated . In silico analysis indicated the presence of T6SS clusters (from zero to four), irrespective origin or virulence, with a high prevalence species (98%). strain CH1157, two T6SS-apparented pathogenicity islands were detected, T6SS-1 and -2, harboring phospholipase-encoding gene ( tle1...
The first proteome-wide analysis of intrinsic disorder in a major plant virus genus.
Viral metagenomics relies on high-throughput sequencing and bioinformatic analyses to access the genetic content diversity of entire viral communities. No universally accepted strategy or tool currently exists define operational taxonomy units (OTUs) evaluate alpha beta from virome data. Here we present a new resource, VirAnnot (automated estimation) pipeline, which performs automated identification OTUs. Reverse-position-specific BLAST (RPS-Blastn) is used detect conserved protein motifs....
Investigating the diversity of a given species could give clues for development autochthonous starter cultures. However, few studies have focused on intraspecies Lactobacillus delbrueckii strains, technologically important lactic acid bacterium dairy industry. For this reason, strains from Saint-Nectaire Protected Designation Origin (PDO) area were isolated and characterized. Genetic was determined based core genome phylogenetic reconstruction pangenome analysis, while phenotypic assessments...
Abstract An exhaustive analysis was performed on more than 2000 microbiotas from French Protected Designation of Origin (PDO) cheeses, covering most cheese families produced throughout the world. Thanks to a complete and accurate set associated metadata, we have carried out deep ecological drivers microbial communities in milk “terroir” cheeses. We show that bacterial fungal microbiota differed significantly across dairy species while sharing core microbiome consisting four species. By...
Little cherry virus 1 (LChV1, Velarivirus, Closteroviridae) is a widespread pathogen of sweet or sour and other Prunus species, which exhibits high genetic diversity lacks putative efficient transmission vector. Thus far, four distinct phylogenetic clusters LChV1 have been described, including isolates from different species. The recent application throughput sequencing (HTS) technologies in fruit tree virology has facilitated the acquisition new viral genomes study diversity. In present...
In declining birches (Betula sp.) from different European stands affected by the "birch leaf-roll disease" (BLRD) a novel virus is identified means of RNA-Seq virome analysis. The represents new member in genus Badnavirus, family Caulimoviridae, tentatively named Birch leaf roll-associated (BLRaV) and it first badnavirus found to infect birch. Complete genome sequences (7,862–7,864 nucleotides) three viral isolates Finnish German origin have been determined. show typical organization with...
Despite the generalized use of cultivars carrying rym4 resistance gene, impact viral mosaic diseases on winter barleys increased in recent years France. This change could reflect i) an prevalence resistance-breaking pathotype Barley yellow virus Y (BaYMV-2), ii) emergence pathotypes mild (BaMMV) or iii) other viruses. A study was undertaken to determine distribution and diversity viruses causing disease. collection 241 symptomatic leaf samples from susceptible, rym5 varieties gathered 117...
The etiology and main pathways for the spread of lavender decline, an infectious disease affecting French production since 1960s, have remained unclear, hampering development efficient control strategies. An extensive survey fields led to conclusion that “ Candidatus Phytoplasma solani” was chronically infecting declining lavenders associated with large populations Hyalesthes obsoletus planthoppers living on crop itself. Lavender appeared be reservoir host lavender-specific phytoplasma...
Abstract Plants are colonized by diverse fungal and viral communities that influence their growth survival as well ecosystem functioning. Viruses interact with both plants the fungi they host. Our understanding of plant–fungi–virus interactions is very limited, especially in wild plants. Combining metagenomic culturomic approaches, we assessed richness, diversity, composition leaf‐associated from pools herbaceous representative four sites corresponding to cultivated or natural ecosystems. We...
Complete genomic sequences of Artichoke latent virus (ArLV) have been obtained by classical or high-throughput sequencing for an ArLV isolate from Italy (ITBr05) and two isolates France (FR37 FR50). The genome is 8,278 to 8,291 nucleotides long has a organization comparable with that Chinese yam necrotic mosaic (CYNMV), the only macluravirus fully sequenced date. cleavage sites viral polyprotein tentatively identified comparison CYNMV, confirming macluraviruses are characterized absence P1...
With the increased use of high-throughput sequencing methods, new viruses infecting
Streptococcus thermophilus is of major importance for cheese manufacturing to ensure rapid acidification; however, studies indicate that intensive use commercial strains leads the loss typical characteristics products. To strengthen link between product and its geographical area improve sensory qualities cheeses, cheese-producing protected designations origin (PDO) are increasingly interested in development specific autochthonous starter cultures. The present study therefore investigating...
In dairy cattle, teat disinfection at the end of milking is commonly applied to limit colonization milk by pathogenic microorganisms via canal. The post-milking products used can irritate skin and unbalance its microbial population. Our study aimed assess impact different on balance communities cows in their milk. For 12 weeks each operation, three groups seven Holstein pasture received either a chlorhexidine gluconate-based product (G) or hydrocolloidal water-in-oil emulsion (A), no (C)....