Biology subjects

Rancurel, C.

Publications and source records attributed to Rancurel, C..

12 recordsLinked to original sources

bioRxiv2026

Transcriptional responses of Solanum lycopersicum to three distinct parasites reveal host hubs and networks underlying parasitic successes

Crops face attacks from a wide range of pathogens and pests that deploy various parasitic strategies. All aggressors must manipulate major plant functions, such as immune signaling, hormone pathways, metabolism, and development, to successfully establish themselves and complete their life cycle. Here, we compared the tomato plant's response to three evolutionary distant pathogens (nematodes, aphids and oomycetes) during compatible interactions using a transcriptomic approach. We identified differentially expressed genes and biological processes, and highlighted potential key host hubs associated with successful parasitism. By integrating recent published datasets, we refined our understanding of the global and tissue-specific mechanisms targeted during compatible interactions and, through co-expression analysis, identified clusters showing shared dysregulation patterns enriched in specific GO terms. Finally, model-to-crop translational analysis using the Arabidopsis interactome network, repositioned tomato candidates within larger interaction networks and emphasized the key positions occupied by some of them. Identifying these pivotal tomato targets is crucial to decipher processes underlying parasitism and, consequently, offers new opportunities to develop sustainable multi-pathogen control strategies.

plant biology↗

bioRxiv2025

Chromosome-scale genome assembly of Xiphinema index uncovers an unparalleled epigenetic toolkit in invertebrates

Nematodes constitute the most speciose animal phylum, occupying an exceptionally broad range of biomes and encompassing free-living microbe-feeders, predators, and notorious plant or animal parasites. However, the limited availability of genome-scale resources for early-branching nematode clades has constrained our understanding of the molecular determinants underlying these multiple evolutionary adaptations. Here, we present the genome of the plant-parasitic nematode Xiphinema index, constituting the first telomere-to-telomere assembly for the order Dorylaimida, an early-branching nematode lineage. Phylogenetic analyses reveal that horizontal gene transfers (HGT) have played a pivotal role in the emergence of plant parasitism in this phylum. Remarkably, we identify the first documented case of a plant-derived HGT in a nematode genome. This gene encodes a predicted secreted parasitic effector, underscoring the diversity of evolutionary events that contributed to the parasitic arsenal. Our results suggest that, beyond bacteria and fungi, plants themselves have provided crucial genes for parasitism that may now be used by the nematodes to manipulate them. Our comparative genomic analyses across more than 70 nematode species further uncover an unprecedented epigenetic toolkit in an invertebrate genome. Indeed, X. index harbors a complete set of canonical DNA methyltransferases, a full-length ATRX chromatin remodeler, and 3D-chromatin architectural CTCF protein coding homolog. Consistent with this repertoire, we detected methylation at CpG genome-wide, which inversely correlates with gene expression and chromatin accessibility. Together, these findings reveal a vertebrate-like epigenetic machinery in an early-branching nematode and call for a fundamental reassessment of the prevailing epigenetic paradigm in nematodes and, more broadly, in animals.

genomics↗

bioRxiv2025

Chronic dietary ingestion of Bacillus thuringiensis spores promotes intestinal inflammation and aging in non-target adult Drosophila

Bacillus thuringiensis (Bt), a spore-forming Gram-positive bacterium, is the leading microbial insecticide used in both organic and conventional agriculture to fight lepidopteran larvae. Bt insecticides, which consist of a mix of Bt spores and crystals of entomopathogenic toxins (Cry toxins), kill target pest larvae rapidly after ingestion by destroying their intestinal epithelium. The potential adverse effects of chronic consumption of Bt spores by non-target organisms have not been thoroughly investigated. In this study, using adult Drosophila melanogaster, a non-target dipteran organism of Bt insecticides, we show that chronic ingestion of agricultural doses of spores in the diet reduces lifespan. Our results demonstrate that Bt spore ingestion affects gut morphology, promotes dysplasia, alters septate junctions and enhances epithelial permeability. In addition, we observed increased levels of inflammatory signaling pathways and reactive oxygen species. Taken together, our results indicate that chronic consumption of Bt spores promotes inflammation and oxidative stress, leading to premature aging of the gut and early lethality in Drosophila. Extended to non-target insects, which account for 85% of animal biodiversity, our study suggests that highly persistent Bt spores may have unintended long-term effects on the environment.

