Biology subjects

Quiobe, S. P.

Publications and source records attributed to Quiobe, S. P..

4 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

Adaptive consequences of transgenerational inheritance of a predatory mouth-form trait in nematodes

A growing body of evidence suggests that environmentally-induced changes in phenotypes can cross the generation barrier and associated molecular mechanisms are being increasingly identified. Such transgenerational epigenetic inheritance (TEI) is repeatedly considered to be adaptive although experimental support for this claim is often missing. We study the adaptive consequences of TEI in the facultative predatory nematode Pristionchus pacificus, which can form two alternative mouth forms dependent on environmental conditions. The choice of feeding structure in P. pacificus can be manipulated through dietary switching and food reversal. Recent studies showed that certain diets cause the induction of the predatory mouth form, which can result in TEI after food reversal. This memory requires the ubiquitin ligase EBAX-1/ZSWIM8 and the destabilization of clustered microRNAs. To study the adaptive potential of transgenerational memory of the predatory morph, we measured brood size as proxy for fitness. We compared naive worms, with those under dietary induction and food reversal, and found a fitness advantage for animals exhibiting TEI of the predatory morph. Specifically, after food reversal worms had higher lifetime reproductive success for up to three generations when compared to diet-induced or naive worms. These results support the adaptive significance of non-genetic inheritance of the predatory trait.

evolutionary 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

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↗