ArticleBMC genomics2018
Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 33 citations in OpenAlex.
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- Unraveling the lncRNA-miRNA-mRNA Regulatory Network Involved in Poplar Coma Development through High-Throughput Sequencing.International journal of molecular sciences · 2024Article
- The Construction of lncRNA/circRNA-miRNA-mRNA Networks Reveals Functional Genes Related to Growth Traits inInternational journal of molecular sciences · 2024Article
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- Identification of birch lncRNAs and mRNAs responding to salt stress and characterization of functions of lncRNA.Horticulture research · 2023Article
- miR172 RegulatesCells · 2022Article
- Cryo-Treatment Enhances the Embryogenicity of Mature Somatic Embryos via the lncRNA-miRNA-mRNA Network in White Spruce.International journal of molecular sciences · 2022Article
- Regulatory non-coding RNAs: Emerging roles during plant cell reprogramming andFrontiers in plant science · 2022Review
- Non-Coding RNAs in Response to Drought Stress.International journal of molecular sciences · 2021Review
- Downregulation of lncRNAInternational journal of molecular sciences · 2021Article
- Identification and characterization of early Fusarium wilt responsive mRNAs and long non-coding RNAs in banana root using high-throughput sequencing.Scientific reports · 2021Article
- Small Non-Coding RNAs at the Crossroads of Regulatory Pathways Controlling Somatic Embryogenesis in Seed Plants.Plants (Basel, Switzerland) · 2021Review
- Selection of reference genes for gene expression analysis in Liriodendron hybrids' somatic embryogenesis and germinative tissues.Scientific reports · 2021Article
- Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation.Computational and structural biotechnology journal · 2021Review
- Article
- From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress.Frontiers in plant science · 2020Review
- Indole-3-acetic acid has long-term effects on long non-coding RNA gene methylation and growth in Populus tomentosa.Molecular genetics and genomics : MGG · 2019Article
- Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Frontiers in plant science · 2019Article
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Authors and funding
11 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundLong non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan (Dimocarpus longan) somatic embryogenesis (SE) system is a good system for research on longan embryo development.
resultsIn this study, 7643 lncRNAs obtained during early SE in D. longan were identified by high-throughput sequencing, among which 6005 lncRNAs were expressed. Of the expressed lncRNAs, 4790 were found in all samples and 160 were specifically expressed in embryogenic callus (EC), 154 in incomplete embryogenic compact structures (ICpECs), and 376 in globular embryos (GEs). We annotated the 6005 expressed lncRNAs, and 1404 lncRNAs belonged to 506 noncoding RNA (ncRNA) families and 4682 lncRNAs were predicted to target protein-coding genes. The target genes included 5051 cis-regulated target genes (5712 pairs) and 1605 trans-regulated target genes (3618 pairs). KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the "plant-pathogen interaction" and "plant hormone signaling" pathways during early longan SE. Real-time quantitative PCR confirmed that 20 selected lncRNAs showed significant differences in expression and that five lncRNAs were related to auxin response factors. Compared with the FPKM expression trends, 16 lncRNA expression trends were the same in qPCR. In lncRNA-miRNA-mRNA relationship prediction, 40 lncRNAs were predicted to function as eTMs for 15 miRNAs and 7 lncRNAs were identified as potential miRNA precursors. In addition, we verified the lncRNA-miRNA-mRNA regulatory relationships by transient expression of miRNAs (miR172a, miR159a.1 and miR398a).
conclusionAnalyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE.
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