Jean‐Marc Aury
A5070886202- Genomics and Phylogenetic Studies
- Microbial Community Ecology and Physiology
- Chromosomal and Genetic Variations
- Protist diversity and phylogeny
- Environmental DNA in Biodiversity Studies
- Genetic diversity and population structure
- Plant Disease Resistance and Genetics
- Insect symbiosis and bacterial influences
- Marine and coastal plant biology
- Plant Pathogens and Fungal Diseases
- Banana Cultivation and Research
- Plant Virus Research Studies
- Legume Nitrogen Fixing Symbiosis
- Coral and Marine Ecosystems Studies
- RNA and protein synthesis mechanisms
- Neurobiology and Insect Physiology Research
- Identification and Quantification in Food
- Nematode management and characterization studies
- Horticultural and Viticultural Research
- Molecular Biology Techniques and Applications
- Yeasts and Rust Fungi Studies
- Toxin Mechanisms and Immunotoxins
- Insect Resistance and Genetics
- Cocoa and Sweet Potato Agronomy
- Plant Pathogens and Resistance
Commissariat à l'Énergie Atomique et aux Énergies Alternatives
2016-2025
Genoscope
2016-2025
CEA Paris-Saclay
2018-2025
Université Paris-Saclay
2018-2025
Centre National de la Recherche Scientifique
2011-2025
The University of Melbourne
2024
Melbourne Bioinformatics
2024
Université d'Évry Val-d'Essonne
2004-2022
University of Göttingen
2021-2022
Direction de la Recherche Fondamentale
2021
The analysis of the first plant genomes provided unexpected evidence for genome duplication events in species that had previously been considered as true diploids on basis their genetics. These polyploidization may have important consequences evolution, particular radiation and adaptation modulation functional capacities. Here we report a high-quality draft sequence grapevine (Vitis vinifera) obtained from highly homozygous genotype. is fourth one produced so far flowering plants, second...
Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and oleracea, followed chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms high gene content. We examined consequences its recent duplication. The constituent An Cn subgenomes are engaged in subtle structural, functional, epigenetic cross-talk, abundant homeologous...
Marine plankton support global biological and geochemical processes. Surveys of their biodiversity have hitherto been geographically restricted not accounted for the full range size. We assessed eukaryotic diversity from 334 size-fractionated photic-zone communities collected across tropical temperate oceans during circumglobal Tara Oceans expedition. analyzed 18S ribosomal DNA sequences intermediate plankton-size spectrum smallest unicellular eukaryotes (protists, >0.8 micrometers) to small...
Plant-parasitic nematodes are major agricultural pests worldwide and novel approaches to control them sorely needed. We report the draft genome sequence of root-knot nematode Meloidogyne incognita, a biotrophic parasite many crops, including tomato, cotton coffee. Most assembled this asexually reproducing nematode, totaling 86 Mb, exists in pairs homologous but divergent segments. This suggests that ancient allelic regions M. incognita evolving toward effective haploidy, permitting new...
Bananas (Musa spp.), including dessert and cooking types, are giant perennial monocotyledonous herbs of the order Zingiberales, a sister group to well-studied Poales, which include cereals. vital for food security in many tropical subtropical countries most popular fruit industrialized countries. The Musa domestication process started some 7,000 years ago Southeast Asia. It involved hybridizations between diverse species subspecies, fostered by human migrations, selection diploid triploid...
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...
Vertebrate evolution has been shaped by several rounds of whole-genome duplications (WGDs) that are often suggested to be associated with adaptive radiations and evolutionary innovations. Due an additional round WGD, the rainbow trout genome offers a unique opportunity investigate early fate duplicated vertebrate genome. Here we show after 100 million years two ancestral subgenomes have remained extremely collinear, despite loss half protein-coding genes, mostly through pseudogenization. In...
The genome of Ectocarpus, a model organism for brown algae, has been sequenced. Brown algae are complex photosynthetic organisms that have adapted to life in rocky coastal environments. Genome analysis sheds light on this adaptation and reveals an extended set light-harvesting pigment biosynthesis genes novel metabolic processes such as halide metabolism. Comparative genomic analyses highlight the likely importance family receptor kinases related molecules evolution multicellularity plants,...
