Biology subjects

Roedelsperger, C.

Publications and source records attributed to Roedelsperger, C..

11 recordsLinked to original sources

bioRxiv2026

Lessons learned from manual curation of thousands of gene models in the nematode Pristionchus pacificus

Continuous developments in sequencing technologies have led to the generation of chromosome-scale genome assemblies across the whole tree of life, but our ability to annotate genomes has lacked behind. One major problem consists in the fact that typically not all genes are expressed at detectable levels at any given life stage or environment. Therefore, available transcriptome data needs to be complemented by gene prediction programs and protein homology evidence. However, how to optimally combine these different data types is not well understood. Here, we present a case study, where we community curated gene annotations of the Pristionchus pacificus strain RSC011. By incorporation of new Iso-seq and RNA-seq data and genome-wide screening, we identified and corrected more than 7,500 ([~]24%) gene models. While the improved gene annotation for the RSC011 strain will be useful for the P. pacificus community, our study reveals several gene annotation problems that may affect data from other species. Among these, we identified assembly errors, artificial transcript fusions resulting from overlapping genes and polycistronic RNAs, falsely called open reading frames, and error propagation based on homology data as frequent sources of gene annotation errors. Thus, our findings may be helpful in guiding future efforts to annotate genomes across different taxonomic groups.

genomics↗

bioRxiv2025

Poly(UG)-tailed RNAs are involved in the control of thousands of genes predominantly in the germline in Pristionchus pacificus

In the nematode Caenorhabditis elegans, the terminal transferase RDE-3 adds a poly(UG)-tail to the free 3 end of RNA molecules generated by the action of primary siRNAs or piRNAs. The tailed RNA serves as a template for RNA-dependent RNA polymerases (RdRp) to generate secondary siRNAs, thereby reinforcing the RNAi effect. In this iterative process, progressively shorter tailed RNAs are formed. In C. elegans, injection of poly(UG)-tailed single-stranded RNA (ssRNA) leads to RNAi-mediated gene silencing, thereby bypassing the need for the processing of double-stranded RNA into siRNAs. We wondered if poly(UG)-tailed ssRNAs could also be used for experimental gene knockdown in nematodes where long dsRNA-mediated RNAi does not work reliably, such as the satellite model organism Pristionchus pacificus or parasitic nematodes of the genus Strongyloides. Here we show that injection of poly(UG)-tailed RNA leads to gene knock down in P. pacificus and that the injected RNA, as well as the corresponding endogenous RNA, serve as substrate for the formation of new poly(UG)-tailed RNAs. Different from C. elegans, in P. pacificus, the knockdown effect depends on the redundant activity of the three rde-1 paralogs present in this species. We detected endogenously occurring poly(UG)-tailed RNAs derived from thousands of genes, more than half of which belong to germline-specific co-expression clusters. Mutations in Ppa-rde-3, lead to sterility. In contrast, in Strongyloides spp., we found poly(UG)-tailed RNAs to be much less abundant, if not absent. Our results show that poly(UG)-tailed RNAs are not restricted to C. elegans and suggest that they play an important function in the germ line in P. pacificus.

molecular biology↗

bioRxiv2025

Diet-derived vitamin B12 induces transgenerational inheritance of nematode predation through elevated vitellogenin provisioning

Dietary and nutritional effects can alter organismal phenotypes and influence trait inheritance over generations, so-called transgenerational epigenetic inheritance. However, the chemical nature of the stimuli and the downstream events inducing such memory remain largely elusive. The nematode Pristionchus pacificus exhibits mouth-form plasticity including predation and was recently shown to respond to a multigenerational Novosphingobium diet with the induction and subsequent transgenerational inheritance of the predatory morph. Here, we show that bacteria-derived vitamin B12 is both necessary and sufficient for transgenerational memory. Different vitamin B12 concentrations are required for the original induction and the subsequent transgenerational inheritance of the predatory morph. Mutant analysis revealed that vitamin B12 functions through methionine-synthase and involves methionine but not vitamin B9. The inherited effect acts through increased multigenerational vitellogenin transcription indicating elevated nutrient provisioning. Consistently, mutants in the vitellogenin receptor Ppa-rme-2 are memory-defective. Thus, vitamin B12 induces vitellogenin provisioning to control organismal physiology and behavior.

genetics↗

bioRxiv2024

Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, behavior, and survival

All animals live in tight association with complex microbial communities, yet studying the effects of individual bacteria remains challenging. Here, we exploit the system of the bacterial feeding nematode Pristionchus pacificus, where specific interactions can be studied in isolation. We sequenced the genomes of 84 Pristionchus-associated bacteria to investigate how differences in bacterial metabolic potential affect nematode traits. Specifically, we identified the Paerucumarin biosynthesis pathway as a strong candidate for nematode survival. Hypothesizing that bacterial production of coumarin derivatives contributed to increased lethality, we demonstrated nematicidal effects of two related compounds using supplementation assays. To explore metabolic interactions at a broader scale, we generated nematode transcriptomes for 38 bacterial diets and constructed a coexpression network that revealed distinct developmental and environmental signatures. Interspecies association studies resulted in a bipartite network with more than 2,800 interactions which may assist future studies to identify metabolites affecting various biological processes.

