Olivier Bouchez's research while affiliated with L’Institut national de la recherche agronomique (Toulouse) and other places
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Publications (252)
Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering and mortality and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones wit...
Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of...
Feed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relative low- (LRFI, more efficient) and high- (HRFI, less efficient) residual feed...
Despite still being a matter of debate, there is growing evidence that pollutant-induced epigenetic changes can be propagated across generations. Whereas such modifications could have long lasting effects on organisms and even on population, environmentally relevant data from long-term exposure combined with follow-up through multiple generations r...
Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering, mortality, and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with...
Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome...
Plant epigenetic regulations are involved in transposable element silencing, developmental processes and responses to the environment1–7. They often involve modifications of DNA methylation, particularly through the DEMETER (DME) demethylase family and RNA-dependent DNA methylation (RdDM)8. Root nodules host rhizobia that can fix atmospheric nitrog...
Honey bee subspecies originate from specific geographic areas in Africa, Europe and the Middle East, and beekeepers interested in specific phenotypes have imported genetic material to regions outside of their original range for use either in pure lines or controlled crosses. Moreover, imported drones are present in the environment and mate naturall...
Plant diseases are an important threat to food production. While major pathogenicity determinants required for disease have been extensively studied, less is known on how pathogens thrive during host colonization, especially at early infection stages. Here, we used randomly barcoded‐transposon insertion site sequencing (RB‐TnSeq) to perform a genom...
Background
Viral Nervous Necrosis (VNN) is major disease affecting of European sea bass. Understanding the biological mechanisms that underlie VNN resistance is thus important for the welfare of farmed fish and the sustainability of production systems. This study aimed at identifying key genomic regions and genes that determine VNN resistance in se...
Hundreds of cytotoxic natural or synthetic lipidic compounds contain chiral alkynylcarbinol motifs, but the mechanism of action of those potential therapeutic agents remains unknown. Using a genetic screen in haploid human cells, we discovered that the enantiospecific cytotoxicity of numerous terminal alkynylcarbinols, including the highly cytotoxi...
Vanilla planifolia, the species cultivated to produce one of the world’s most popular flavors, is highly prone to partial genome endoreplication (PE) which leads to highly unbalanced DNA content in cells. We report here first molecular evidence of PE at chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. pla...
Accurate species phylogenies are a prerequisite for evolutionary research. Teleosts are by far the largest and the most diversified group of extant vertebrates, but relationships among the three oldest lineages of extant teleosts remain unresolved. Based on seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the to...
Evolution of sex determination (SD) in teleosts is amazingly dynamic, as reflected by the variety of different master sex‐determining genes identified. Pangasiids are economically important catfishes in South‐Asian countries, but little is known about their SD system. Here, we generated novel genomic resources for 12 Pangasiids and characterized th...
Plant diseases are an important threat to food production. While major pathogenicity determinants required for disease have been extensively studied, less is known on how pathogens thrive during host colonization especially at early infection stages. Here, we used randomly barcoded-transposon insertion site sequencing (RB-TnSeq) to perform a genome...
The evolution of sex determination (SD) mechanisms in teleost fishes is amazingly dynamic, as reflected by the variety of different master sex-determining genes identified, even sometimes among closely related species. Pangasiids are a group of economically important catfishes in many South-Asian countries, but little is known about their sex deter...
Background
In the early 20th century, Cuban farmers imported Charolais cattle (CHFR) directly from France. These animals are now known as Chacuba (CHCU) and have become adapted to the rough environmental tropical conditions in Cuba. These conditions include long periods of drought and food shortage with extreme temperatures that European taurine ca...
Mycobacterium tuberculosis , the main causative agent of human tuberculosis, is transmitted from person to person via small droplets containing very few bacteria. Optimizing the chance to seed in the lungs is therefore a major adaptation to favor survival and dissemination in the human population. Here we used TnSeq to identify genes important for...
Honey bee subspecies originate from specific geographic areas in Africa, Europe and the Middle East. The interest of beekeepers in specific phenotypes has led them to import subspecies to regions outside of their original range. The resulting admixture complicates population genetics analyses and populations stratification can be a major problem fo...
Hundreds of cytotoxic natural or synthetic lipidic compounds contain chiral alkynylcarbinol motifs, but the mechanism of action of those potential therapeutic agents remains unknown. Using a genetic screen in haploid human cells, we discovered that the enantiospecific cytotoxicity of numerous terminal alkynylcarbinols, including the highly cytotoxi...
G-quadruplexes (G4) are non-canonical DNA structures found in the genome of most species including human. Small molecules stabilizing these structures, called G4 ligands, have been identified and, for some of them, shown to induce cytotoxic DNA double-strand breaks. Through the use of an unbiased genetic approach, we identify here topoisomerase 2-a...
