ArticleGenome research2008
Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 238 papers.
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Who cites it
238 citing papers in PubMed, 468 citations in OpenAlex.
- Function and mechanism of double-stranded RNA-binding protein 1 in small RNA metabolism in tomato.The Plant journal : for cell and molecular biology · 2026Article
- Transcriptional control of tomato fruit development and ripening.Journal of experimental botany · 2025Review
- An intron-split microRNA mediates cleavage of the mRNA encoded by low phosphate root in Solanaceae.Planta · 2025Article
- Detection of Ethylene Signaling Using Bioinformatics Tools in Plants.Methods in molecular biology (Clifton, N.J.) · 2025Article
- MicroRNA Nobel Prize: Timely Recognition and High Anticipation of Future Products-A Prospective Analysis.International journal of molecular sciences · 2024Review
- Involvement of MicroRNAs in the Hypersensitive Response of Capsicum Plants to the Capsicum Chlorosis Virus at Elevated Temperatures.Pathogens (Basel, Switzerland) · 2024Article
- Interfamily Grafted HybridsPlants (Basel, Switzerland) · 2024Article
- Epigenetic insights into an epimutantFrontiers in plant science · 2024Review
- Differential expression of microRNAs in response toFrontiers in plant science · 2024Article
- Article
- Coordinating Diverse Functions of miRNA and lncRNA in Fleshy Fruit.Plants (Basel, Switzerland) · 2023Review
- Tomato MicroRNAs and Their Functions.International journal of molecular sciences · 2022Review
- Parasitic plant small RNA analyses unveil parasite-specific signatures of microRNA retention, loss, and gain.Plant physiology · 2022Article
- miR390-tasiRNA3-ARF4 pathway is involved in regulating flowering time in woodland strawberry.Plant cell reports · 2022Article
- Exploring the Effect of Methyl Jasmonate on the Expression of microRNAs Involved in Biosynthesis of Active Compounds of Rosemary Cell Suspension Cultures through RNA-Sequencing.International journal of molecular sciences · 2022Article
- Small RNA profiling reveals the involvement of microRNA-mediated gene regulation in response to symbiosis in raspberry.Frontiers in microbiology · 2022Article
- Transcriptional regulatory networks in response to drought stress and rewatering in maize (Zea mays L.).Molecular genetics and genomics : MGG · 2021Review
- Identification and Characterization of Downy Mildew-Responsive microRNAs in IndianJournal of fungi (Basel, Switzerland) · 2021Article
- The NAM/ATAF1/2/CUC2 transcription factor PpNAC.A59 enhances PpERF.A16 expression to promote ethylene biosynthesis during peach fruit ripening.Horticulture research · 2021Article
- Deep Sequencing Discovery and Profiling of Known and Novel miRNAs Produced in Response to DNA Damage in Rice.International journal of molecular sciences · 2021Article
178 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 1 institution in 2 countries.
Funding
Abstract
In plants there are several classes of 21-24-nt short RNAs that regulate gene expression. The most conserved class is the microRNAs (miRNAs), although some miRNAs are found only in specific species. We used high-throughput pyrosequencing to identify conserved and nonconserved miRNAs and other short RNAs in tomato fruit and leaf. Several conserved miRNAs showed tissue-specific expression, which, combined with target gene validation results, suggests that miRNAs may play a role in fleshy fruit development. We also identified four new nonconserved miRNAs. One of the validated targets of a novel miRNA is a member of the CTR family involved in fruit ripening. However, 62 predicted targets showing near perfect complementarity to potential new miRNAs did not validate experimentally. This suggests that target prediction of plant short RNAs could have a high false-positive rate and must therefore be validated experimentally. We also found short RNAs from a Solanaceae-specific foldback transposon, which showed a miRNA/miRNA*-like distribution, suggesting that this element may function as a miRNA gene progenitor. The other Solanaceae-specific class of short RNA was derived from an endogenous pararetrovirus sequence inserted into the tomato chromosomes. This study opens a new avenue in the field of fleshy fruit biology by raising the possibility that fruit development and ripening may be under miRNA regulation.
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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.