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

434
Publications
85,656
Reads
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12,613
Citations
Citations since 2016
236 Research Items
10080 Citations
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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 co-leading the local bio-informatic platform (http://bioinfo.genotoul.fr/). We develop software packages, train biologists and take part in research projects. @ChristopheKlopp
Additional affiliations
May 2002 - present
French National Institute for Agriculture, Food, and Environment (INRAE)
Position
  • Bioinformatician

Publications

Publications (434)
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...
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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
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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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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...
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...
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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...
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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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...
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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...
Article
Full-text available
Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bra-dyrhizobia. Despite the significance of these symbiotic features, their understanding...
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Full-text available
The understanding of the evolution of variable sex determination mechanisms across taxa requires comparative studies among closely related species. Following the fate of a known master sex-determining gene, we traced the evolution of sex determination in an entire teleost order (Esociformes). We discovered that the northern pike (Esox lucius) maste...
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Motivation Long-read sequencing technologies can be employed to detect and map DNA modifications at the nucleotide resolution on a genome-wide scale. However, published software packages neglect the integration of genomic annotation and comprehensive filtering when analyzing patterns of modified bases detected using Pacific Biosciences (PacBio) or...
Article
Le séquençage du génome entier est devenu abordable chez la poule. Le projet « Mille Génomes Gallus » a pour objectif de rassembler les séquences d’animaux du genre Gallus, produites dans des projets de recherche. L’intérêt est d’augmenter la puissance des analyses génomiques en augmentant le nombre de génomes comparés. Les applications possibles c...
Article
Nanometric revolution is underway, promising technical innovations in a wide range of applications, leading to a potential boost in environmental discharges. Nanoparticle propensity to be transferred throughout trophic chains and to generate toxicity was mainly assessed in primary consumers while a lack of knowledge for higher trophic levels persis...
Preprint
Full-text available
Among legumes (Fabaceae) capable of nitrogen-fixing nodulation, several Aeschynomene spp. use a unique symbiotic process that is independent of Nod factors and infection threads. They are also distinctive in developing root and stem nodules with photosynthetic bradyrhizobia. Despite the significance of these symbiotic features, their understanding...
Article
Full-text available
Motivation: Siberian sturgeon is a long lived and late maturing fish farmed for caviar production in 50 countries. Functional genomics enable to find genes of interest for fish farming. In the absence of a reference genome, a reference transcriptome is very useful for sequencing based functional studies. Results: We present here a high-quality tran...
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Full-text available
Long non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken genes enriched in LNC (http://www.fragencode.org/), built from the Ensembl reference extended using novel LNC modelled here from 364 RNA-seq and...
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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...
Preprint
Full-text available
Several hypotheses explain the prevalence of undifferentiated sex chromosomes 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-rever...
Article
We investigated the toxicity of Iron oxide and Zinc oxide engineered nanoparticles (ENPs) on Paracentrotus lividus sea urchin embryos and three species of microalgae. Morphological responses, internalization, and potential impacts of Fe2O3 and ZnO ENPs on physiology and metabolism were assessed. Both types of ENPs affected P. lividus larval develop...
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Full-text available
Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxes functional constraints. Subterranean vertebrates are outstanding models to analyze this process, and gene decay can serve as a readout. We sought to understand some general principles on the extent and tempo of the deca...
Preprint
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 noc...
Article
Full-text available
Background: Goldfish is an important model for various areas of research, including neural development and behavior and a species of significant importance in aquaculture, especially as an ornamental species. It has a male heterogametic (XX/XY) sex determination system that relies on both genetic and environmental factors, with high temperatures b...
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Full-text available
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...
Article
Pikeperch, Sander lucioperca, is a species of high interest to the aquaculture. The expansion of its production can only be achieved by furthering domestication level. However, the mechanisms driving the domestication process in finfishes are poorly understood. Transcriptome profiling of eggs was found to be a useful tool allowing understanding of...
Article
The lean-to-fat ratio is a major issue in beef meat industry both for carcass and meat production perspectives. This industrial perspective has motivated meat physiologists to use transcriptomics technologies to decipher mechanisms behind fat deposition within muscle during the time course of muscle growth. However, synthetic biological information...
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Biological rhythms are a fundamental property of life. The deep ocean covers 66% of our planet surface and is one of the largest biomes. The deep sea has long been considered as an arrhythmic environment because sunlight is totally absent below 1,000 m depth. In the present study, we have sequenced the temporal transcriptomes of a deep-sea species,...
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Full-text available
White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here we combined comparative genomics, transcriptomics and secreto...
Article
Full-text available
Sturgeons seem to be frozen in time. The archaic characteristics of this ancient fish lineage place it in a key phylogenetic position at the base of the ~30,000 modern teleost fish species. Moreover, sturgeons are notoriously polyploid, providing unique opportunities to investigate the evolution of polyploid genomes. We assembled a high-quality chr...
Preprint
Full-text available
Sexual reproduction is a ubiquitous basic feature of life and genetic sex determination is thus widespread, at least among eukaryotes. Understanding the remarkable diversity of sex determination mechanisms, however, is limited by the paucity of empirical studies. Here, we traced back the evolution of sex determination in an entire clade of vertebra...
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Full-text available
Siberian sturgeon, Acipenser baerii, is a commercially valuable fish for flesh and caviar production and a threatened species. We produced transcriptomic data for ten tissues with relevance to puberty, reproduction, early development, growth and food intake. The data includes RNA-Seq read sets of brain, pituitary, anterior-kidney, kidney, stomach,...
Article
Full-text available
White-rot (WR) fungi are pivotal decomposers of dead organic matter in forest ecosystems and typically use a large array of hydrolytic and oxidative enzymes to deconstruct lignocellulose. However, the extent of lignin and cellulose degradation may vary between species and wood type. Here we combined comparative genomics, transcriptomics and secreto...
Article
Full-text available
RNA-Seq transcriptome data from twenty Siberian sturgeon gonads at different developmental stages is described: ten undifferentiated gonads, six gonads of immature males and four gonads from immature females. Siberian sturgeon, Acipenser baerii, is long-lived, late-maturing fish farmed in 50 countries but its production remains on a craftsman scale...
Article
Full-text available
Background Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce. Result Chromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates informati...
Preprint
Full-text available
The study of sex determination and sex chromosome organisation in non-model species has long been technically challenging, but new sequencing methodologies are now enabling precise and high-throughput identification of sex-specific genomic sequences. In particular, Restriction Site-Associated DNA Sequencing (RAD-Seq) is being extensively applied to...
Article
Full-text available
Although ants are amongst the most abundant venomous terrestrial organisms, only a few studies have investigated the entire repertoire of peptides in the venom of a single ant species, or identified the toxins involved in insecticidal activity. In this study, the venom peptidome of the red ant, Manica rubida, was characterized using an integrated t...
Preprint
Evolution sometimes proceeds by loss, especially when structures and genes become dispensable after an environmental shift relaxing functional constraints. Gene decay can serve as a read-out of this evolutionary process. Animals living in the dark are outstanding models, in particular cavefishes as hundreds of species evolved independently during v...
Article
Full-text available
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...
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Full-text available
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...