Article

Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100094, PR China.
BMC Plant Biology (Impact Factor: 3.81). 04/2011; 11(1):61. DOI: 10.1186/1471-2229-11-61
Source: PubMed

ABSTRACT

Biotic and abiotic stresses, such as powdery mildew infection and high temperature, are important limiting factors for yield and grain quality in wheat production. Emerging evidences suggest that long non-protein coding RNAs (npcRNAs) are developmentally regulated and play roles in development and stress responses of plants. However, identification of long npcRNAs is limited to a few plant species, such as Arabidopsis, rice and maize, no systematic identification of long npcRNAs and their responses to abiotic and biotic stresses is reported in wheat.
In this study, by using computational analysis and experimental approach we identified 125 putative wheat stress responsive long npcRNAs, which are not conserved among plant species. Among them, some were precursors of small RNAs such as microRNAs and siRNAs, two long npcRNAs were identified as signal recognition particle (SRP) 7S RNA variants, and three were characterized as U3 snoRNAs. We found that wheat long npcRNAs showed tissue dependent expression patterns and were responsive to powdery mildew infection and heat stress.
Our results indicated that diverse sets of wheat long npcRNAs were responsive to powdery mildew infection and heat stress, and could function in wheat responses to both biotic and abiotic stresses, which provided a starting point to understand their functions and regulatory mechanisms in the future.

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Available from: Mingming Xin, Jun 13, 2014
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    • "e l s e v i e r . c o m / l o c a t e / g e n e responses (factors limiting crop yield) for plant lncRNAs (Xin et al., 2011; Liu et al., 2012). For example, the Pol III-transcribed conserved lncRNA AtR8 acts negatively to hypoxic conditions in both Arabidopsis and Brassicaceae (Wu et al., 2012). "
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    ABSTRACT: Accumulating published reports have confirmed the critical biological role (e.g., cell differentiation, gene regulation, stress response) for plant long non-coding RNAs (lncRNAs). However, a literature-derived database with the aim of lncRNA curation, data deposit and further distribution remains still absent for this particular lncRNA clade. PLNlncRbase has been designed as an easy-to-use resource to provide detailed information for experimentally identified plant lncRNAs. In the current version, PLNlncRbase has manually collected data from nearly 200 published literature, covering a total of 1187 plant lncRNAs in 43 plant species. The user can retrieve plant lncRNA entries from a well-organized interface through a keyword search by using the name of plant species or a lncRNA identifier. Each entry upon a query will be returned with detailed information for a specific plant lncRNA, including the species name, a lncRNA identifier, a brief description of the potential biological role, the lncRNA sequence, the lncRNA classification, an expression pattern of the lncRNA, the tissue/developmental stage/condition for lncRNA expression, the detection method for lncRNA expression, a reference literature, and the potential target gene(s) of the lncRNA extracted from the original reference. This database will be regularly updated to greatly facilitate future investigations of plant lncRNAs pertaining to their biological significance. The PLNlncRbase database is now freely available at http://bioinformatics.ahau.edu.cn/PLNlncRbase. Copyright © 2015. Published by Elsevier B.V.
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    • "Recent studies revealed that lncRNAs exert a crucial role in various biological processes of plants (Zhang and Chen, 2013). Although many lncRNAs have been identified from model plants, such as Arabidopsis (Ben et al., 2009; Liu et al., 2012; Zhu et al., 2013; Wang et al., 2014), wheat (Xin et al., 2011), rice (Li et al., 2007), and maize (Boerner and McGinnis, 2012; Li et al., 2014), much work still remains to be done with tomato. In the present study, a total of 3679 lncRNA loci (3981 isoforms) were identified in tomato, a model plant for study of fruit ripening (Fig. 1). "
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    Full-text · Article · May 2015 · Journal of Experimental Botany
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    • "In animals, lncRNAs are involved in development [17]–[19] and disease response [10], [20]. In plants, lncRNAs have been systematically screened from Arabidopsis thaliana, Triticum aestivum, Digitalis purpurea and Medicago truncatura [7], [21]–[28]. These lncRNAs are important in phosphate-starvation response, gender-specific expression, nodulation, and cold-stress response. "
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    ABSTRACT: Ganoderma lucidum is a white-rot fungus best-known for its medicinal activities. We have previously sequenced its genome and annotated the protein coding genes. However, long non-coding RNAs in G. lucidum genome have not been analyzed. In this study, we have identified and characterized long intergenic non-coding RNAs (lincRNA) in G. lucidum systematically. We developed a computational pipeline, which was used to analyze RNA-Seq data derived from G. lucidum samples collected from three developmental stages. A total of 402 lincRNA candidates were identified, with an average length of 609 bp. Analysis of their adjacent protein-coding genes (apcGenes) revealed that 46 apcGenes belong to the pathways of triterpenoid biosynthesis and lignin degradation, or families of cytochrome P450, mating type B genes, and carbohydrate-active enzymes. To determine if lincRNAs and these apcGenes have any interactions, the corresponding pairs of lincRNAs and apcGenes were analyzed in detail. We developed a modified 3' RACE method to analyze the transcriptional direction of a transcript. Among the 46 lincRNAs, 37 were found unidirectionally transcribed, and 9 were found bidirectionally transcribed. The expression profiles of 16 of these 37 lincRNAs were found to be highly correlated with those of the apcGenes across the three developmental stages. Among them, 11 are positively correlated (r>0.8) and 5 are negatively correlated (r<-0.8). The co-localization and co-expression of lincRNAs and those apcGenes playing important functions is consistent with the notion that lincRNAs might be important regulators for cellular processes. In summary, this represents the very first study to identify and characterize lincRNAs in the genomes of basidiomycetes. The results obtained here have laid the foundation for study of potential lincRNA-mediated expression regulation of genes in G. lucidum.
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