A5085749572- Horticultural and Viticultural Research
- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Plant Pathogenic Bacteria Studies
- Plant Virus Research Studies
- Banana Cultivation and Research
- Coffee research and impacts
- Cocoa and Sweet Potato Agronomy
- Legume Nitrogen Fixing Symbiosis
- Chromosomal and Genetic Variations
- Wheat and Barley Genetics and Pathology
- Phytoplasmas and Hemiptera pathogens
- Plant Disease Resistance and Genetics
- Plant-Microbe Interactions and Immunity
- Gene expression and cancer classification
- Fermentation and Sensory Analysis
- Genetics, Bioinformatics, and Biomedical Research
- CRISPR and Genetic Engineering
- Nematode management and characterization studies
- Cassava research and cyanide
- Plant biochemistry and biosynthesis
- Plant tissue culture and regeneration
- Plant Physiology and Cultivation Studies
- Rice Cultivation and Yield Improvement
- Scientific Computing and Data Management
Institut Pasteur
2022-2024
Institut Pasteur de la Guadeloupe
2022-2023
Université de Montpellier
2013-2023
Institut de Recherche pour le Développement
2013-2023
Institut Agro Montpellier
2010-2023
Centre de Coopération Internationale en Recherche Agronomique pour le Développement
2014-2023
Centre Occitanie-Montpellier
2021-2023
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2020-2023
Genetic Improvement and Adaptation of Mediterranean and Tropical Plants
2011-2023
Institut Français de Bioinformatique
2022
Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, phylogenetic reconstruction graphical representation inferred tree. The Phylogeny.fr platform transparently chains programs automatically perform these tasks. It is primarily designed for biologists with no experience phylogeny, but can also meet needs specialists; first ones will find up-to-date tools chained a phylogeny pipeline...
Abstract Background The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality which can have significant impact on final interpretation study. There no single way constructing datasets suitable analysis, because this task intimately depends scientific question we want to address, Moreover, database mining softwares such as BLAST are routinely used searching not specifically optimized task. Results To fill gap, designed...
Coffee, tea, and chocolate converge Caffeine has evolved multiple times among plant species, but no one knows whether these events involved similar genes. Denoeud et al. sequenced the Coffea canephora (coffee) genome identified a conserved gene order (see Perspective by Zamir). Although this species underwent fewer duplications than related relevant caffeine genes experienced tandem that expanded their numbers within species. Scientists have seen independent expansions in distantly of tea...
Banana is one of the world's favorite fruits and most important crops for developing countries. The banana reference genome sequence (Musa acuminata) was recently released. Given taxonomic position Musa, completed genomic has particular comparative value to provide fresh insights about evolution monocotyledons. study been enhanced by a number tools resources that allows harnessing its sequence. First, we set up essential such as Community Annotation System, phylogenomics metabolic pathways....
As for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. In perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked agronomic traits variation. However, due the juvenile period of these establishing numerous highly recombinant populations high resolution mapping both costly time-consuming. Genome wide association studies in germplasm panels an alternative...
Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity grape. Clonal provided such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir 777 which all produce wines superior quality. The economic impact selection is therefore very high: since approx. 95% grapevines produced French nurseries originate from selection. In this study we provide first broad description polymorphism different a...
Transcription Activators-Like Effectors (TALEs) belong to a family of virulence proteins from the Xanthomonas genus bacterial plant pathogens that are translocated into cell. In nucleus, TALEs act as transcription factors inducing expression susceptibility genes. A code for TALE-DNA binding specificity and high-resolution three-dimensional structures complexes were recently reported. Accurate prediction TAL Effector Binding Elements (EBEs) is essential elucidate biological functions many...
Both hybridization and allopolyploidization generate novel phenotypes by conciliating divergent genomes regulatory networks in the same cellular context.To understand rewiring of gene expression hybrids, total 21,025 genes allele-specific over 11,000 were quantified interspecific hybrids their parental species, Coffea canephora eugenioides using RNA-seq technology.Between cis-and trans-regulatory divergences affected around 32% 35% analyzed genes, respectively, with nearly 17% them showing...
High-throughput re-sequencing, new genotyping technologies and the availability of reference genomes allow extensive characterization Single Nucleotide Polymorphisms (SNPs) insertion/deletion events (indels) in many plant species. The rapidly increasing amount re-sequencing data generated by large-scale genetic diversity projects requires development integrated bioinformatics tools able to efficiently manage, analyze, combine these with genome structure external data. In this context, we...
Summary Polyploidy has occurred throughout the evolutionary history of plants and led to diversification plant ecological adaptation. Functional plasticity duplicate genes is believed play a major role in environmental adaptation polyploids. In this context, we characterized genome‐wide homoeologous gene expression Coffea arabica , recent allopolyploid combining two subgenomes that derive from closely related diploid species, investigated its variation response changing environment. The...
SNiPlay is a web-based tool for detection, management and analysis of genetic variants including both single nucleotide polymorphisms (SNPs) InDels. Version 3 now extends functionalities in order to easily manage exploit SNPs derived from next generation sequencing technologies, such as GBS (genotyping by sequencing), WGRS (whole gre-sequencing) RNA-Seq technologies. Based on the standard VCF (variant call format) format, application offers an intuitive interface filtering comparing using...
