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Zou C, Zhao S, Yang B, Chai W, Zhu L, Zhang C, Gai Z. Genome-wide characterization of drought-responsive long non-coding RNAs in sorghum (Sorghum bicolor). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 214:108908. [PMID: 38976942 DOI: 10.1016/j.plaphy.2024.108908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/08/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
Drought stress strongly affects crop yield. Although knowledge of long non-coding RNAs (lncRNAs) has been updated continuously and rapidly, information about lncRNAs in drought resistance regulation is extremely limited in sorghum. Here, lncRNA-sequencing was performed with seedlings of a sorghum cultivar (Jinza29) under three water control treatments to investigate the mechanism of lncRNAs responsible for drought resistance in sorghum. A total of 377 differentially expressed lncRNAs (DElncRNAs) were identified. We also predicted 4322 and 2827 transcripts as potential cis-target and trans-target genes for drought-responsive lncRNAs, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that those target genes exhibited marked enrichment into "oxidoreductase activity", "signal transducer activity", "DNA repair", "photosynthesis", "glutathione metabolism", and "phenylpropanoid biosynthesis" and other terms associated with abiotic stress resistance. Moreover, several lncRNAs were estimated to modulate the expression of other genes related to stress response and photosynthetic carbon metabolism. Additionally, we found 107 DElncRNAs that might be candidate target mimics for 56 miRNAs. LncRNAs play important roles in drought adaptation of sorghum through interacting with protein-encoding genes. The obtained results provided novel insights into the biological characteristics of lncRNAs and offered potential regulatory factors for genetically enhancing drought resistance in sorghum.
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Affiliation(s)
- Chunlei Zou
- College of Agronomy, Shanxi Agricultural University, 030800, Taigu, Shanxi, China
| | - Shanshan Zhao
- College of Agronomy, Shanxi Agricultural University, 030800, Taigu, Shanxi, China
| | - Bohui Yang
- College of Agronomy, Shanxi Agricultural University, 030800, Taigu, Shanxi, China
| | - Wenting Chai
- College of Agronomy, Shanxi Agricultural University, 030800, Taigu, Shanxi, China
| | - Lixun Zhu
- College of Agronomy, Shanxi Agricultural University, 030800, Taigu, Shanxi, China
| | - Chunlai Zhang
- College of Agronomy, Shanxi Agricultural University, 030800, Taigu, Shanxi, China.
| | - Zhijia Gai
- Jiamusi Branch, Heilongjiang Academy of Agricultural Sciences, 154000, Jiamusi, Heilongjiang, China
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Zou C, Guo Z, Zhao S, Chen J, Zhang C, Han H. Genome-wide analysis of long non-coding RNAs in sugar beet ( Beta vulgaris L.) under drought stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1118011. [PMID: 36866366 PMCID: PMC9971629 DOI: 10.3389/fpls.2023.1118011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
Drought stress is one of the most severe abiotic stresses that restrict global crop production. Long non-coding RNAs (lncRNAs) have been proved to play a key role in response to drought stress. However, genome-wide identification and characterization of drought-responsive lncRNAs in sugar beet is still lacking. Thus, the present study focused on analyzing lncRNAs in sugar beet under drought stress. We identified 32017 reliable lncRNAs in sugar beet by strand-specific high-throughput sequencing. A total of 386 differentially expressed lncRNAs (DElncRNAs) were found under drought stress. The most significantly upregulated and downregulated lncRNAs were TCONS_00055787 (upregulated by more than 6000 fold) and TCONS_00038334 (downregulated by more than 18000 fold), respectively. Quantitative real-time PCR results exhibited a high concordance with RNA sequencing data, which conformed that the expression patterns of lncRNAs based on RNA sequencing were highly reliable. In addition, we predicted 2353 and 9041 transcripts that were estimated to be the cis- and trans-target genes of the drought-responsive lncRNAs. As revealed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the target genes of DElncRNAs were significantly enriched in organelle subcompartment, thylakoid, endopeptidase activity, catalytic activity, developmental process, lipid metabolic process, RNA polymerase activity, transferase activity, flavonoid biosynthesis and several other terms associated with abiotic stress tolerance. Moreover, 42 DElncRNAs were predicted as potential miRNA target mimics. LncRNAs have important effects on plant adaptation to drought conditions through the interaction with protein-encoding genes. The present study leads to greater insights into lncRNA biology and offers candidate regulators for improving the drought tolerance of sugar beet cultivars at the genetic level.
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Eiteneuer C, Velasco D, Atemia J, Wang D, Schwacke R, Wahl V, Schrader A, Reimer JJ, Fahrner S, Pieruschka R, Schurr U, Usadel B, Hallab A. GXP: Analyze and Plot Plant Omics Data in Web Browsers. PLANTS 2022; 11:plants11060745. [PMID: 35336631 PMCID: PMC8952246 DOI: 10.3390/plants11060745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/15/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022]
Abstract
Next-generation sequencing and metabolomics have become very cost and work efficient and are integrated into an ever-growing number of life science research projects. Typically, established software pipelines analyze raw data and produce quantitative data informing about gene expression or concentrations of metabolites. These results need to be visualized and further analyzed in order to support scientific hypothesis building and identification of underlying biological patterns. Some of these tools already exist, but require installation or manual programming. We developed “Gene Expression Plotter” (GXP), an RNAseq and Metabolomics data visualization and analysis tool entirely running in the user’s web browser, thus not needing any custom installation, manual programming or uploading of confidential data to third party servers. Consequently, upon receiving the bioinformatic raw data analysis of RNAseq or other omics results, GXP immediately enables the user to interact with the data according to biological questions by performing knowledge-driven, in-depth data analyses and candidate identification via visualization and data exploration. Thereby, GXP can support and accelerate complex interdisciplinary omics projects and downstream analyses. GXP offers an easy way to publish data, plots, and analysis results either as a simple exported file or as a custom website. GXP is freely available on GitHub (see introduction)
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Affiliation(s)
- Constantin Eiteneuer
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - David Velasco
- Faculty of Natural Sciences, Norges Teknisk-Naturvitenskapelige Universitet, 7034 Trondheim, Norway;
| | - Joseph Atemia
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
| | - Dan Wang
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Rainer Schwacke
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
| | - Vanessa Wahl
- Max Planck Institute for Molecular Plant Physiology, 14476 Potsdam, Germany;
| | - Andrea Schrader
- Institute for Biology I, RWTH Aachen University, 52062 Aachen, Germany; (A.S.); (J.J.R.)
| | - Julia J. Reimer
- Institute for Biology I, RWTH Aachen University, 52062 Aachen, Germany; (A.S.); (J.J.R.)
- Faculty of Technology, University of Applied Science Emden/Leer, Molecular Biosciences, 26723 Emden, Germany
| | - Sven Fahrner
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Roland Pieruschka
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Ulrich Schurr
- IBG-2 Plant Sciences, Forschungszentrum Jülich, 52428 Jülich, Germany; (C.E.); (D.W.); (S.F.); (R.P.); (U.S.)
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
| | - Asis Hallab
- IBG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany; (J.A.); (R.S.); (B.U.)
- Correspondence:
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Malečková E. Plant PhysioSpace: navigating the "space" of plant stress responses. PLANT PHYSIOLOGY 2021; 187:1286-1287. [PMID: 34734284 PMCID: PMC8566250 DOI: 10.1093/plphys/kiab403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Eva Malečková
- Institute for Microbiology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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