The duplication of entire genomes has long been recognized as having great potential for evolutionary novelties, but the mechanisms underlying their resolution through gene loss are poorly understood. Here we show that in unicellular eukaryote Paramecium tetraurelia, a ciliate, most nearly 40,000 genes arose at least three successive whole-genome duplications. Phylogenetic analysis indicates recent coincides with an explosion speciation events gave rise to P. aurelia complex 15 sibling...
Xavier Argout and colleagues report the draft genome of Theobroma cacao, tropical crop that is source chocolate. The sequence assembly covers approximately 80% genome. We sequenced assembled an economically important tropical-fruit tree This corresponds to 76% estimated size contains almost all previously described genes, with 82% these genes anchored on 10 T. cacao chromosomes. Analysis this information highlighted specific expansion some gene families during evolution, for example,...
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...
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...
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...
We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel's original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes suggest a major role repetitive elements in pea evolution. Compared to other sequenced Leguminosae genomes, shows intense gene dynamics, most likely associated with size expansion when Fabeae diverged from its sister tribes. During Pisum evolution, translocation transposition differentially...
Quantifying the impact of heritable epigenetic variation on complex traits is an emerging challenge in population genetics. Here, we analyze a isogenic Arabidopsis lines that segregate experimentally induced DNA methylation changes at hundreds regions across genome. We demonstrate several these differentially methylated (DMRs) act as bona fide quantitative trait loci (QTL(epi)), accounting for 60 to 90% heritability two traits, flowering time and primary root length. These QTL(epi) are...
Roses have high cultural and economic importance as ornamental plants in the perfume industry. We report rose whole-genome sequencing assembly resequencing of major genotypes that contributed to domestication. generated a homozygous genotype from heterozygous diploid modern progenitor, Rosa chinensis 'Old Blush'. Using single-molecule real-time meta-assembly approach, we obtained one most comprehensive plant genomes date. Diversity analyses highlighted mosaic origin 'La France', first...
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...
Teleost fishes provide the first unambiguous support for ancient whole-genome duplication in an animal lineage. Studies yeast or plants have shown that effects of such duplications can be mediated by a complex pattern gene retention and changes evolutionary pressure. To explore patterns fishes, we determined phylogenetic analysis origin 675 Tetraodon duplicated genes assigned to chromosomes, using additional data from other species actinopterygian fishes. The subset genes, which was retained...
The genome of the asexual rotifer Adineta vaga lacks homologous chromosomes; instead, its allelic regions are rearranged and sometimes found on same chromosome in a palindromic fashion, structure reminiscent primate Y other mitotic lineages such as cancer cells. Bdelloid rotifers thought to have persisted diversified asexually for millions years, which is odd because loss sexual reproduction widely considered be an evolutionary dead end metazoans. suspicion remained that they might engage...
While our knowledge about the roles of microbes and viruses in ocean has increased tremendously due to recent advances genomics metagenomics, research on marine microbial eukaryotes zooplankton benefited much less from these new technologies because their larger genomes, enormous diversity, largely unexplored physiologies. Here, we use a metatranscriptomics approach capture expressed genes open Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster...
Red seaweeds are key components of coastal ecosystems and economically important as food a source gelling agents, but their genes genomes have received little attention. Here we report the sequencing 105-Mbp genome florideophyte Chondrus crispus (Irish moss) annotation 9,606 genes. The features an unusual structure characterized by gene-dense regions surrounded repeat-rich dominated transposable elements. Despite its fairly large size, this shows typical compact genomes, e.g., on average...
Abstract Background The dung-inhabiting ascomycete fungus Podospora anserina is a model used to study various aspects of eukaryotic and fungal biology, such as ageing, prions sexual development. Results We present 10X draft sequence P. genome, linked the sequences large expressed tag collection. Similar higher eukaryotes, transcription/splicing machinery generates numerous non-conventional transcripts. Comparison genome orthologous gene set with one its close relatives, Neurospora crassa ,...
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...