Among crop fruit trees, the apricot (Prunus armeniaca) provides an excellent model to study divergence and adaptation processes. Here, we obtain nearly 600 Armeniaca apricot genomes and four high-quality assemblies anchored on genetic maps. Chinese and European apricots form two differentiated gene pools with high genetic diversity, resulting from...
In addition to their common usages to study gene expression, RNA-seq data accumulated over the last 10 years are a yet-unexploited resource of SNPs in numerous individuals from different populations. SNP detection by RNA-seq is particularly interesting for livestock species since whole genome sequencing is expensive and exome sequencing tools are u...
The identification of quantitative trait loci (QTL) through genome‐wide association studies (GWAS) is a powerful method for unravelling the genetic background of selected traits and improving early‐stage predictions. In honey bees (Apis mellifera), past genetic analyses have particularly focused on individual queens and workers. In this study, we u...
Background:
The reconstruction of metagenome-assembled genomes (MAGs) has emerged as a powerful approach for combining the taxonomic and functional content of microbial populations.
Aim:
To use this new approach to highlight mechanisms linking gut microbiota to NAFLD severity METHODS: Stool samples were collected from 96 NAFLD patients on the da...
Background
The impact of individual genetic and genomic variations on immune responses is an emerging lever investigated in vaccination strategies. In our study, we used genetic and pre-vaccination blood transcriptomic data to study vaccine effectiveness in pigs.
Results
A cohort of 182 Large White pigs was vaccinated against Mycoplasma hyopneumon...
Characterizing the genetic diversity of populations allows to better understand their demographic history and their adaptation to selective pressures. Social insects, such as honeybee, live in colonies which ultimately are the relevant evolutionary and selective units for such species. However, performing large scale genetic analyses of honeybees i...
The evolutionary and adaptive potential of a pathogen is a key determinant for successful host colonization and proliferation, but remains poorly known for most of the pathogens. Here, we used experimental evolution combined with phenotyping, genomics and transcriptomics to estimate the adaptive potential of the bacterial plant pathogen Ralstonia s...
Discovered in the 1960s, Meloidogyne graminicola is a root-knot nematode species considered as a major threat to rice production. Yet, its origin, genomic structure, and intraspecific diversity are poorly understood. So far, such studies have been limited by the unavailability of a sufficiently complete and well-assembled genome. In this study, usi...
Rainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY. Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenoty...
Phenotypic plasticity is a key component of the ability of organisms to respond to changing environmental conditions. In this study, we aimed to study the establishment of DNA methylation marks in response to an environmental stress in rainbow trout and to assess whether these marks depend on the genetic background. The environmental stress chosen...
Photosynthetic microbial mats are stable, self-supported communities. Due to their coastal localization, these mats are frequently exposed to hydrocarbon contamination and are able to grow on it. To decipher how this contamination disturbs the functioning of microbial mats, we compared two mats: a contaminated mat exposed to chronic petroleum conta...
Mating types are self-incompatibility systems that promote outcrossing in plants, fungi, and oomycetes. Mating-type genes have been widely studied in plants and fungi but have yet to be identified in oomycetes, eukaryotic organisms closely related to brown algae that cause many destructive animal and plant diseases. We identified the mating-type lo...
Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we investigate mous...
Early introduction of a nutritional substrate is a promising biomimetic strategy for controlling the implantation of the microbiota and preserving the health of young animals. In this study, we provided experimental solid substrate in a gel form to stimulate suckling rabbits' intake and to investigate its effects on microbiota implantation and colo...
Rainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY . Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenot...
Understanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstruc...
Mating types are self-incompatibility systems that promote outcrossing in plants, fungi and oomycetes. Mating-type genes have been widely studied in plants and fungi, but have yet to be identified in oomycetes, eukaryotic organisms closely related to brown algae that cause many destructive animal and plant diseases. We identified the mating-type lo...
Some species of parasitic wasps have domesticated viral machineries to deliver immunosuppressive factors to their hosts. Up to now, all described cases fall into the Ichneumonoidea superfamily, which only represents around 10% of hymenoptera diversity, raising the question of whether such domestication occurred outside this clade. Furthermore, the...
G-quadruplexes (G4), non-canonical DNA structures, are involved in several essential processes. Stabilization of G4 structures by small compounds (G4 ligands) affects almost all DNA transactions, including telomere maintenance and genomic stability. Here, thanks to a powerful and unbiased genetic approach, we identify topoisomerase 2-alpha (TOP2A)...
Rhizobia are soil bacteria from unrelated genera able to form a mutualistic relationship with legumes. Bacteria induce the formation of root nodules, invade nodule cells, and fix nitrogen to the benefit of the plant. Rhizobial lineages emerged from the horizontal transfer of essential symbiotic genes followed by genome remodeling to activate and/or...
The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behaviour, morphology or adaptation through comparative genomic approa...
Yellow perch, Perca flavescens, is an ecologically and economically important species native to a large portion of the northern United States and southern Canada and is also a promising candidate species for aquaculture. No yellow perch reference genome, however, has been available to facilitate improvements in both fisheries and aquaculture manage...
