ArticlePLoS genetics2009
A genome-wide characterization of microRNA genes in maize.
Article in PLoS genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 178 papers, 1 of them a synthesis that pooled it.
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Who cites it
178 citing papers in PubMed, 1 synthesis or guideline pooled it, 371 citations in OpenAlex.
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- miRScore: A rapid and precise microRNA validation tool.PLoS computational biology · 2025Article
- The MIR157-SPL15 module regulates flowering and inflorescence development in Arabidopsis thaliana under short days and in Arabis alpina.PLoS genetics · 2025Article
- MicroRNA528 and Its Regulatory Roles in Monocotyledonous Plants.International journal of molecular sciences · 2025Review
- An intron-split microRNA mediates cleavage of the mRNA encoded by low phosphate root in Solanaceae.Planta · 2025Article
- MicroRNA408 negatively regulates salt tolerance by affecting secondary cell wall development in maize.Plant physiology · 2023Article
- INDETERMINATE1 autonomously regulates phosphate homeostasis upstream of the miR399-ZmPHO2 signaling module in maize.The Plant cell · 2023Article
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- Genome-Wide Expression Analysis of Long Noncoding RNAs and Their Target Genes in MetafemaleInternational journal of molecular sciences · 2023Article
- Small RNA and Degradome Sequencing in Floral Bud Reveal Roles of miRNAs in Dormancy Release ofInternational journal of molecular sciences · 2023Article
- Recent Insights into Plant miRNA Biogenesis: Multiple Layers of miRNA Level Regulation.Plants (Basel, Switzerland) · 2023Review
- Phylogenetic and functional analysis of tiller angle control homeologs in allotetraploid cotton.Frontiers in plant science · 2023Article
- Functional role of microRNA in the regulation of biotic and abiotic stress in agronomic plants.Frontiers in genetics · 2023Review
- Article
- Integrated High-Throughput Sequencing, Microarray Hybridization and Degradome Analysis Uncovers MicroRNA-Mediated Resistance Responses of Maize to PathogenInternational journal of molecular sciences · 2022Article
- Identification of miRNAs Mediating Seed Storability of Maize during Germination Stage by High-Throughput Sequencing, Transcriptome and Degradome Sequencing.International journal of molecular sciences · 2022Article
- Parallel analysis of RNA ends reveals global microRNA-mediated target RNA cleavage in maize.The Plant journal : for cell and molecular biology · 2022Article
- Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain.Plant physiology · 2022Article
- Rapid sequence and functional diversification of a miRNA superfamily targeting calcium signaling components in seed plants.The New phytologist · 2022Article
- The multiple fates of gene duplications: Deletion, hypofunctionalization, subfunctionalization, neofunctionalization, dosage balance constraints, and neutral variation.The Plant cell · 2022Article
118 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling identified 150 high-confidence genes within 26 miRNA families. For 25 families, expression was verified by deep-sequencing of small RNA libraries that were prepared from an assortment of maize tissues. PCR-RACE amplification of 68 miRNA transcript precursors, representing 18 families conserved across several plant species, showed that splice variation and the use of alternative transcriptional start and stop sites is common within this class of genes. Comparison of sequence variation data from diverse maize inbred lines versus teosinte accessions suggest that the mature miRNAs are under strong purifying selection while the flanking sequences evolve equivalently to other genes. Since maize is derived from an ancient tetraploid, the effect of whole-genome duplication on miRNA evolution was examined. We found that, like protein-coding genes, duplicated miRNA genes underwent extensive gene-loss, with approximately 35% of ancestral sites retained as duplicate homoeologous miRNA genes. This number is higher than that observed with protein-coding genes. A search for putative miRNA targets indicated bias towards genes in regulatory and metabolic pathways. As maize is one of the principal models for plant growth and development, this study will serve as a foundation for future research into the functional roles of miRNA genes.
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