A5091774062- Marine Ecology and Invasive Species
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Legume Nitrogen Fixing Symbiosis
- Ichthyology and Marine Biology
- Protist diversity and phylogeny
- Marine Biology and Ecology Research
- Genetic diversity and population structure
- Environmental DNA in Biodiversity Studies
- Bone and Dental Protein Studies
- Business Strategy and Innovation
- Marine Invertebrate Physiology and Ecology
- Forensic Anthropology and Bioarchaeology Studies
- Photosynthetic Processes and Mechanisms
- Identification and Quantification in Food
- Aquatic Ecosystems and Phytoplankton Dynamics
- Insect-Plant Interactions and Control
- Study of Mite Species
- Chromosomal and Genetic Variations
- Marine Sponges and Natural Products
- Subterranean biodiversity and taxonomy
- Cooperative Studies and Economics
- CRISPR and Genetic Engineering
- Venomous Animal Envenomation and Studies
- Coastal wetland ecosystem dynamics
University of Namur
2019-2024
Ecosystèmes, Biodiversité, Evolution
2024
Université de Rennes
2024
Institut des Sciences de l'Evolution de Montpellier
2015-2022
Ecologie & Evolution
2020
École Pratique des Hautes Études
2017-2019
Université de Montpellier
2017-2019
Centre National de la Recherche Scientifique
2014-2019
Institut de Recherche pour le Développement
2017-2019
Sorbonne Université
2014
Tunicates are the closest relatives of vertebrates and widely used as models to study evolutionary developmental biology chordates. Their phylogeny, however, remains poorly understood, date, only 18S rRNA nuclear gene mitogenomes have been delineate major groups tunicates. To resolve their relationships provide a first estimate divergence times, we transcriptomic approach build phylogenomic dataset including all tunicate lineages, consisting 258 evolutionarily conserved orthologous genes...
ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions nine ascidian species. It provides increased integration with external molecular taxonomy databases, better support epigenomics datasets, in particular RNA-seq, ChIP-seq SELEX-seq, features novel interactive interfaces existing datatypes. In particular, cross-species navigation...
Multiple RNA samples are frequently processed together and often mixed before multiplex sequencing in the same run. While different can be separated post using sample barcodes, possibility of cross contamination between biological from species that have been or sequenced parallel has potential to extremely deleterious for downstream analyses. We present CroCo, a software package identifying removing such contaminants assembled transcriptomes. Using multiple, recently published sequence...
Whether adaptation is limited by the beneficial mutation supply a long-standing question of evolutionary genetics, which more generally related to determination adaptive substitution rate and its relationship with species effective population size (Ne) genetic diversity. Empirical evidence reported so far equivocal, some but not all studies supporting higher in large-Ne than small-Ne species. We gathered coding sequence polymorphism data estimated amino-acid ωa, 50 from ten distant groups...
Ascidians belong to the tunicates, sister group of vertebrates and are recognized model organisms in field embryonic development, regeneration stem cells. ANISEED is main information system ascidian developmental biology. This article reports development since its initial publication 2010. Over past five years, we refactored from an custom schema extended version Chado redesigned all user back end interfaces. new architecture was used improve enrich description Ciona intestinalis based on...
ANISEED (https://www.aniseed.cnrs.fr) is the main model organism database for worldwide community of scientists working on tunicates, vertebrate sister-group. Information provided each species includes functionally-annotated gene and transcript models with orthology relationships within echinoderms, cephalochordates vertebrates. Beyond genes system describes other genetic elements, including repeated elements cis-regulatory modules. Gene expression profiles several thousand are formalized in...
Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing well-assembled reference genome is critical step developing an understanding of the effects long-term asexuality DNA breakage on evolution. To this end, we present first high-quality chromosome-level assemblies for Adineta vaga, composed six pairs...
The shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generated reference genomes for five independently evolved parthenogenetic species stick insect genus Timema and their closest relatives. Using these references population genomic data, we show that results an extreme reduction heterozygosity often leads genetically uniform populations. also find evidence less effective...
Significance Putatively ancient asexual species pose a challenge to theory because they appear escape the predicted negative long-term consequences of asexuality. Although asexuality is difficult demonstrate, specific signatures haplotype divergence, called “Meselson effect,” are regarded as strong support for Here, we provide evidence Meselson effect in an oribatid mite species, Oppiella nova , and show that not caused by hybridization or polyploidization. Our findings conclusive absence...
