ArticlePlant physiology2023
Phylogenetic analyses of seven protein families refine the evolution of small RNA pathways in green plants.
Article in Plant physiology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 31 citations in OpenAlex.
- Sequence Conservation and Functional Significance of Charged Clusters in Mitochondria-Located Proteins of Green Plants.Journal of molecular evolution · 2026Article
- Reproductive phasiRNAs are the piRNAs of plants.Trends in genetics : TIG · 2026Review
- Molecular basis of plant DCL4 action that outcompetes DCL2.Nature plants · 2026Article
- Article
- Epigenetic control of seed development and dormancy in cereals.Plant signaling & behavior · 2025Review
- Distinct classes of 21- and 24-nt phasiRNAs suggests diverse mechanisms of biogenesis and function in rice anther development.The plant genome · 2025Article
- Article
- Targeted seed EMS mutagenesis reveals a basic helix-loop-helix transcription factor underlying male sterility in sorghum.Genetics · 2025Article
- Importance of an N-terminal structural switch in the distinction between small RNA-bound and free ARGONAUTE.Nature structural & molecular biology · 2025Article
- Identification and characterization of DICER-LIKE genes and their roles in Marchantia polymorpha development and salt stress response.The Plant journal : for cell and molecular biology · 2025Article
- Decoding the Dialog Between Plants and Arbuscular Mycorrhizal Fungi: A Molecular Genetic Perspective.Genes · 2025Review
- Comparative RNA profiling identifies stage-specific phasiRNAs and coexpressed Argonaute genes in Bambusoideae and Pooideae species.The Plant cell · 2024Article
- Genome-wide identification, characterization and expression analysis of key gene families in RNA silencing in centipedegrass.BMC genomics · 2024Article
- Conservation of molecular responses upon viral infection in the non-vascular plant Marchantia polymorpha.Nature communications · 2024Article
- Charophytic Green Algae Encode Ancestral Polymerase IV/Polymerase V Subunits and a CLSY/DRD1 Homolog.Genome biology and evolution · 2024Article
- Premeiotic 24-nt phasiRNAs are present in theProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Premeiotic 24-nt phasiRNAs are present in thebioRxiv : the preprint server for biology · 2024Article
- Beyond Loading: Functions of Plant ARGONAUTE Proteins.International journal of molecular sciences · 2023Review
- Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development.Plant molecular biology · 2023Review
- Recent Insights into Plant miRNA Biogenesis: Multiple Layers of miRNA Level Regulation.Plants (Basel, Switzerland) · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Several protein families participate in the biogenesis and function of small RNAs (sRNAs) in plants. Those with primary roles include Dicer-like (DCL), RNA-dependent RNA polymerase (RDR), and Argonaute (AGO) proteins. Protein families such as double-stranded RNA-binding (DRB), SERRATE (SE), and SUPPRESSION OF SILENCING 3 (SGS3) act as partners of DCL or RDR proteins. Here, we present curated annotations and phylogenetic analyses of seven sRNA pathway protein families performed on 196 species in the Viridiplantae (aka green plants) lineage. Our results suggest that the RDR3 proteins emerged earlier than RDR1/2/6. RDR6 is found in filamentous green algae and all land plants, suggesting that the evolution of RDR6 proteins coincides with the evolution of phased small interfering RNAs (siRNAs). We traced the origin of the 24-nt reproductive phased siRNA-associated DCL5 protein back to the American sweet flag (Acorus americanus), the earliest diverged, extant monocot species. Our analyses of AGOs identified multiple duplication events of AGO genes that were lost, retained, or further duplicated in subgroups, indicating that the evolution of AGOs is complex in monocots. The results also refine the evolution of several clades of AGO proteins, such as AGO4, AGO6, AGO17, and AGO18. Analyses of nuclear localization signal sequences and catalytic triads of AGO proteins shed light on the regulatory roles of diverse AGOs. Collectively, this work generates a curated and evolutionarily coherent annotation for gene families involved in plant sRNA biogenesis/function and provides insights into the evolution of major sRNA pathways.
Indexed as
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.