Biology subjects

Richaud, A.

Publications and source records attributed to Richaud, A..

8 recordsLinked to original sources

bioRxiv2026

Repeated mutation of a GT92 glycosyltransferase gene confers antiviral resistance in two Caenorhabditis species

Host-pathogen interactions evolve rapidly within species, providing natural genetic resources for the identification of specific ecological interaction factors. We previously identified RNA viruses that infect the nematodes C. elegans and C. briggsae in a species-specific manner. Wild strains of both host species demonstrate ample variation in viral sensitivity. Specifically, the wild C. elegans strain MY10, despite carrying a deletion in a key immunity factor, was among the most resistant strains. Here we use recombinant inbred lines and pool-sequencing approaches to genetically map the major MY10 resistance locus, narrowing down its position by CRISPR/Cas9 mediated recombination and testing candidates by genome editing. A rare non-synonymous polymorphism in the gtnt-1 gene, encoding a putative glycosyltransferase of the GT92 family, causes resistance to viral infection in MY10. We find that viral resistance through gtnt-1 mutation occurred repeatedly in C. elegans, with diverse resistance alleles each remaining at low frequency (<1%). Furthermore, leveraging closely related C. briggsae strains differing in viral susceptibility, we demonstrate that repeated reduction-of-function alleles of the Cbr-gtnt-1 ortholog similarly impair viral infection and enhance host fitness upon infection. In conclusion, we found recurrent evolution in two host species of reduction-of-function alleles of the gtnt-1 orthologs, which repeatedly lead to viral resistance yet remain at low frequency. These repeated events provide a case of transient ecological adaptation to a pathogen through recurrent mutation of the same gene in two species. The low population frequencies of the resistant alleles point to a changing eco-evolutionary context that prevents their spread in populations, resulting in high allelic heterogeneity.

evolutionary biology↗

bioRxiv2025

Caenorhabditis briggsae ancestral genomic hyper-diversity contrasts with globally distributed genome-wide haplotypes

Comparative genomics provides a powerful framework to uncover the molecular and evolutionary mechanisms that shape genetic diversity within and across species, revealing how shared and lineage-specific processes influence their evolutionary trajectories through time. The nematode Caenorhabditis briggsae is distributed world-wide and is a comparative model to Caenorhabditis elegans in the biology of development, cellular mechanisms, neurobiology, genetic mappings of complex traits, and genome evolution. Following massive collection efforts by the nematode research community, we present the isolation of over 2,000 wild strains and analyses of genome sequences that catalog over six million single-nucleotide and insertion-deletion variants. This genome and strain resource provide a powerful means to interrogate the causal genetic bases of phenotypic variation for diverse traits. Additionally, we describe its global population structure and discover new and genetically distinct groups within this primarily self-fertilizing species, including groups of highly related strains that were sampled across different continents. We leverage expansive genetic variation to decipher the effects of linkage and selection on the distribution of genetic diversity across the genome and across geographic regions. Within the species, we find genomic regions with extremely high levels of genetic variation similar to hyper-divergent regions found in C. elegans and other species. These regions harbor new genes and variation enriched for environmental sensing and pathogen responses. In comparison to the outbreeding sister species Caenorhabditis nigoni, we conclude that long-term balancing selection has maintained substantial functional variation since the divergence from their outbreeding ancestor, likely in response to differences in the ecological niche. Overall, this massive strain resource enables future comparative genetics and genomics studies, including genome-wide association studies between Caenorhabditis species.

genomics↗

bioRxiv2025

Mutational divergence in local populations of the selfing nematode Caenorhabditis elegans

