ArticleThe Plant cell2014
An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers, 2 of them syntheses that pooled it.
What it found
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Who cites it
87 citing papers in PubMed, 2 syntheses or guidelines pooled it, 160 citations in OpenAlex.
- The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea).The plant genome · 2023Pooled it
- The Brassicaceae Family Displays Divergent, Shoot-Skewed NLR Resistance Gene Expression.Plant physiology · 2018Pooled it
- Epigenomics and Non-Coding RNAs in Soybean Adaptation to Abiotic Stresses.International journal of molecular sciences · 2025Review
- Tissue- and Condition-Specific Biosynthesis of Ascorbic Acid inInternational journal of molecular sciences · 2025Article
- Deciphering the impact of microRNAs in plant biology: a review of computational insights and experimental validation.Molecular biology reports · 2025Review
- The biogenesis, regulation and functions of transitive siRNA in plants.Acta biochimica et biophysica Sinica · 2024Review
- The role of microRNAs in NBS-LRR gene expression and its implications for plant immunity and crop development.Transgenic research · 2024Review
- Regulation of plant immunity via small RNA-mediated control of NLR expression.Journal of experimental botany · 2023Article
- Identification and characterization of miRNAs and PHAS loci related to the early development of the embryo and endosperm in Fragaria × ananassa.BMC genomics · 2022Article
- Heightened miR6024-NLR interactions facilitate necrotrophic pathogenesis in tomato.Plant molecular biology · 2022Article
- 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
- Progress in soybean functional genomics over the past decade.Plant biotechnology journal · 2022Review
- Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs.BMC genomics · 2022Article
- Epigenetic Mechanisms of Senescence in Plants.Cells · 2022Review
- microRNAs and Their Roles in Plant Development.Frontiers in plant science · 2022Review
- tRNA derived small RNAs-Small players with big roles.Frontiers in genetics · 2022Review
- Review
- Uncovering miRNA-mRNA Regulatory Modules in Developing Xylem ofInternational journal of molecular sciences · 2021Article
- MiR1885 Regulates Disease Tolerance Genes inInternational journal of molecular sciences · 2021Article
- Pre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants.Nature communications · 2021Article
27 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
12 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed from mRNA forming stem-loops; and (2) small interfering RNAs (siRNAs), the latter derived in plants by a process typically requiring an RNA-dependent RNA polymerase. We constructed and analyzed an expression atlas of soybean (Glycine max) small RNAs, identifying over 500 loci generating 21-nucleotide phased siRNAs (phasiRNAs; from PHAS loci), of which 483 overlapped annotated protein-coding genes. Via the integration of miRNAs with parallel analysis of RNA end (PARE) data, 20 miRNA triggers of 127 PHAS loci were detected. The primary class of PHAS loci (208 or 41% of the total) corresponded to NB-LRR genes; some of these small RNAs preferentially accumulate in nodules. Among the PHAS loci, novel representatives of TAS3 and noncanonical phasing patterns were also observed. A noncoding PHAS locus, triggered by miR4392, accumulated preferentially in anthers; the phasiRNAs are predicted to target transposable elements, with their peak abundance during soybean reproductive development. Thus, phasiRNAs show tremendous diversity in dicots. We identified novel miRNAs and assessed the veracity of soybean miRNAs registered in miRBase, substantially improving the soybean miRNA annotation, facilitating an improvement of miRBase annotations and identifying at high stringency novel miRNAs and their targets.
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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.