ArticleGenome biology and evolution2015
Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway.
Article in Genome biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 51 citations in OpenAlex.
- RdDM-Dependent Epigenetic Regulation Coordinates Systemic Immunity and Compatibility withMicroorganisms · 2026Article
- Genome-Wide Identification of DNA Methyltransferase and Demethylase inPlants (Basel, Switzerland) · 2025Article
- Genome-Wide Identification and Analysis of DNA Methyltransferase and Demethylase Gene Families in Sweet Potato and Its Diploid Relative.Plants (Basel, Switzerland) · 2025Article
- Genome-wide identification and characterization of DNA methyltransferases and demethylases inFrontiers in plant science · 2025Article
- The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza.G3 (Bethesda, Md.) · 2024Article
- The Role of Chromatin Modifications in the Evolution of Giant Plant Genomes.Plants (Basel, Switzerland) · 2023Article
- Article
- The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine.Nature communications · 2023Article
- DDM1-Mediated TE Silencing in Plants.Plants (Basel, Switzerland) · 2023Review
- Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba.Scientific reports · 2021Article
- RNA-directed DNA Methylation.PLoS genetics · 2020Article
- RNA directed DNA methylation and seed plant genome evolution.Plant cell reports · 2020Review
- Establishment, maintenance, and biological roles of non-CG methylation in plants.Essays in biochemistry · 2019Review
- Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce.BMC genomics · 2019Article
- Tracing the origin and evolution history of methylation-related genes in plants.BMC plant biology · 2019Article
- Small RNA-seq reveals novel regulatory components for apomixis in Paspalum notatum.BMC genomics · 2019Article
- RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs.Nature communications · 2019Article
- Modeling Interactions between Transposable Elements and the Plant Epigenetic Response: A Surprising Reliance on Element Retention.Genome biology and evolution · 2018Article
- Review
- Small RNA-Omics for Plant Virus Identification, Virome Reconstruction, and Antiviral Defense Characterization.Frontiers in microbiology · 2018Review
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The RNA-directed DNA methylation (RdDM) pathway can be divided into three phases: 1) small interfering RNA biogenesis, 2) de novo methylation, and 3) chromatin modification. To determine the degree of conservation of this pathway we searched for key genes among land plants. We used OrthoMCL and the OrthoMCL Viridiplantae database to analyze proteomes of species in bryophytes, lycophytes, monilophytes, gymnosperms, and angiosperms. We also analyzed small RNA size categories and, in two gymnosperms, cytosine methylation in ribosomal DNA. Six proteins were restricted to angiosperms, these being NRPD4/NRPE4, RDM1, DMS3 (defective in meristem silencing 3), SHH1 (SAWADEE homeodomain homolog 1), KTF1, and SUVR2, although we failed to find the latter three proteins in Fritillaria persica, a species with a giant genome. Small RNAs of 24 nt in length were abundant only in angiosperms. Phylogenetic analyses of Dicer-like (DCL) proteins showed that DCL2 was restricted to seed plants, although it was absent in Gnetum gnemon and Welwitschia mirabilis. The data suggest that phases (1) and (2) of the RdDM pathway, described for model angiosperms, evolved with angiosperms. The absence of some features of RdDM in F. persica may be associated with its large genome. Phase (3) is probably the most conserved part of the pathway across land plants. DCL2, involved in virus defense and interaction with the canonical RdDM pathway to facilitate methylation of CHH, is absent outside seed plants. Its absence in G. gnemon, and W. mirabilis coupled with distinctive patterns of CHH methylation, suggest a secondary loss of DCL2 following the divergence of Gnetales.
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