Background and Aims The root-knot nematode Meloidogyne graminicola is responsible for production losses in rice (Oryza sativa) Asia Latin America. accession TOG5681 of African rice, O. glaberrima, presents improved resistance to several biotic abiotic factors, including nematodes. aim this study was assess the cytological molecular mechanisms underlying accession. Methods Penetration development M. susceptible sativa genotype 'Nipponbare' were compared by microscopic observation infected...
Abstract Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent Nod factors and infection threads. They are also distinctive in developing root stem nodules with photosynthetic bradyrhizobia. Despite the significance these features, their understanding remains limited. To overcome such limitations, we conduct genetic studies nodulation evenia , supported by development genome sequence for A. transcriptomic...
Abstract Motivation As pan-genome approaches are largely employed for bacterial comparative genomics and evolution analyses, but still difficult to be carried out by non-bioinformatician biologists, there is a need an innovative tool facilitating the exploration of pan-genomes. Results PanExplorer web application providing various genomic analyses reports, giving intuitive views that enable better understanding example, we produced 121 Anaplasmataceae strains (including 30 Ehrlichia, 15...
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,...
Summary Root‐knot nematodes secrete proteinaceous effectors into plant tissues to facilitate infection by suppressing host defences and reprogramming the metabolism their benefit. Meloidogyne graminicola is a major pest of rice ( Oryza sativa ) in Asia Latin America, causing important crop losses. The goal this study was identify M. pathogenicity genes expressed during plant–nematode interaction. Using dual RNA‐sequencing (RNA‐seq) strategy, we generated transcriptomic data samples covering...
Summary Allopolyploidization is widespread and has played a major role in flowering plant diversification. Genomic changes are common consequences of allopolyploidization, but their mechanisms occurrence dynamics over time still poorly understood. Coffea arabica , recently formed allotetraploid, was chosen as model to investigate genetic allopolyploid using an approach that exploits next‐generation sequencing technologies. Genes affected by putative homoeolog loss were inferred comparing the...
Summary Quantitative trait loci ( QTL ) that confer broad‐spectrum resistance BSR ), or is effective against multiple and diverse plant pathogens, have been elusive targets of crop breeding programmes. Multiparent advanced generation intercross MAGIC populations, with their genetic composition high levels recombination, are potential resources for the identification . In this study, a rice population was used to map conferring two major diseases, bacterial leaf streak BLS blight BB caused by...
Abstract Background and Aims Reticulate evolution, coupled with reproductive features limiting further interspecific recombinations, results in admixed mosaics of large genomic fragments from the ancestral taxa. Whole-genome sequencing (WGS) data are powerful tools to decipher such complex genomes but still too costly be used for populations. The aim this work was develop an approach infer phylogenomic structures diploid, triploid tetraploid individuals reduced genome complexity libraries....
Guadeloupe (French West Indies), a Caribbean island, is an ideal place to study the reservoirs of Klebsiella pneumoniae species complex (KpSC) and identify routes transmission between human nonhuman sources due its insularity, small population size, area. Here, we report analysis 590 biological samples, 546 KpSC isolates, 331 genome sequences collected January 2018 May 2019. The appears be common whatever source. Extended-spectrum-β-lactamase (ESBL)-producing isolates (21.4%) belonged K....
Introduction Free-living amoebae of the Naegleria genus belong to major protist clade Heterolobosea and are ubiquitously distributed in soil freshwater habitats. Of 47 species described, N. fowleri is only one being pathogenic humans, causing a rare but fulminant primary amoebic meningoencephalitis. Some genome sequences publicly available, genetic basis for diversity ability thrive diverse environments (including human brain) remains unclear. Methods Herein, we constructed high-quality...
Cotton (Gossypium) fiber is the most prevalent natural product used in textile industry. The two major cultivated species, G. hirsutum (Gh) and barbadense (Gb), are allotetraploids with contrasting quality properties. To better understand molecular basis for their differences, EST pyrosequencing was to document transcriptomes at key development stages, 10 days post anthesis (dpa), representing peak of elongation, 22 dpa, transition secondary cell wall synthesis. 617,000 high reads (89% total...
Polyploidy impacts the diversity of plant species, giving rise to novel phenotypes and leading ecological diversification. In order observe adaptive evolutionary capacities polyploids, we compared growth, primary metabolism transcriptomic expression level in leaves newly formed allotetraploid Coffea arabica species with its two diploid parental ( eugenioides canephora ), exposed four thermal regimes (TRs; 18–14, 23–19, 28–24 33–29°C). The growth rate allopolyploid C. was similar that under...
Abstract Allopolyploidization is a biological process that has played major role in plant speciation and evolution. Genomic changes are common consequences of polyploidization, but their dynamics over time still poorly understood. Coffea arabica, recently formed allotetraploid, was chosen to study genetic accompany allopolyploid formation. Both RNA-seq DNA-seq data were generated from two genetically distant C. arabica accessions. structural variation investigated using canephora, one its...
It is now well documented that moonlight affects the life cycle of invertebrates, birds, reptiles, and mammals. The lunisolar tide also well-known to alter plant growth development. However, although plants are known be very photosensitive, few studies have been undertaken explore effect on physiology.Here for first time we report a massive transcriptional modification in Coffea arabica genes under full conditions, particularly at moon zenith 3 h later. Among 3387 deregulated found our...