ArticleBMC biology2015
A dynamic evolutionary and functional landscape of plant phased small interfering RNAs.
Article in BMC biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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
34 citing papers in PubMed, 1 synthesis or guideline pooled it, 76 citations in OpenAlex.
- The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea).The plant genome · 2023Pooled it
- Evolutionarily New Solanaceous DCL2 Family Members Acquire Functions in Tomato.Molecular plant pathology · 2025Article
- Dynamics of small RNAs in a red-fruited wine grape cultivar infected with Grapevine red blotch virus.BMC genomics · 2025Article
- Tweaking the Small Non-Coding RNAs to Improve Desirable Traits in Plant.International journal of molecular sciences · 2023Review
- Role of phasiRNAs in plant-pathogen interactions: molecular perspectives and bioinformatics tools.Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Review
- fIdentification of B. napus small RNAs responsive to infection by a necrotrophic pathogen.BMC plant biology · 2021Article
- Transgenerational conditioned male fertility of HD-ZIP IV transcription factor mutant ocl4: impact on 21-nt phasiRNA accumulation in pre-meiotic maize anthers.Plant reproduction · 2021Article
- Degradome sequencing-based identification of phasiRNAs biogenesis pathways in Oryza sativa.BMC genomics · 2021Article
- License to Regulate: Noncoding RNA Special Agents in Plant Meiosis and Reproduction.Frontiers in plant science · 2021Review
- Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology.Frontiers in plant science · 2021Review
- PhasiRNAs in Plants: Their Biogenesis, Genic Sources, and Roles in Stress Responses, Development, and Reproduction.The Plant cell · 2020Review
- Role of phasiRNAs from two distinct phasing frames of GhMYB2 loci in cis- gene regulation in the cotton genome.BMC plant biology · 2020Article
- Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants.Genome research · 2020Article
- The small RNA locus map for Chlamydomonas reinhardtii.PloS one · 2020Article
- Genome-Wide Analysis of Cotton miRNAs During Whitefly Infestation Offers New Insights into Plant-Herbivore Interaction.International journal of molecular sciences · 2019Article
- Small RNA discovery in the interaction between barley and the powdery mildew pathogen.BMC genomics · 2019Article
- Identification of miRNAs and Their Response to Cold Stress inBiomolecules · 2019Article
- Tapetum-Dependent Male Meiosis Progression in Plants: Increasing Evidence Emerges.Frontiers in plant science · 2019Review
- Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA-dominatedPlant direct · 2018Article
- Genome-wide comparative analysis in Solanaceous species reveals evolution of microRNAs targeting defense genes in Capsicum spp.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSecondary, phased small interfering RNAs (phasiRNAs) derived from protein-coding or noncoding loci (PHAS) are emerging as a new type of regulators of gene expression in plants. However, the evolution and function of these novel siRNAs in plant species remain largely unexplored.
resultsWe systematically analyzed PHAS loci in 23 plant species covering major phylogenetic groups spanning alga, moss, gymnosperm, basal angiosperm, monocot, and dicot. We identified over 3,300 PHAS loci, among which ~1,600 were protein-coding genes. Most of these PHAS loci were novel and clade- or species-specific and showed distinct expression patterns in association with particular development stages, viral infection, or abiotic stresses. Unexpectedly, numerous PHAS loci produced phasiRNAs from introns or exon-intron junction regions. Our comprehensive analysis suggests that phasiRNAs predominantly regulate protein-coding genes from which they are derived and genes from the same families of the phasiRNA-deriving genes, in contrast to the dominant trans-regulatory mode of miRNAs. The stochastic occurrence of many PHAS loci in the plant kingdom suggests their young evolutionary origins.
conclusionsOur study discovered an unprecedented diversity of protein-coding genes that produce phasiRNAs in a wide variety of plants, and set a kingdom-wide foundation for investigating the novel roles of phasiRNAs in shaping phenotype diversities of plants.
Indexed as
Identifiers
What OpenQuestion 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 OpenQuestion graph.