Asexual propagation and whole body regeneration are forms of nonembryonic development (NED) widespread across animal phyla central in life history evolutionary diversification metazoans. Whereas it is challenging to reconstruct the gains or losses NED at large phylogenetic scale, comparative studies could benefit from being conducted more restricted taxonomic groups for which relationships well established. The ascidian family Styelidae encompasses strictly sexually reproducing solitary as...
Abstract In order to characterize the molecular bases of mineralizing cell evolution, we targeted type X collagen, a nonfibrillar network forming collagen encoded by Col10a1 gene. It is involved in process endochondral ossification ray-finned fishes and tetrapods (Osteichthyes), but until now unknown cartilaginous (Chondrichthyes). We show that holocephalans elasmobranchs have respectively five six tandemly duplicated gene copies display conserved genomic synteny with osteichthyan genes. All...
Bdelloid rotifers are part of the restricted circle multicellular animals that can withstand a wide range genotoxic stresses at any stage their life cycle. In this study, bdelloid rotifer Adineta vaga is used as model to decipher molecular basis extreme tolerance. Proteomic analysis shows specific DNA ligase, different from those usually involved in repair eukaryotes, strongly over-represented upon ionizing radiation. A phylogenetic reveals its orthology prokaryotic ligase E, and horizontal...
The molecular bases explaining the diversity of dental tissue mineralization across gnathostomes are still poorly understood. Odontodes, such as teeth and body denticles, serial structures that develop through deployment a gene regulatory network shared between all gnathostomes. Dentin, inner odontode mineralized tissue, is produced by odontoblasts appears well-conserved evolution. In contrast, hypermineralized external layer (enamel or enameloid) ameloblasts epithelial origin, shows...
Among semi-aquatic species of the legume genus Aeschynomene, some have property being nodulated by photosynthetic Bradyrhizobium lacking nodABC genes necessary for synthesis Nod factors. Knowledge specificities underlying this Nod-independent symbiosis has been gained from model Aeschynomene evenia but our understanding remains limited due to lack comparative genetics with related taxa using a factor-dependent process. To fill gap, we combined different approaches perform thorough analysis...
ABSTRACT The several hundreds of species bdelloid rotifers are notorious because they represent an ancient clade comprising only asexual lineages 1 . Moreover, most have the ability to withstand complete desiccation and high doses ionizing radiation, being able repair their DNA after massive genome breakage 2 To better understand impact long-term asexuality on evolution, a telomere-to-tolemere reference assembly is critical 3, 4 Here we present first, quality chromosome-scale for A. vaga...
Abstract Ostracods are one of the oldest crustacean groups with an excellent fossil record and high importance for phylogenetic analyses but genome resources this class still lacking. We have successfully assembled annotated first reference genomes three species nonmarine ostracods; two obligate sexual reproduction (Cyprideis torosa Notodromas monacha) putative ancient asexual Darwinula stevensoni. This kind genomic research has so far been impeded by small size most ostracods absence...
ABSTRACT Whether adaptation is limited by the beneficial mutation supply a long-standing question of evolutionary genetics, which more generally related to determination adaptive substitution rate and its relationship with effective population size N e . Empirical evidence reported so far equivocal, some but not all studies supporting higher in large-N than small-N species. We gathered coding sequence polymorphism data estimated amino-acid ω , 50 species from ten distant groups animals...
Abstract The shift from sexual reproduction to parthenogenesis has occurred repeatedly in animals, but how the loss of sex affects genome evolution remains poorly understood. We generated de novo reference genomes for five independently evolved parthenogenetic species stick insect genus Timema and their closest relatives. Using these references combination with population genomic data, we show that results an extreme reduction heterozygosity, often leads genetically uniform populations. also...
Homologous recombination is an essential DNA repair mechanism that promotes chromosome pairing and ensures allele segregation during meiosis in sexual organisms. Here, we explore the dual function of homologous bdelloid rotifer Adineta vaga , ancient asexual species known for its remarkable resilience to extreme genotoxic stresses. Genomic analyses reveal A. uses meiotic recombination, both promote spontaneous crossovers gene conversion oogenesis genome response damage. Our study identifies...
Abstract Background Tunicates are the closest relatives of vertebrates and widely used as models to study evolutionary developmental biology chordates. Their phylogeny, however, remains poorly understood date, only 18S rRNA nuclear gene mitogenomes have been delineate major groups tunicates. To resolve their relationships provide a first estimate divergence times, we transcriptomic approach build phylogenomic dataset including all tunicate lineages, consisting 258 evolutionarily conserved...