physiology↗

bioRxiv2025

Genomic rearrangements promote diversification of a facultative meiotic parthenogenetic nematode pest (Meloidogyne graminicola)

Meloidogyne graminicola (Mg), commonly known as the rice root-knot nematode, is a highly destructive pest that inflicts significant damage on rice crops worldwide. Mg is thought to reproduce primarily by meiotic parthenogenesis, but its success across diverse habitats and hosts raises important questions about its adaptation mechanisms, particularly those driving the evolution of its virulence. Documenting the origin of the pathogen, its reproductive strategies and other evolutionary processes shaping its genome are thus crucial to understand its recent, rapid expansion. In this study, we first improved gene annotations of the Mg genome to enhance identification of potential secreted parasitism genes. Next, comparative genomics analyses of 13 Mg isolates from diverse geographic locations revealed evolutionary changes in the genome, including single nucleotide variations (SNVs), loss of heterozygosity (LoH), and copy number variations (CNVs). These events affected a substantial number of genes, including those coding for secreted proteins, suggesting their roles in nematode adaptation. LoH, the reduction of linkage disequilibrium between SNPs with distance as well as the 4-gamete test all provide evidence for meiotic recombination, supporting some sexual reproduction in Mg. Clustering of populations, based on LoH profiles and SNVs, allowed the definition of groups of isolates not correlating with current geographic distribution. The low sequence divergence at the genome level and the lack of clear phylogeographic structure among isolates support the hypothesis of a recent, widespread dissemination of the parasite, especially across Southeast Asia. Overall, our study supports a dual reproductive mode (sexual/asexual) in Mg, which offers an evolutionary advantage by balancing clonal proliferation in favorable conditions with occasional sexual reproduction allowing generation of new allelic combinations in adverse environments.

genomics↗

bioRxiv2025

A tumor-suppressive role of the PRC1 Polycomb epigenetic complex in the maintenance of adult Drosophila intestinal stem cell identity

Chromatin modulators, like Polycomb group proteins, are key epigenetic regulators of gene expression and are frequently mutated in cancers. In adult stem cells, epigenetic regulation maintains their identity and controls their differentiation during homeostasis or aging, but its direct role in tumorigenesis remains unclear. Here we developed a novel tumor model in Drosophila by exploring the function of Polycomb Repressive Complex 1 (PRC1) in adult intestinal stem cells (ISCs). Disrupting core PRC1 components in ISCs induces the formation of small cell clusters devoid of intestinal markers, a novel phenotype linked to premature mortality under stress. These clusters exhibit neoplastic characteristics such as overproliferation and continuous growth in serial transplantations, leading to their designation as tumor-initiating intestinal cells (TIICs). While JAK/STAT signaling contributes to TIIC growth, the NF-{kappa}B-related Toll/Imd immune pathways restrict their expansion independently of cell death. Altogether, our results highlight PRC1 as an epigenetic tumor suppressor in adult stem cells. AUTHOR SUMMARYOur research explores how stem cells in the adult intestine stay healthy and avoid becoming cancerous. We focused on a group of proteins called Polycomb Repressive Complex 1 (PRC1), which help regulate which genes are turned off in a cell. While these proteins are known to play important roles during development and cancer prevention, their function in the adult intestine has been less clear. Using the fruit fly Drosophila, we discovered that when PRC1 function is lost in intestinal stem cells, abnormal clusters of cells begin to form. These clusters grow uncontrollably, lose their normal identity, and can keep growing when transplanted--traits that are typical of cancer. Interestingly, we also found that parts of the immune system, specifically NF-{kappa}B-related pathways, can act inside these tumor cells to limit their growth--revealing a protective role that hasnt been seen before in the adult gut. This work provides new insights into how epigenetic regulation and immune signaling work together to keep stem cells from turning cancerous. It opens up new possibilities for understanding how cancers begin and how the body may naturally resist them, even at the level of the tissue.

cancer biology↗

bioRxiv2024

Unveiling the genome assembly of the polyploid and quarantine root-knot nematode, Meloidogyne enterolobii

