ArticlePLoS genetics2014
Evolution of DNA methylation patterns in the Brassicaceae is driven by differences in genome organization.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
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98 citing papers in PubMed.
- Transposon expansion is associated with reorganization of small RNA and DNA methylation landscapes in the morphologically minimal angiosperm Wolffia brasiliensis.The Plant journal : for cell and molecular biology · 2026Article
- Convergence and divergence of DNA methylation and gene expression patterns in neopolyploid Arabidopsis kamchatica.Nature communications · 2026Article
- A dynamic epigenetic perspective on above- and belowground phenotypic responses to drought: Insights from global DNA methylation in Erodium cicutarium.Plant biology (Stuttgart, Germany) · 2026Article
- DNA methylation in invertebrate genomes and cell lineage plasticity.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Genotype-dependent DNA methylation patterns are negatively associated with allelic variation rather than heat-induced gene expression in two contrasting potato genotypes.The Plant journal : for cell and molecular biology · 2026Article
- Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducingGenome research · 2025Article
- Bridging micro and macroevolution: insights from chromosomal dynamics in plants.Frontiers in plant science · 2025Review
- Almond Grafting for Plum Pox Virus Resistance Triggers Significant Transcriptomic and Epigenetic Shifts in Peaches.International journal of molecular sciences · 2024Article
- Genome-wide DNA methylation and their transgenerational pattern differ in Arabidopsis thaliana populations originated along the elevation of West Himalaya.BMC plant biology · 2024Article
- The evolutionary consequences of interactions between the epigenome, the genome and the environment.Evolutionary applications · 2024Review
- DNA Methylation Analysis of Growth Differences between Upright and Inverted Cuttings ofInternational journal of molecular sciences · 2024Article
- High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features.EMBO reports · 2024Article
- Complementing model species with model clades.The Plant cell · 2024Review
- Differentiation of Morphological Traits and Genome-Wide Expression Patterns between Rice SubspeciesGenes · 2023Article
- Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants.Genome biology · 2023Article
- Warmer temperature during asexual reproduction induce methylome, transcriptomic, and lasting phenotypic changes inHorticulture research · 2023Article
- Multi-omic analyses reveal the unique properties of chia (Salvia hispanica) seed metabolism.Communications biology · 2023Article
- DNA methylation signatures of duplicate gene evolution in angiosperms.Plant physiology · 2023Article
- 6mA DNA Methylation on Genes in Plants Is Associated with Gene Complexity, Expression and Duplication.Plants (Basel, Switzerland) · 2023Article
- Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor.PLoS genetics · 2022Article
38 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA methylation is an ancient molecular modification found in most eukaryotes. In plants, DNA methylation is not only critical for transcriptionally silencing transposons, but can also affect phenotype by altering expression of protein coding genes. The extent of its contribution to phenotypic diversity over evolutionary time is, however, unclear, because of limited stability of epialleles that are not linked to DNA mutations. To dissect the relative contribution of DNA methylation to transposon surveillance and host gene regulation, we leveraged information from three species in the Brassicaceae that vary in genome architecture, Capsella rubella, Arabidopsis lyrata, and Arabidopsis thaliana. We found that the lineage-specific expansion and contraction of transposon and repeat sequences is the main driver of interspecific differences in DNA methylation. The most heavily methylated portions of the genome are thus not conserved at the sequence level. Outside of repeat-associated methylation, there is a surprising degree of conservation in methylation at single nucleotides located in gene bodies. Finally, dynamic DNA methylation is affected more by tissue type than by environmental differences in all species, but these responses are not conserved. The majority of DNA methylation variation between species resides in hypervariable genomic regions, and thus, in the context of macroevolution, is of limited phenotypic consequence.
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