microbiology↗

bioRxiv2024

EBAX-1/ZSWIM8 destabilizes miRNAs resulting in transgenerational memory of a predatory trait

Environmental influences on traits and associated transgenerational epigenetic inheritance have widespread implications, but remain controversial and underlying mechanisms poorly understood. We introduce long-term environmental induction experiments on alternative diets in Pristionchus pacificus, a nematode exhibiting mouth-form plasticity including predation, by propagating 110 isogenic lines for 101 generations with associated food-reversal experiments. We found dietary induction and subsequent transgenerational memory of the predatory morph and identified a role of ubiquitin ligase EBAX-1/ZSWIM8 in this process. Ppa-ebax-1 mutants have no memory and Ppa-EBAX-1 destabilizes the clustered microRNA family miR-2235a/miR-35. Deletions of a cluster of 44 identical miR-2235a copies resulted in precocious and extended transgenerational inheritance of the predatory morph. These findings indicate that EBAX-1/ZSWIM8 destabilizes miRNAs resulting in transgenerational memory, suggesting a role for target-directed miRNA degradation.

genetics↗

bioRxiv2024

The genome assembly of Rhabditoides inermis from a complex microbial community reveals further evidence for parallel gene family expansions across multiple nematodes

BackgroundFree-living nematodes such as Caenorhabditis elegans and Pristionchus pacificus are powerful model systems for linking specific traits to their underlying genetic basis. To trace the evolutionary history of a candidate gene, a robust phylogenomic framework is indispensable. ResultsIn this work, we generated a near chromosome-scale genome assembly of the nematode Rhabditoides inermis which had previously been proposed as the sister group of the family Diplogastridae to which P. pacificus belongs. The genome was assembled from a complex microbial community that consists of multiple bacteria and a fungus of the genus Vanrija. The R. inermis genome has five chromosomes that likely arose from recent fusions of different Nigon elements. Phylogenomic analysis grouped R. inermis within a clade including C. elegans, Mesorhabditis belari and other rhabditids and thus, did not support a sister group relationship between R. inermis and the family Diplogastridae. Comparative genomic analyses identified abundant lineage-specific orthogroups which reveal evidence for parallel expansions of environmentally responsive gene families. ConclusionsOur work demonstrates the value of the R. inermis genome as a resource for future phylogenomic analysis and for studying gene family evolution.

genomics↗

bioRxiv2022

Did Caenorhabditis nematodes recycle transposons to fight pathogens?

Animal genomes consist largely of sequences derived from transposons which were previously considered as junk DNA and active transposons can even be deleterious for organismal fitness. Nevertheless, the huge pool of transposon-derived sequences also forms the raw material for molecular innovations. Here, we follow up on the incidental finding of a transposon-derived DNA binding domain in a subset of F-box genes in Caenorhabditis elegans. Based on phylogenetic analysis, we show that a single gene fusion followed by individual losses explains most members of this novel gene family. Phylogenomic data of available Caenorhabditis genomes allowed us to trace this fusion event to the ancestor of the Elegans group. Additional homology searches suggest endogenous Mariner transposons as the likely source of the coopted sequence. Further bioinformatic characterization of different F-box families by Gene Ontology analysis, gene module comparisons, and literature research identified first evidence that some F-box genes might be involved in innate immunity, as it had been proposed previously based on adaptive signatures of molecular evolution. Specifically, the F-box gene fbxa-158 contains one of the transposon-derived domains and was shown to interact with the components of the intracellular pathogen response machinery targeting Microsporidia and viruses. Thus, cooption of transposon-derived sequences likely contributed to the adaptive evolution of the F-box superfamily in Caenorhabditis nematodes. Significance statementWhen considering transposons as genomic junk or selfish elements that are detrimental for organismal fitness, we often neglect the potential of transposon-derived sequences as a source of molecular innovation. Here, we characterize a case where a transposon-derived sequence has been coopted by one of the largest and fastest evolving gene superfamilies in Caenorhabditis nematodes which include the model organism C. elegans. The resulting chimeric gene family has been stably maintained for about 20 million years and bioinformatic analysis reveals first evidence for potential functions in innate immunity. Thus, strong evolutionary pressure might have forced Caenorhabditis nematodes to recycle transposons in order to fight pathogens.

evolutionary biology↗

bioRxiv2021

Influence of environmental temperature on mouth-form plasticity in Pristionchus pacificus acts through daf-11-dependent cGMP signaling

