Christophe Klopp

Christophe Klopp
French National Institute for Agriculture, Food, and Environment (INRAE) | INRAE · Mathématiques et Informatique Appliquées (MIA)

MS
Bio-informatic platform coordinator. Interested in genome assembly, phasing and annotation.

About

475
Publications
114,474
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Introduction
I'm currently working at the Department of Applied Mathematics and Informatics, French National Institute for Agricultural Research, leading a group of bioinformaticians (http://www.sigenae.fr) providing services to INRAE biologists working in animal genomics and taking part in the local bio-informatic platform (http://bioinfo.genotoul.fr/). We develop software packages, train biologists and take part in research projects.
Additional affiliations
May 2002 - present
French National Institute for Agriculture, Food, and Environment (INRAE)
Position
  • Bioinformatician

Publications

Publications (475)
Article
Full-text available
Background Dairy cattle breeds are populations of limited effective size, subject to recurrent outbreaks of recessive defects that are commonly studied using positional cloning. However, this strategy, based on the observation of animals with characteristic features, may overlook a number of conditions, such as immune or metabolic genetic disorders...
Article
Full-text available
The common bean (Phaseolus vulgaris L.) is a crucial legume crop and an ideal evolutionary model to study adaptive diversity in wild and domesticated populations. Here, we present a common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. It reveals ~234 Mb of additional sequences containing 6,905...
Preprint
Full-text available
Many plants interact symbiotically with arbuscular mycorrhizal (AM) fungi to enhance inorganic phosphorus uptake, and legumes also develop a nodule symbiosis with rhizobia for nitrogen acquisition. Establishment and functioning of both symbioses rely on a common plant signaling pathway activated by structurally related Myc- and Nod-factors. Recentl...
Article
Full-text available
Background The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera , often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing int...
Article
Full-text available
Background The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determina...
Article
Full-text available
Bovine mastitis remains a major disease in cattle world-wide. In the mammary gland, mammary epithelial cells (MEC) are sentinels equipped with receptors allowing them to detect and respond to the invasion by bacterial pathogens, in particular Escherichia coli . Lipopolysaccharide (LPS) is the major E. coli motif recognized by MEC through its intera...
Article
Full-text available
Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus;...
Poster
The poster is already online with a doi !
Poster
Full-text available
Understanding the evolution of wild species is crucial for developing effective population management strategies and predicting their future trajectories. In my doctoral research, we opted for genomics approaches to explore the demographic history of two iconic diadromous fishes: Anguilla anguilla (European eel) and Salmo salar (Atlantic salmon). W...
Article
Full-text available
Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specif...
Preprint
Full-text available
Background: Plant cell walls are the main carbon sources for ruminal bacteria, which have evolved to produce sophisticated multi-functional enzyme cocktails in response to the structural diversity of lignocelulloses. Since a large proportion of ruminal bacteria are not yet cultured, we developed a high-throughput activity-based metagenomic approach...
Preprint
Full-text available
The great pond snail Lymnaea stagnalis has served as a model organism for over a century in diverse disciplines such as neurophysiology, evolution, ecotoxicology and developmental biology. To support both established uses and newly emerging research interests we have performed whole genome sequencing (~ 176 x depth), assembly and annotation of a si...
Article
Full-text available
Background Venoms have evolved independently over a hundred times in the animal kingdom to deter predators and/or subdue prey. Venoms are cocktails of various secreted toxins, whose origin and diversification provide an appealing system for evolutionary researchers. Previous studies of the ant venom of Tetramorium bicarinatum revealed several Myrmi...
Preprint
Full-text available
Background The actual honey bee reference genome, HAv3.1, was produced from a commercial line sample, thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing inter...
Article
Full-text available
Legumes establish symbiotic interactions with nitrogen-fixing rhizobia that are accomodated in root-derived organs known as nodules. Rhizobial recognition triggers a plant symbiotic signalling pathway that activates two coordinated processes: infection and nodule organogenesis. How these processes are orchestrated in legume species utilizing interc...
Preprint
Full-text available
The common bean (Phaseolus vulgaris L.) is an important grain legume crop [1,2] whose life history offers an ideal evolutionary model to identify adaptive variants suitable for breeding programs [3]. Here we present the first common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. We found ~243 M...
Article
Full-text available
Background The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many o...
Preprint
Full-text available
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems...
Preprint
Full-text available
The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems...
Preprint
Full-text available
