ArticlePlanta2015
Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq.
Article in Planta, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
What it found
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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
47 citing papers in PubMed, 108 citations in OpenAlex.
- Advances of Long Non-Coding RNA in Perennial Plants: Development and Stress Responses.Plants (Basel, Switzerland) · 2025Review
- Genome-wide characterization of post-transcriptional processes related to wood formation in Dalbergia odorifera.BMC genomics · 2024Article
- Deciphering the intricate hierarchical gene regulatory network: unraveling multi-level regulation and modifications driving secondary cell wall formation.Horticulture research · 2024Article
- Different transcription of novel, functional long non-coding RNA genes by UV-B in green algae, Volvox carteri.International microbiology : the official journal of the Spanish Society for Microbiology · 2024Article
- Characterization and analysis of multi-organ full-length transcriptomes in Sphaeropteris brunoniana and Alsophila latebrosa highlight secondary metabolism and chloroplast RNA editing pattern of tree ferns.BMC plant biology · 2024Article
- Comparative proteomic analysis provides insights into wood formation in immature xylem at different ages inFrontiers in plant science · 2024Article
- Integrated microRNA and whole-transcriptome sequencing reveals the involvement of small and long non-coding RNAs in the fiber growth of ramie plant.BMC genomics · 2023Article
- Exploring the Seasonal Dynamics and Molecular Mechanism of Wood Formation in Gymnosperm Trees.International journal of molecular sciences · 2023Review
- Characterization of microRNAs and Target Genes inPlants (Basel, Switzerland) · 2023Article
- Identification of long non-coding RNAs and microRNAs involved in anther development in the tropical Camellia oleifera.BMC genomics · 2022Article
- Genome-wide identification and characterization of Fusarium circinatum-responsive lncRNAs in Pinus radiata.BMC genomics · 2022Article
- Article
- Comprehensive Transcriptome Analysis of Stem-Differentiating Xylem Upon Compression Stress in Cunninghamia Lanceolata.Frontiers in genetics · 2022Article
- Identification of long non-coding RNAs involved in floral scent ofFrontiers in plant science · 2022Article
- Root-to-Shoot Long-Distance Mobile miRNAs Identified fromInternational journal of molecular sciences · 2021Article
- Genome-Wide Identification of Barley Long Noncoding RNAs and Analysis of Their Regulatory Interactions during Shoot and Grain Development.International journal of molecular sciences · 2021Article
- MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development.International journal of molecular sciences · 2021Review
- Identification and functional prediction of long non-coding RNAs of rice (Oryza sativa L.) at reproductive stage under salinity stress.Molecular biology reports · 2021Article
- RNA Sequencing Reveals Phenylpropanoid Biosynthesis Genes and Transcription Factors forFrontiers in genetics · 2021Article
- Genome-wide analysis of lncRNA and mRNA expression and endogenous hormone regulation during tension wood formation in Catalpa bungei.BMC genomics · 2020Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Increasing evidence shows that long non-coding RNAs (lncRNAs) function as important regulatory factors during plant development, but few reports have examined lncRNAs in trees. Here, we report our genome-scale identification and characterization of lncRNAs differentially expressed in the xylem of tension wood, opposite wood and normal wood in Populus tomentosa, by high-throughput RNA sequencing. We identified 1,377 putative lncRNAs by computational analysis, and expression and structure analyses showed that the lncRNAs had lower expression levels and shorter lengths than protein-coding transcripts in Populus. Of the 776 differently expressed (log2FC ≥1 or ≤-1, FDR ≤0.01) lncRNAs, 389 could potentially target 1,151 genes via trans-regulatory effects. Functional annotation of these target genes demonstrated that they are involved in fundamental processes, and in specific mechanisms such as response to stimuli. We also identified 16 target genes involved in wood formation, including cellulose and lignin biosynthesis, suggesting a potential role for lncRNAs in wood formation. In addition, three lncRNAs harbor precursors of four miRNAs, and 25 were potentially targeted by 44 miRNAs where a negative expression relationship between them was detected by qRT-PCR. Thus, a network of interactions among the lncRNAs, miRNAs and mRNAs was constructed, indicating widespread regulatory interactions between non-coding RNAs and mRNAs. Lastly, qRT-PCR validation confirmed the differential expression of these lncRNAs, and revealed that they have tissue-specific expression in P. tomentosa. This study presents the first global identification of lncRNAs and their potential functions in wood formation, providing a starting point for detailed dissection of the functions of lncRNAs in Populus.
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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.