ArticleGenome research2020
Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it, 81 citations in OpenAlex.
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- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- Regulatory Landscapes of Non-Coding RNAs During Drought Stress in Plants.International journal of molecular sciences · 2025Review
- Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network.International journal of molecular sciences · 2025Article
- Advancing ornamental plant breeding through genomic technologies: opportunities, challenges, and future directions.Functional & integrative genomics · 2025Review
- Identification and Characterization of Copper-Responsive miRNAs and Their Target Genes in Jerusalem Artichoke.Plants (Basel, Switzerland) · 2025Article
- Widespread impact of transposable elements on the evolution of post-transcriptional regulation in the cotton genus Gossypium.Genome biology · 2025Article
- Artificial Sweet Cherry miRNA 396 Promotes Early Flowering in Vernalization-Dependent Arabidopsis Edi-0 Ecotype.Plants (Basel, Switzerland) · 2025Article
- Evolution of Plant Conserved microRNAs After Whole-Genome Duplications.Genome biology and evolution · 2025Article
- TIPPo: A User-Friendly Tool for De Novo Assembly of Organellar Genomes with High-Fidelity Data.Molecular biology and evolution · 2025Article
- Class-agnostic annotation of small RNAs balances sensitivity and specificity in diverse organisms.Computational and structural biotechnology journal · 2025Article
- A telomere-to-telomere cotton genome assembly reveals centromere evolution and a Mutator transposon-linked module regulating embryo development.Nature genetics · 2024Article
- Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures.Pathogens (Basel, Switzerland) · 2024Article
- Identification of Arabidopsis thaliana small RNAs responsive to the fungal pathogen Botrytis cinerea at an early stage of interaction.PloS one · 2024Article
- Small RNAs >26 nt in length associate with AGO1 and are upregulated by nutrient deprivation in the alga Chlamydomonas.The Plant cell · 2023Article
- Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Small RNAs and Karma methylation in Elaeis guineensis mother palms are linked to high clonal mantling.Plant molecular biology · 2023Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Plant endogenous small RNAs (sRNAs) are important regulators of gene expression. There are two broad categories of plant sRNAs: microRNAs (miRNAs) and endogenous short interfering RNAs (siRNAs). MicroRNA loci are relatively well-annotated but compose only a small minority of the total sRNA pool; siRNA locus annotations have lagged far behind. Here, we used a large data set of published and newly generated sRNA sequencing data (1333 sRNA-seq libraries containing more than 20 billion reads) and a uniform bioinformatic pipeline to produce comprehensive sRNA locus annotations of 47 diverse plants, yielding more than 2.7 million sRNA loci. The two most numerous classes of siRNA loci produced mainly 24- and 21-nucleotide (nt) siRNAs, respectively. Most often, 24-nt-dominated siRNA loci occurred in intergenic regions, especially at the 5'-flanking regions of protein-coding genes. In contrast, 21-nt-dominated siRNA loci were most often derived from double-stranded RNA precursors copied from spliced mRNAs. Genic 21-nt-dominated loci were especially common from disease resistance genes, including from a large number of monocots. Individual siRNA sequences of all types showed very little conservation across species, whereas mature miRNAs were more likely to be conserved. We developed a web server where our data and several search and analysis tools are freely accessible.
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