Laboratory mutation accumulation experiments allow the assessment of spontaneous mutation rates and patterns with minimal selection. Here, we aimed to follow the accumulation and fate of mutations in natural populations, in a spatial context. The nematode Caenorhabditis elegans is particularly suited for such endeavor, as it reproduces almost exclusively by selfing. We analyzed the evolution of clonal C. elegans genotypes along a 300-m long stream bank in the Santeuil wood (France), based on short-read whole-genome sequencing of individuals collected between 2009 and 2022. We followed along years two of these quasi-clones composed of individuals only differing by recent mutations. Recombination was scarce. A temporal signal was detected: strains from earlier years were found close to inner nodes of the tree, while recent ones were found on outer tips. This signal allowed us to estimate a substitution rate of 4 to 5x10-8 mutations per base pair per year, which can be used to calibrate divergence times among and within species. Mutation densities were higher on the X chromosome, on chromosome arms, and in non-exonic regions. We detected a high transition-to-transversion ratio, not observed in C. elegans laboratory mutation accumulation lines. Based on the spontaneous mutation rate per generation in laboratory lines of intergenic regions under minimal purifying selection, we estimated that C. elegans locally undergoes around 25 effective generations per year. Finally, using these recent mutations, we detected a spatio-temporal pattern within the field site, indicating limited dispersal at the scale of 100 meters within 10 years.

evolutionary biology↗

bioRxiv2025

Five new Caenorhabditis species from Indonesia provide exceptions to Haldane's rule and partial fertility of interspecific hybrids

Given the interest in the biogeography and diversity of the Caenorhabditis genus, we established a collection of these nematodes from field surveys on four Indonesian islands. We isolated over 60 Caenorhabditis strains belonging to ten species. Five species were previously known from other locations: C. briggsae, which was predominant, C. tropicalis, C. nigoni, C. brenneri and C. elegans. The five other species are new, and we describe them here as Caenorhabditis indonesiana, Caenorhabditis malino, Caenorhabditis ceno, Caenorhabditis brawijaya and Caenorhabditis ubi. RNA sequence analysis of 1,861 orthologous genes placed all species from Indonesia in the Elegans group of Caenorhabditis species. Four of the new species belong to a Sinica subclade of species so far only found in an East Asia-Indo-Pacific world region. The fifth new species, C. indonesiana, appears as the sister of the C. tropicalis-C. wallacei pair, both also found in Indonesia. The present findings are thus consistent with diversification in the Elegans group having occurred in this world region. Crosses between closely related species showed counterexamples to Haldanes "rule": for two pairs of species, in one cross direction we only found hybrid males. In addition, we found a pair of species that could partially interbreed: Caenorhabditis ubi (East Java) with C. sp. 41 (Solomon islands), with the hybrid males in one cross direction being fertile. Such closesly related species pairs are good models for genetic studies of incompatibilities arising during speciation. SummaryThis work addresses their biodiversity, phylogenetic relationships and genetic incompatibilities of Caenorhabditis nematodes, which are laboratory model organisms. Through field studies, the authors isolated 60 Caenorhabditis strains in Indonesia, representing ten species, including five new. From RNA sequencing and phylogenetic reconstruction, all ten species belong to the Elegans group of Caenorhabditis. In crosses between closely related species, the hybrid progeny can be all females, abiding by Haldanes rule, but in other cases all males. In one species pair, partially fertile hybrids are produced in one cross direction. These closely related species are good models for studying genetic incompatibilities.

genetics↗

bioRxiv2024

Natural variation in infection specificityof Caenorhabditis briggsae isolates by two RNA viruses