Characterising the genetic diversity of populations allows to better understand their demographic history and their adaptation to selective pressures. In honey bees, this characterisation is facilitated by a relatively small genome size, but is hindered by the fact that often the unit of observation and sampling is the colony rather than a single i...
Pythium oligandrum is a soil born free living oomycete able to parasitize fungi and oomycetes prey, including important plant and animals pathogens. Pythium oligandrum can colonize endophytically the root tissues of diverse plants where it induces plant defences. Here we report the first long-read genome sequencing of a P. oligandrum strain sequenc...
Transcriptomic and proteomic analyses were performed on three replicates of tomato fruit pericarp samples collected at nine developmental stages, each replicate resulting from the pooling of at least 15 fruits. For transcriptome analysis, Illumina-sequenced libraries were mapped on the tomato genome with the aim to obtain absolute quantification of...
In third generation sequencing, the production of quality data requires the selection of molecules longer than ~20 kbp, but the size selection threshold of most purification technologies is smaller than this target. Here, we describe a technology operated in a capillary with an accordable selection threshold in the range of 3 to 40 kbp controlled b...
Like many other species, the duck genome has been sequenced thanks to the technological breakthrough provided by the emergence of Next Generation Sequencing (NGS). The resulting de novo assemblies are however made of thousands of scattered scaffolds. To achieve chromosome-scale contiguity, long-range intermediate genome maps remain indispensable. R...
Gammarids are amphipods found worldwide distributed in fresh and marine waters. They play an important role in aquatic ecosystems and are well established sentinel species in ecotoxicology. In this study, we sequenced the transcriptomes of a male individual and a female individual for seven different taxonomic groups belonging to the two genera Gam...
Streptomycetes are soil-dwelling filamentous actinobacteria and represent a prominent bacterial clade inside the plant root microbiota. The ability of streptomycetes to produce a broad spectrum of antifungal metabolites suggests that these bacteria could be used to manage plant diseases. Here we describe the identification of a soil Streptomyces st...
Characterising the genetic diversity of populations allows to better understand their demographic history and their adaptation to selective pressures. In honey bees, this characterisation is facilitated by a relatively small genome size, but is hindered by the fact that often the unit of observation and sampling is the colony rather than a single i...
A bstract
Mouse lemurs ( Microcebus ) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic explosion has prompted understandable concern that there has been substantial oversplitting in the mouse lemur clade. Here, we tak...
Low temperature stress affects growth and development in pea (Pisum sativum L.) and decreases yield. In this study, RNA sequencing time series analyses performed on lines, Champagne frost-tolerant and Térèse frost-sensitive, during a low temperature treatment versus a control condition, led us to identify 4981 differentially expressed genes. Thanks...
Background: Yellow perch, Perca flavescens, is an ecologically and commercially important species native to a large portion of the northern United States and southern Canada. It is also a promising candidate species for aquaculture. No yellow perch reference genome, however, has been available to facilitate improvements in both fisheries and aquacu...
Plasmopara viticola is a biotrophic oomycete pathogen causing grapevine downy mildew. We characterized the repertoire of P. viticola effector proteins which may be translocated into plants to support the disease. We found several secreted proteins that contain canonical dEER motifs and conserved WY-domains but lack the characteristic RXLR motif rep...
The Venturia genus comprises fungal species that are pathogens on Rosaceae host plants, including V. inaequalis and V. asperata on apple, V. aucupariae on sorbus and V. pirina on pear. Although the genetic structure of V. inaequalis populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood....
Understanding how new species arise through the progressive establishment of reproductive isolation barriers between diverging populations is a major goal in Evolutionary Biology. One important result of speciation genomics studies is that the genomic regions involved in reproductive isolation frequently harbor anciently diverged haplotypes that pr...
O. cumana (the sunflower broomrape) is an obligate parasitic plant that needs to fix to the sunflower roots for collecting water and nutrients from sunflower. For sunflower physiology, O. cumana can be considered as a new sink that leads to yield losses. During the early stages of the interaction, the connection of O. cumana to the vascular system...
This study aimed to evaluate how the feeding strategy of rabbit kits at the onset of solid feed intake could affect ecological diversity and co-occurrence patterns of the cecal bacterial community. From birth to 18 days of age kits were exclusively milk-fed, and between 18 and 35 days the young rabbits also had access to solid feed. After weaning a...
Seeds are involved in the vertical transmission of microorganisms in plants and act as reservoirs for the plant microbiome. They could serve as carriers of pathogens, making the study of microbial interactions on seeds important in the emergence of plant diseases. We studied the influence of biological disturbances caused by seed transmission of tw...
Protein synthesis and degradation are essential processes that regulate cell status. Because labeling in bulky organs, such as fruits, is difficult, we developed a modeling approach to study protein turnover at the global scale in developing tomato (Solanum lycopersicum) fruit. Quantitative data were collected for transcripts and proteins during fr...