Most vertebrates develop separate females and males, where sex is determined by repeatedly-evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master gene is known in >8650 species, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs...
Preprint
Full-text available
We present a data-mining framework designed to detect recessive defects in livestock that have been previously missed due to a lack of specific signs, incomplete penetrance, or incomplete linkage disequilibrium. This approach leverages the massive data generated by genomic selection. Its basic principle is to compare the observed and expected numbe...
Preprint
Full-text available
Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specif...
Article
Full-text available
The Creole cattle from Guadeloupe (GUA) are well adapted to the tropical environment. Its admixed genome likely played an important role in such adaptation. Here, we sought to detect genomic signatures of selection in the GUA genome. For this purpose, we sequenced 23 GUA individuals and combined our data with sequenced genomes of 99 animals represe...
Preprint
Full-text available
A bstract Cyathostomins are a complex of 50 intestinal parasite species infecting horses and wild equids. The massive administration of modern anthelmintic drugs has increased their relative abundance in horse helminth communities and selected drug-resistant isolates worldwide. Cylicocyclus nassatus is the most prevalent and the most abundant speci...
Poster
Full-text available
Figure 4: Linkage disequilibrium across four chromosomes in the populations of the white gum complex. Pairwise estimates of LD decay were obtained using 20,000 markers anchored to the phased Eucalyptus gunnii reference genome assembly (maternal). Different coloured markers indicate average LD within different populations as computed across 2 MB sli...
Preprint
Full-text available
Background. The red junglefowl, the wild progenitor of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, man...
Article
Full-text available
Inspired by the production of reference data sets in the Genome in a Bottle project, we sequenced one Charolais heifer with different technologies: Illumina paired-end, Oxford Nanopore, Pacific Biosciences (HiFi and CLR), 10X Genomics linked-reads, and Hi-C. In order to generate haplotypic assemblies, we also sequenced both parents with short reads...
Preprint
Full-text available
Bovine mastitis remains a major disease in cattle world-wide. In the mammary gland, epithelial cells are sentinels equipped with receptors allowing them to detect and respond to the invasion by bacterial pathogens, in particular Escherichia coli . Lipopolysaccharide (LPS) is the major E. coli motif recognized by MEC through its interaction with the...
Preprint
Full-text available
Bovine mastitis remains a major disease in cattle world-wide. In the mammary gland, epithelial cells are sentinels equipped with receptors allowing them to detect and respond to the invasion by bacterial pathogens, in particular Escherichia coli . Lipopolysaccharide (LPS) is the major E. coli motif recognized by MEC through its interaction with the...
Article
Full-text available
Candida lusitaniae is an emerging opportunistic pathogenic yeast capable of shifting from yeast to pseudohyphae form, and it is one of the few Candida species with the ability to reproduce sexually. In this study, we showed that a dpp3Δ mutant, inactivated for a putative pyrophosphatase, is impaired in cell separation, pseudohyphal growth and matin...
Article
Diffuse pollution of the environment by pesticides has become a major soil threat to non-target organisms, such as earthworms for which declines have been reported. However some endogeic species are still abundant and persist in intensively cultivated fields, suggesting they become tolerant to long-term anthropogenic pressure. We thus considered th...
Article
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...
Article
Full-text available
The chicken continues to hold its position as a leading model organism within many areas of research, as well as a being major source of protein for human consumption. The First Report on Chicken Genes and Chromosomes [Schmid et al., 2000], which was published in 2000, was the brainchild of the late, and sadly missed, Prof Michael Schmid of the Uni...
Preprint
Admixture is an evolutionary process that enables short-term adaptation. The Creole cattle from Guadeloupe is a tropically adapted breed. Its three-way admixture and long-term isolation offer a unique opportunity for understanding the genetic determinants of adaptive admixture in livestock. Here, we sequenced 23 Creole cattle from Guadeloupe (GUA)...
Article
Full-text available
This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. Abstract The deep-sea corals Dendrophyllia ramea and Dendrophyllia...
Article
Among ants, Myrmicinae represents the most speciose subfamily. The venom composition previously described for these social insects is extremely variable, with alkaloids predominant in some genera while, conversely, proteomics studies have revealed that some myrmicine ant venoms are peptide-rich. Using integrated transcriptomic and proteomic approac...
Article
Full-text available
Unraveling the origin of molecular pathways underlying the evolution of adaptive traits is essential for understanding how new lineages emerge, including the relative contribution of conserved ancestral traits and newly evolved derived traits. Here, we investigated the evolutionary divergence of sex pheromone communication from moths (mostly noctur...
Article
Full-text available
