bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.10.29.762914

DNA demethylases constrain multigenerational methylome and transcriptome divergence

Dmitrieva, A. D.·Christensen, K. I.·Williams, B. P.
View original source ↗Export metadata ↓

Abstract

In plants, animals and fungi, DNA methylation is important for the silencing of repetitive DNA and impacts the expression of a subset of genes. DNA methylation landscapes exhibit a high degree of stability over generations, yet this stability is the product of multiple dynamic methylation and demethylation pathways. How these dynamic pathways function over longer multigenerational timescales is unclear. To address this, we inbred quadruple DNA demethylase Arabidopsis mutants and closely related wild type lines for nine generations by single-seed descent. In inbred mutant lines, methylation gains accumulated across generations, with regions of preexisting methylation becoming progressively reinforced or spreading to proximal sequences. Additionally, each inbred line possessed hundreds of de novo methylation gains in unmethylated regions. Two-thirds of all methylation gains and 85% of de novo methylated loci were unique to only one inbred line, suggesting a high degree of stochasticity in multigenerational methylation dynamics. Individual inbred lines also exhibited substantial divergence in both their transcriptomes and small RNA profiles. Our data lead to a model in which DNA demethylases constrain the epigenome and transcriptome space accessible over multigenerational timescales. Long-term loss of DNA demethylase activity causes lineages to drift further apart to more diverged epigenetic landscapes.

Explore related subjects

plant biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Dmitrieva, A. D., Christensen, K. I., Williams, B. P.. 2026-10-30. DNA demethylases constrain multigenerational methylome and transcriptome divergence. https://doi.org/10.64898/2026.10.29.762914

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Spatial expression evolution of duplicated genes post-whole genome duplication in cultivated tomato

The mechanisms by which whole genome duplication contributes to expression divergence of duplicate genes, which can impact the evolution of form and function, has been a long-standing question in evolutionary biology. We compared expression patterns of paralogs derived from the most recent Solanaceae-specific genome triplication event across 23 tissues and inferred ancestral expression states to investigate patterns of expression evolution. While the partitioning of ancestral expression states is traditionally considered the second most common (after the gene loss) trajectory of duplicate expression evolution, we found that the ancestral expression states tended to be retained by most (~66%) duplicates, with ~6% of gene lineages experiencing expression gain events and ~20% experiencing expression losses. The genes that gained expression in fruit tissues are significantly enriched with functions associated with fruit quality. Notably, asymmetrical expression divergence is prevalent among duplicates, especially when ancestral genes were either not expressed or were highly expressed. Our study demonstrates the utility of integrating paralog expression comparisons with phylogenetic analyses to document the potential evolutionary history of spatial expression patterns and gain insight into how expression divergence contributes to the evolution of function across tissues.

plant biology↗
bioRxiv2026

On the asymbiotic germination of some New Zealand spider orchids (Corybas).

Corybas is a large and widespread genus of terrestrial orchids, but little has been done to understand their germination. We tested germination of five species of helmet orchid (C. cheesemanii, C. dienemus, C. iridescens, C. macranthus and C. oblongus) on a range of asymbiotic media. Corybas macranthus germinated on four of seven tested media. From other species there was limited germination; for C. cheesemanii germination occurred for only two of five capsules collected concurrently and sown under the same conditions. The failure of filled seeds to germinate under optimal conditions could suggests the presence of seed dormancy. We trialed desiccation and warm moist stratification as methods to break dormancy, however this was unsuccessful.

plant biology↗
bioRxiv2026

Compost from urban biowaste shapes the bacterial community and its functional traits in the rhizosphere of tomato plants

Industrial compost derived from urban biowaste is a sustainable biofertilizer made from food waste and plant matter. It has long been used as a fertilizer in agriculture and horticulture for its rich nutrient content. However, the composition of the microbiota in industrial biowaste compost has been studied only partially, and the effects of this bacterial community on soil, rhizosphere, and plant root communities have received limited attention. In this study, we conducted community and functional analyses to examine how the microbiota in biowaste compost influences bacterial diversity, community composition, and metabolic potential in tomato plants, compared with plants fertilized with conventional, unsustainable chemical fertilizer. Source contribution analysis tracking bacterial taxa indicated a significant contribution of compost-derived taxa to the soil, rhizosphere, and roots. The community analysis revealed distinct clustering by fertilizer type, with biowaste compost promoting a unique, more diverse rhizosphere community, enriched in Firmicutes species. Functional analysis highlighted increased microbial pathways in the rhizosphere treated with biowaste compost, including enzymes for cellulolytic and xylanolytic activity, nitrogenase, phytase, and 1-ACC deaminase. Overall, food-derived industrial biowaste compost enhances bacterial diversity and the predicted functional and plant growth-promoting potential in the rhizosphere of tomato plants, underscoring its potential as a sustainable biofertilizer that supports soil health, microbial biodiversity, and crop productivity.

plant biology↗