Mouth-form plasticity in the nematode Pristionchus pacificus has become a powerful system to identify the genetic and molecular mechanisms associated with phenotypic (developmental) plasticity. In particular, the identification of developmental switch genes that can sense environmental stimuli and reprogram developmental processes has confirmed long-standing evolutionary theory. Together with the associated gene regulatory networks, these developmental switch genes have been important to show that plasticity is consistent with the Modern Synthesis of evolution. However, how these genes are involved in the direct sensing of the environment, or if the switch genes act downstream of another, primary environmental sensing mechanism, remains currently unknown. Here, we study the influence of environmental temperature on mouth-form plasticity. Using forward and reverse genetic technology including CRISPR/Cas9, we show that mutations in the guanylyl cyclase Ppa-daf-11, the Ppa-daf-25/AnkMy2 and the cyclic nucleotide-gated channel Ppa-tax-2 eliminate the response to elevated temperatures. Together, our study indicates that DAF-11, DAF-25 and TAX-2 have been co-opted for environmental sensing during mouth-form plasticity regulation in P. pacificus. This work suggests that developmental switch genes integrate environmental signals including perception by cGMP signaling.

genetics↗

bioRxiv2020

A simplified workflow for the analysis of whole-genome sequencing data from Pristionchus pacificus mutant lines

Nematodes are attractive model systems to understand the genetic basis of various biological processes ranging from development to complex behaviors. In particular, mutagenesis experiments combined with whole-genome sequencing has been proven as one of the most effective methods to identify core players of multiple biological pathways. To enable experimentalists to apply such integrative genetic and bioinformatic analysis in the case of the satellite model organism Pristionchus pacificus, I present a simplified workflow for the analysis of whole-genome data from mutant lines and corresponding mapping panels. Individual components are based on well-maintained and widely used software packages and are extended by 50 lines of code for the analysis and visualization of allele frequencies. The effectiveness of this workflow is demonstrated by an application to recently generated data of a P. pacificus mutant line, where it reduced the number of candidate mutations from an initial set of 3,500 single nucleotide variants to ten.

bioinformatics↗

bioRxiv2019

Bacterial derived vitamin B12 enhances predatory behaviors in nematodes

The microbiome is known to affect host development, metabolism and immunity, however, its impact on behaviors is only beginning to be understood. Here, we investigate how bacteria modulate complex behaviors in the nematode model organism Pristionchus pacificus. P. pacificus is a predator feeding on the larvae of other nematodes including Caenorhabditis elegans. Growing P. pacificus on different bacteria and testing their ability to kill C. elegans reveals drastic differences in killing efficiencies with a Novosphingobium species showing the strongest enhancement. Strikingly, increased killing was not accompanied by an increase in feeding, a phenomenon known as surplus-killing whereby predators kill more prey than necessary for sustenance. RNA-seq revealed widespread metabolic rewiring upon exposure to Novosphingobium, which facilitated the screening for bacterial mutants leading to an altered transcriptional response. This identified bacterial derived vitamin B12 as a major micronutrient enhancing predatory behaviors. Vitamin B12 is an essential cofactor for detoxification and metabolite biosynthesis and has previously been shown to accelerate development in C. elegans. In P. pacificus vitamin B12 supplementation amplified, whereas mutants in vitamin B12-dependent pathways reduced surplus-killing. This demonstrates that bacterial vitamin B12 affects complex behaviors and thus establishes a connection between microbial diet and the nervous system.

microbiology↗

bioRxiv2016

Parallel adaptation to higher temperatures in divergent clades of the nematode Pristionchus pacificus

Studying the effect of temperature on fertility is particularly important in the light of ongoing climate change. We need to know if organisms can adapt to higher temperatures and, if so, what are the evolutionary mechanisms behind such adaptation. Such studies have been hampered by the lack different populations of sufficient sizes with which to relate the phenotype of temperature tolerance to the underlying genotypes. Here, we examined temperature adaptation in populations of the nematode Pristionchus pacificus, in which individual strains are able to successfully reproduce at 30{degrees}C. Analysis of the frequency of heat tolerant strains in different temperature zones on La Reunion supports that this trait is subject to natural selection. Reconstruction of ancestral states along the phylogeny of highly differentiated P. pacificus clades suggests that heat tolerance evolved multiple times independently. This is further supported by genome wide association studies showing that heat tolerance is a polygenic trait and that different loci are used by individual P. pacificus clades to develop heat tolerance. More precisely, analysis of allele frequencies indicated that most genetic markers that are associated with heat tolerance are only polymorphic in individual clades. While in some P. pacificus clades, parallel evolution of heat tolerance can be explained by ancestral polymorphism or by gene flow across clades, we observe at least one clearly distinct and independent scenario where heat tolerance emerged by de novo mutation. Thus, temperature tolerance evolved at least two times independently in the evolutionary history of this species. Our data suggest that studies of wild populations of P. pacificus will reveal distinct cellular mechanisms driving temperature adaptation.

evolutionary biology↗