Root-knot nematodes of the genus Meloidogyne are obligatory plant endoparasites that cause substantial economic losses to the agricultural production and impact the global food supply. These plant parasitic nematodes belong to the most widespread and devastating genus worldwide, yet few measures of control are available. The most efficient way to control root-knot nematodes (RKN) is deployment of resistance genes in plants. However, current resistance genes that control other Meloidogyne species are mostly inefficient on M. enterolobii. Consequently, M. enterolobii was listed as a European Union quarantine pest implementing regulation. To gain insight into the molecular characteristics underlying its parasitic success, exploring the genome of M. enterolobii is essential. Here, we report a high-quality genome assembly of Meloidogyne enterolobii using the high-fidelity long-read sequencing technology developed by Pacific Biosciences, combined with a gap-aware sequence transformer, DeepConsensus. The resulting genome assembly spans 273 Mbp with 556 contigs, a GC% of 30 {+/-} 0.042 and an N50 value of 2.11Mb, constituting a useful platform for comparative, population and functional genomics.

genomics↗

bioRxiv2023

Unzipped assemblies of polyploid root-knot nematode genomes reveal new kinds of unilateral complex telomeric repeats

Telomeres play central roles in senescence, aging and chromosome integrity. Using ONT long read sequencing we have assembled the genomes of Meloidogyne incognita, M. javanica and M. arenaria, the three most devastating plant-parasitic nematodes at unparalleled contiguity. The telomeric repeat (TTAGGC)n, evolutionarily conserved in nematodes, was not found in these genomes. Furthermore, no evidence for a telomerase enzyme or for orthologs of C. elegans telomere-associated proteins could be found. Instead, we identified species-specific composite repeats mostly present at one end of contigs. These repeats were G-rich, oriented and transcribed, similarly to known telomeric repeats. Using FISH we confirmed these repeats were present at one single end of M. incognita chromosomes. The discovery of a new kind of telomeric repeat in these species highlights the evolutionary diversity of chromosome protection systems despite their central roles and opens new perspectives towards the development of more specific control methods against these pests.

genomics↗

bioRxiv2023

Genome sequence and annotation of Periconia digitata, a promising biocontrol agent of phytopathogenic oomycetes

The Periconia fungal genus belongs to the phylum Ascomycota, order Pleosporales, family Periconiaceae. Periconia are found in many habitats but little is known about their ecology. Several species from this genus produce bioactive molecules. Periconia digitata extracts were shown to be deadly active against the pine wilt nematode. Furthermore, P. digitata was shown to inhibit plant pathogenic oomycete Phytophthora parasitica. Because P. digitata has great potential as a biocontrol agent and high quality genomic resources are still lacking in the Periconiaceae family, we generated long-read genomic data for P. digitata. Using the PacBio Hifi sequencing technology, we obtained a highly-contiguous genome assembled in 13 chromosomes and totalling ca. 39 Mb. In addition, we produced a reference transcriptome, based on 12 different culture conditions, and proteomic data to support the genome annotation. Besides representing a new reference genome within the Periconiaceae, this work will contribute to our better understanding of the Eukaryotic tree of life and opens new possibilities in terms of biotechnological applications.

microbiology↗

bioRxiv2022

AvP: a software package for automatic phylogenetic detection of candidate horizontal gene transfers.

Horizontal gene transfer (HGT) is the transfer of genes between species outside the transmission from parent to offspring. Due to their impact on the genome and biology of various species, HGTs have gained broader attention, but high-throughput methods to robustly identify them are lacking. One rapid method to identify HGT candidates is to calculate the difference in similarity between the most similar gene in closely related species and the most similar gene in distantly related species. Although metrics on similarity associated with taxonomic information can rapidly detect putative HGTs, these methods are hampered by false positives that are difficult to track. Furthermore, they do not inform on the evolutionary trajectory and events such as duplications. Hence, phylogenetic analysis is necessary to confirm HGT candidates and provide a more comprehensive view of their origin and evolutionary history. However, phylogenetic reconstruction requires several time-consuming manual steps to retrieve the homologous sequences, produce a multiple alignment, construct the phylogeny and analyze the topology to assess whether it supports the HGT hypothesis. Here, we present AvP which automatically performs all these steps and detects candidate HGTs within a phylogenetic framework. Availability and implementationAvP is written in Python and is available under GNU General Public License v3.0 at (https://github.com/GDKO/AvP).

