ArticleBMC genomics2015
Global identification and analysis of long non-coding RNAs in diploid strawberry Fragaria vesca during flower and fruit development.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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Who cites it
62 citing papers in PubMed, 150 citations in OpenAlex.
- Transcriptome Dynamics Reveal the Potential Roles of Long Non-Coding RNAs in Regulating Flower Color of Safflowers (International journal of molecular sciences · 2026Article
- Epigenetic Regulation of Root-Associated Microbiota: Mechanisms and Horticultural Applications.Plants (Basel, Switzerland) · 2026Review
- A long noncoding RNA functions in pumpkin fruit development through S-adenosyl-L-methionine synthetase.Plant physiology · 2024Article
- Emerging roles and mechanisms of lncRNAs in fruit and vegetables.Horticulture research · 2024Review
- Post-transcriptional regulation shapes the transcriptome of quiescent budding yeast.Nucleic acids research · 2024Article
- Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing.The Plant cell · 2023Article
- Construction of ceRNA Networks at Different Stages of Somatic Embryogenesis in Garlic.International journal of molecular sciences · 2023Article
- Coordinating Diverse Functions of miRNA and lncRNA in Fleshy Fruit.Plants (Basel, Switzerland) · 2023Review
- Plant long non-coding RNAs: identification and analysis to unveil their physiological functions.Frontiers in plant science · 2023Review
- Long non-coding RNA-mediated competing endogenous RNA regulatory network during flower development and color formation inFrontiers in plant science · 2023Article
- Article
- Whole-transcriptome analyses identify key differentially expressed mRNAs, lncRNAs, and miRNAs associated with male sterility in watermelon.Frontiers in plant science · 2023Article
- Genome-wide identification and characterization of long noncoding RNAs during peach (Prunus persica) fruit development and ripening.Scientific reports · 2022Article
- Repetitive Sequence Barcode Probe for Karyotype Analysis inInternational journal of molecular sciences · 2022Article
- Expression Profiles and Characteristics of Apple lncRNAs in Roots, Phloem, Leaves, Flowers, and Fruit.International journal of molecular sciences · 2022Article
- Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis).Scientific reports · 2022Article
- Genome-wide identification and comprehensive analysis reveal potential roles of long non-coding RNAs in fruit development of southern highbush blueberry (Frontiers in plant science · 2022Article
- Investigating nicotine pathway-related long non-coding RNAs in tobacco.Frontiers in genetics · 2022Article
- Comprehensive identification and analysis of circRNAs during hickory (Frontiers in plant science · 2022Article
- Identification and Analysis of Long Non-Coding RNAs Related to UV-B-Induced Anthocyanin Biosynthesis During Blood-Fleshed Peach (Frontiers in genetics · 2022Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLong non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes. While much effort has been invested in the analysis of lncRNAs from established plant models Arabidopsis, maize, and rice, almost nothing is known about lncRNAs from fruit crops, including those in the Rosaceae family.
resultsHere, we present a genome-scale identification and characterization of lncRNAs from a diploid strawberry, Fragaria vesca, based on rich RNA-seq datasets from 35 different flower and fruit tissues. 5,884 Fve-lncRNAs derived from 3,862 loci were identified. These lncRNAs were carefully cataloged based on expression level and whether or not they contain repetitive sequences or generate small RNAs. About one fourth of them are termed high-confidence lncRNAs (hc-lncRNAs) because they are expressed at a level of FPKM higher than 2 and produce neither small RNAs nor contain repetitive sequence. To identify regulatory interactions between lncRNAs and their potential protein-coding (PC) gene targets, pairs of lncRNAs and PC genes with positively or negatively correlated expression trends were identified based on their expression; these pairs may be candidates of cis- or trans-acting lncRNAs and their targets. Finally, blast searches within plant species indicate that lncRNAs are not well conserved.
conclusionsOur study identifies a large number of tissue-specifically expressed lncRNAs in F. vesca, thereby highlighting their potential contributions to strawberry flower and fruit development and paving the way for future functional studies.
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