Antagonistic relationships such as host-virus interactions potentially lead to rapid evolution and specificity in interactions. The Orsay virus is so far the only horizontal virus naturally infecting the nematode C. elegans. In contrast, several related RNA viruses infect its congener C. briggsae, including Santeuil (SANTV) and Le Blanc (LEBV) viruses. Here we focus on the hosts intraspecific variation in sensitivity to these two intestinal viruses. Many temperate-origin C. briggsae strains, including JU1264 and JU1498, are sensitive to both, while many tropical strains, such as AF16, are resistant to both. Interestingly, some C. briggsae strains exhibit a specific resistance, such as the HK104 strain, specifically resistant to LEBV. The viral sensitivity pattern matches the strains geographic and genomic relationships. The heavily infected strains mount a seemingly normal small RNA response that is insufficient to suppress viral infection, while the resistant strains show no small RNA response, suggesting an early block in viral entry or replication. We use a genetic approach from the host side to map genomic regions participating in viral resistance polymorphisms. Using Advanced Intercrossed Recombinant Inbred Lines (RILs) between virus-resistant AF16 and SANTV-sensitive HK104, we detect Quantitative Trait Loci (QTLs) on chromosomes IV and III. Building RILs between virus-sensitive JU1498 and LEBV-resistant HK104 followed by bulk segregant analysis, we identify a chromosome II QTL. In both cases, further introgressions of the regions confirmed the QTLs. This diversity provides an avenue for studying virus entry, replication, and exit mechanisms, as well as host-virus specificity and the host response to a specific virus infection.

genetics↗

bioRxiv2023

Genome-wide association and environmental suppression of the mortal germline phenotype of wild C. elegans

The animal germline lineage needs to be maintained along generations. However, some Caenorhabditis elegans wild isolates display a mortal germline phenotype, whereby the lineage becomes sterile after several generations at 25{degrees}C. We used a genome-wide association approach to study the genetic basis for this phenotype in C. elegans populations. We detected a significant peak on chromosome III around 5 Mb, which was confirmed using introgression lines. These results indicate that a seemingly deleterious genotype is maintained at intermediate frequency in the species. Environmental rescue is a likely explanation and we indeed find that naturally associated bacteria and microsporidia suppressed the phenotype. The tested bacteria also suppressed the temperature-sensitive mortal germline phenotype of mutants in small RNA inheritance (nrde-2) and histone modifications (set-2). Even Escherichia coli strains of the K-12 lineage suppressed the phenotype compared to B strains. By shifting a strain cultured on E. coli K-12 back to E. coli B, we found that C. elegans can keep over several generations the memory of the suppressing conditions. Thus, the mortal germline phenotype of wild C. elegans is lin part revealed by laboratory conditions and may represent variation in epigenetic inheritance and environmental interactions. This study also points to the importance of non-genetic memory in the face of environmental variation.

evolutionary biology↗

bioRxiv2018

Comparative genomics of ten new Caenorhabditis species

The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for ten new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We show unexpected complexity in the evolutionary history of key developmental pathway genes. The genomic data also permit large scale analysis of gene structure, which we find to be highly variable within the genus. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.

evolutionary biology↗

bioRxiv2018

Pristionchus nematodes occur frequently in diverse rotting vegetal substrates and are not exclusively necromenic, while Panagrellus redivivoides is found specifically in rotting fruits

The lifestyle and feeding habits of nematodes are highly diverse. Several species of Pristionchus (Nematoda: Diplogastridae), including Pristionchus pacificus, have been reported to be necromenic, i.e. to associate with beetles in their dauer diapause stage and wait until the death of their host to resume development and feed on microbes in the decomposing beetle corpse. We review the literature and suggest that the association of Pristionchus to beetles may be phoretic and not necessarily necromenic. The view that Pristionchus nematodes have a necromenic lifestyle is based on studies that have sought Pristionchus only by sampling live beetles. By surveying for nematode genera in different types of rotting vegetal matter, we found Pristionchus spp. at a similar high frequency as Caenorhabditis, often in large numbers and in feeding stages. Thus, these Pristionchus species may feed in decomposing vegetal matter. In addition, we report that one species of Panagrellus (Nematoda: Panagrolaimidae), Panagrellus redivivoides, is found in rotting fruits but not in rotting stems, with a likely association with Drosophila fruitflies. Based on our sampling and the observed distribution of feeding and dauer stages, we propose a life cycle for Pristionchus nematodes and Panagrellus redivivoides that is similar to that of C. elegans, whereby they feed on the microbial blooms on decomposing vegetal matter and are transported between food patches by coleopterans for Pristionchus spp., fruitflies for Panagrellus redivivoides and isopods and terrestrial molluscs for C. elegans.

ecology↗