Biology subjects

Gawehns, F.

Publications and source records attributed to Gawehns, F..

3 recordsLinked to original sources

bioRxiv2023

Epigenetic variation causes heritable variation in complex traits in the mollusk Biomphalaria glabrata, vector of the human parasite Schistosoma mansoni

DNA methylation variation may play a role in phenotypic variation as it can be directly affected by the environment and be inherited. DNA methylation variations were introduced into the parasite vector snail Biomphalaria glabrata with low genetic diversity by chemical treatment in F0 and followed over 3 generations using epigenetic recombinant inbred lines (epiRILs). We observed phenotypic variation in complex traits such as fecundity and susceptibility to infestation by Schistosoma mansoni and DNA methylation differences in F3. Both, increase and decrease of infestation success (up to 100% and down to 20% prevalence in epiRILs and from 86% to 94% in control RILs) indicated variation in complex resistance/compatibility trait. Average prevalence in control RILs was 84{+/-}5% but only 68{+/-}21 % in epiRILs. Fecundity also changed and was in average 47{+/-}7% in control RILs and 59{+/-}18% in epiRILs, being 12% higher in epiRILs. We found that the heritability h2 of the fecundity in the epiRILs was between 0.5 and 0.6 depending on the method used to estimate it. We developed a model for introducing epimutant offspring snails into resident susceptible populations. If genetic assimilation of the resistant phenotype occured in a small fraction of the introduced epimutant snails, we predict that the susceptible phenotype is replaced by the resistant phenotype after 50-70 generations.

ecology↗

bioRxiv2022

DNA methylation in clonal Duckweed lineages (Lemna minor L.) reflects current and historical environmental exposures.

While some DNA methylation variants are transgenerationally stable in plants, DNA methylation modifications that are specifically induced by environmental exposure are typically transient and subject to resetting in germ lines, limiting the potential for transgenerational epigenetics stress memory. Asexual reproduction circumvents germlines, and may be more conducive to long-term memory and inheritance of epigenetic marks. This, however, has been poorly explored. Taking advantage of the rapid clonal reproduction of the common duckweed Lemna minor, we tested the hypothesis that a long-term, transgenerational stress memory from exposure to high temperature can be detected in DNA methylation profiles. Using a reduced representation bisulfite sequencing approach (epiGBS), we show that high temperature stress induces DNA hypermethylation at many cytosines in CG and CHG contexts but not in CHH. In addition, a subset of the temperature responsive CHG cytosines, showed differential DNA methylation between in lineages exposed to 30{degrees}C and 24{degrees}C, 3-12 clonal generations after subsequent culturing in a common environment, demonstrating a memory effect of stress that persists over many clonal generations and that is reflected in DNA methylation. Structural annotation revealed that this memory effect in CHG methylation was enriched in TEs. We argue that the observed epigenetic stress memory is likely caused by stable transgenerational persistence of high temperature-induced DNA methylation variants across multiple clonal generations. To the extent that such epigenetic memory has functional consequences for gene expression and phenotypes, this result suggests potential for long-term modulation of stress responses in asexual plants and vegetatively propagated crops.

evolutionary biology↗

bioRxiv2020

epiGBS2: an improved protocol and automated snakemake workflow for highly multiplexed reduced representation bisulfite sequencing

epiGBS is an existing reduced representation bisulfite sequencing method to determine cytosine methylation and genetic polymorphisms de novo. Here, we present epiGBS2, an improved epiGBS laboratory protocol and user-friendly bioinformatics pipeline for a wide range of species with or without reference genome. epiGBS2 decreases costs and time investment and increases user-friendliness and reproducibility. The library protocol was adjusted to allow for a flexible choice of restriction enzymes and a double digest. Instead of fully methylated adapters, semi-methylated adapters are now used. The bioinformatics pipeline was improved in speed and integrated in the snakemake workflow management system, which now makes the pipeline easy to execute, modular, and parameter settings flexible. We also provide a detailed description of the laboratory protocol, an extensive manual of the bioinformatics pipeline, which is publicly accessible on github (https://github.com/nioo-knaw/epiGBS2) and zenodo (https://doi.org/10.5281/zenodo.3819996), and example output.

bioinformatics↗