Biology subjects

Postuma, M.

Publications and source records attributed to Postuma, M..

3 recordsLinked to original sources

bioRxiv2023

DNA methylation responses to stress across different plant species

O_LIChanges in environments trigger plant DNA methylation responses, potentially modulating stress responses. Studies on stress-induced DNA methylation typically focus on single species, limiting our understanding of what are general and specific responses between species. C_LIO_LIUsing reduced-representation bisulfite sequencing epiGBS, we compared DNA methylation stress-responses across seven plant species. Because methylation can be targeted at transposable elements (TEs) and because environmental plasticity may be particularly relevant in asexual species, we hypothesize that genome size and reproduction mode explain differences in methylation responses between species. C_LIO_LIWe show that enrichment of environmentally-induced methylation responses in genes and TEs is a general feature across plant species. While previous studies have emphasized methylation responses in CHH-cytosines, we observed that cytosines in all sequence contexts (CG, CHG, CHH) are equally likely to respond to stress. Larger-genome species showed a higher proportion of stress-responding cytosines, and asexual species showed more cytosines with a strong methylation response to stress than sexually responding species. C_LIO_LIOur study highlights the role of TEs in methylome plasticity and identifies causes of variation in methylome plasticity. This provides guidance to extrapolating results from models to other plant species, and may contribute to better understanding of functionality of the response. C_LI

plant 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↗

bioRxiv2019

A tradeoff between robustness to environmental fluctuations and speed of evolution

Organisms must cope with both short- and long-term environmental changes to persist. In this study we investigated whether life histories trade-off between their robustness to short-term environmental perturbations and their ability to evolve directional trait changes. We could confirm the tradeoff by modeling the eco-evolutionary dynamics of life-histories along the fast-slow pace-of-life continuum. Offspring dormancy and high adult survival rates allowed for large population sizes to be maintained in face of interannual environmental fluctuations but limited the speed of trait evolution with ongoing environmental change. In contrast, precocious offspring maturation and short-living adults promoted evolvability while lowering demographic robustness. This tradeoff had immediate consequences on extinction dynamics in variable environments. High evolvability allowed short-lived species to cope with long-lasting gradual environmental change, but came at the expense of more pronounced population declines and extinction rates from environmental variability. Higher robustness of slow life-histories helped them persist better on short timescales.

evolutionary biology↗