Intensive research on nitrogen-fixing symbiosis in two model legumes has uncovered the molecular mechanisms whereby rhizobial Nod factors activate a plant symbiotic signaling pathway that controls infection and nodule organogenesis. By constrast, the so-called Nod-independent symbiosis found between Aeschynomene evenia and photosynthetic bradyrhizo...
Article
Full-text available
Since 2004, a tuberculosis surveillance protocol has been carried out in Aragon, thereby managing to detect all tuberculosis outbreaks that take place in the community. The largest outbreak was caused by a strain named Mycobacterium tuberculosis Zaragoza (MtZ), causing 242 cases as of 2020. The main objective of this work was to analyze this outbre...
Article
Full-text available
DNA methylations play an important role in the biology of bacteria. Often associated with restriction modification (RM) systems, they are important drivers of bacterial evolution interfering in horizontal gene transfer events by providing a defence against foreign DNA invasion or by favouring genetic transfer through production of recombinogenic DN...
Article
Full-text available
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...
Article
Full-text available
The Pacific halibut (Hippoglossus stenolepis) is a key species in the North Pacific Ocean and Bering Sea ecosystems, where it also supports important fisheries. However, the lack of genomic resources limits our understanding of evolutionary, environmental and anthropogenic forces affecting key life history characteristics of Pacific halibut and pre...
Preprint
Full-text available
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...
Article
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...
Preprint
Full-text available
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...
Article
Full-text available
Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chrom...
Article
Full-text available
The earth harbors trillions of bacterial species adapted to very diverse ecosystems thanks to specific metabolic function acquisition. Most of the genes responsible for these functions belong to uncultured bacteria and are still to be discovered. Functional metagenomics based on activity screening is a classical way to retrieve these genes from mic...
Article
Sex chromosomes are generally derived from a pair of classical type-A chromosomes, and relatively few alternative models have been proposed up to now.¹,² B chromosomes (Bs) are supernumerary and dispensable chromosomes with non-Mendelian inheritance found in many plant and animal species³,⁴ that have often been considered as selfish genetic element...
Article
The aim of this study was to investigate the respective contribution of maternally-inherited mRNAs and proteins to egg molecular cargo and to its developmental competence in fish using pikeperch as a model. Our study provides novel insights into the understanding of type-specific roles of maternally-inherited molecules in fish. Here we show, for th...
Article
Full-text available
Chub mackerel Scomber japonicus and blue mackerel S. australasicus have become important aquaculture target species in Japan. For an efficient and stable aquaculture production of mackerels, it is desirable to work with a female-biased broodstock and thus to be able to manage precisely their sex ratio. As these two mackerel species do not have any...
Article
Full-text available
The neuropeptides involved in the regulation of reproduction in the Pacific oyster (Cras- sostrea gigas) are quite diverse. To investigate this diversity, a transcriptomic survey of the visceral ganglia (VG) was carried out over an annual reproductive cycle. RNA-seq data from 26 samples corresponding to VG at different stages of reproduction were d...
Article
Full-text available
Several hypotheses explain the prevalence of undifferentiated sex chromo- somes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-rev...
Article
Full-text available
Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the fraction usually studied is harbored in protein-coding regions because potential impacts on proteins are relatively easy to predict by popular tools such as the Variant Effect Predictor. These tools annotate variants independently without considering the potentia...
Article
Full-text available
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...
Preprint
DNA methylation plays an important role in the biology of bacteria. Often associated with restriction-modification (RM) systems, they also provide a defence against foreign DNA. Little is known regarding the methylome of the mycoplasma genus, which encompasses several pathogenic species with small genomes. Here, single molecule real-time (SMRT) and...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
Full-text available
Background In Metazoans, embryonic development relies on maternally-inherited mRNAs and proteins that are critical for early developmental success and known to play major roles at later stages, beyond zygotic genome activation. However, very poor concordance between transcript and protein levels in oocytes and embryos of vertebrates suggest that ma...
Article
Full-text available
Sturgeon immunity is relevant for basic evolutionary and applied research, including caviar-and meat-producing aquaculture, protection of wild sturgeons and their re-introduction through conservation aquaculture. Starting from a comprehensive overview of immune organs, we discuss pathways of innate and adaptive immune systems in a vertebrate phylog...
Article
The study of sex determination and sex chromosome organisation in non-model species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, Restriction Site-Associated DNA Sequencing (RAD-Seq) is being extensively applied to explo...