bioinformatics↗

bioRxiv2021

Improvement of eukaryotic proteins prediction from soil metagenomes

BackgroundDuring the last decades, shotgun metagenomics and metabarcoding have highlighted the diversity of microorganisms from environmental or host-associated samples. Most assembled metagenome public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs and metagenome-assembled genomes (MAGs). Consequently, eukaryotic contigs and MAGs, with intrinsically different gene features, are not optimally annotated, resulting in an incorrect representation of the eukaryotic component of biodiversity, despite their biological relevance. ResultsUsing an automated analysis pipeline, we have filtered 7.9 billion of contigs from 6,873 soil metagenomes in the IMG/M database of the Joint Genome Institute to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins. Of these, 5.6 million could be traced back to non-chimeric higher confidence eukaryotic contigs. Our pipeline improves eukaryotic proteins completeness, contiguity and quality. Moreover, the better quality of eukaryotic proteins combined with a more comprehensive assignment method improves the taxonomic annotation as well. ConclusionsUsing public soil metagenomic data, we provide a dataset of eukaryotic soil proteins with improved completeness and quality as well as a more reliable taxonomic annotation. This unique resource is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes. O_TEXTBOXKey Points O_LIEukaryotic micro-organisms have key roles in soil microbial communities and ecosystems. C_LIO_LIEukaryotic genes and proteins are incorrectly represented in metagenomic libraries due to inappropriate methods dedicated to prokaryotes. C_LIO_LIWe have improved the quality and completeness of the de novo proteins prediction and taxonomic annotation of eukaryotic organisms from soil or plant-associated microbiome. C_LI C_TEXTBOX

genomics↗

bioRxiv2018

Family-Companion: analyse, visualise, browse, query and share your homology clusters

Identifying homology groups in predicted proteomes from different biological sources allows biologists to address questions as diverse as inferring species-specific proteins or retracing the phylogeny of gene families. Nowadays, command-line software exists to infer homology clusters. However, computing and interpreting homology groups with this software remains challenging for biologists and requires computational skills.\n\nWe propose Family-Companion, a web server dedicated to the computation, the analysis and the exploration of homology clusters. Family-Companion aims to fill the gap between analytic software and databases presenting orthologous groups based on a set of public data. It offers a user-friendly interface to launch or upload precomputed homology cluster analysis, to explore and share the results with other users. The exploration of the results is highly facilitated by interactive solutions to visualize proteome intersections via Venn diagrams, phylogenetic trees, multiple alignments, and also by querying the results by blast or by keywords.\n\nFamily-Companion is available at http://family-companion.toulouse.inra.fr with a demo dataset and a set of video tutorials. Source code and installation protocol can be found at https://framagit.org/BBRIC/family-companion/. A container-based package simplifies the installation of the web-suite.

bioinformatics↗

bioRxiv2017

Signatures of the evolution of parthenogenesis and cryptobiosis in the genomes of panagrolaimid nematodes

Most animal species reproduce sexually, but parthenogenesis, asexual reproduction of various forms, has arisen repeatedly. Parthenogenetic lineages are usually short lived in evolution; though in some environments parthenogenesis may be advantageous, avoiding the cost of sex. Panagrolaimus nematodes have colonised environments ranging from arid deserts to arctic and antarctic biomes. Many are parthenogenetic, and most have cryptobiotic abilities, being able to survive repeated complete desiccation and freezing. It is not clear which genomic and molecular mechanisms led to the successful establishment of parthenogenesis and the evolution of cryptobiosis in animals in general. At the same time, model systems to study these traits in the laboratory are missing.\n\nWe compared the genomes and transcriptomes of parthenogenetic and sexual Panagrolaimus able to survive crybtobiosis, as well as a non-cryptobiotic Propanogrolaimus species, to identify systems that contribute to these striking abilities. The parthenogens are most probably tripoids originating from hybridisation (allopolyploids). We identified genomic singularities like expansion of gene families, and selection on genes that could be linked to the adaptation to cryptobiosis. All Panagrolaimus have acquired genes through horizontal transfer, some of which are likely to contribute to cryptobiosis. Many genes acting in C. elegans reproduction and development were absent in distant nematode species (including the Panagrolaimids), suggesting molecular pathways cannot directly be transferred from the model system.\n\nThe easily cultured Panagrolaimus nematodes offer a system to study developmental diversity in Nematoda, the molecular evolution of parthenogens, the effects of triploidy on genomes stability, and the origin and biology of cryptobiosis.

evolutionary biology↗