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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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Fahad M, Tariq L, Muhammad S, Wu L. Underground communication: Long non-coding RNA signaling in the plant rhizosphere. PLANT COMMUNICATIONS 2024; 5:100927. [PMID: 38679911 PMCID: PMC11287177 DOI: 10.1016/j.xplc.2024.100927] [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: 01/31/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/01/2024]
Abstract
Long non-coding RNAs (lncRNAs) have emerged as integral gene-expression regulators underlying plant growth, development, and adaptation. To adapt to the heterogeneous and dynamic rhizosphere, plants use interconnected regulatory mechanisms to optimally fine-tune gene-expression-governing interactions with soil biota, as well as nutrient acquisition and heavy metal tolerance. Recently, high-throughput sequencing has enabled the identification of plant lncRNAs responsive to rhizosphere biotic and abiotic cues. Here, we examine lncRNA biogenesis, classification, and mode of action, highlighting the functions of lncRNAs in mediating plant adaptation to diverse rhizosphere factors. We then discuss studies that reveal the significance and target genes of lncRNAs during developmental plasticity and stress responses at the rhizobium interface. A comprehensive understanding of specific lncRNAs, their regulatory targets, and the intricacies of their functional interaction networks will provide crucial insights into how these transcriptomic switches fine-tune responses to shifting rhizosphere signals. Looking ahead, we foresee that single-cell dissection of cell-type-specific lncRNA regulatory dynamics will enhance our understanding of the precise developmental modulation mechanisms that enable plant rhizosphere adaptation. Overcoming future challenges through multi-omics and genetic approaches will more fully reveal the integral roles of lncRNAs in governing plant adaptation to the belowground environment.
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Affiliation(s)
- Muhammad Fahad
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Leeza Tariq
- National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sajid Muhammad
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Liang Wu
- Hainan Institute, Zhejiang University, Sanya, Hainan 572000, China; Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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3
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Zhang P, Li F, Tian Y, Wang D, Fu J, Rong Y, Wu Y, Gao T, Zhang H. Transcriptome Analysis of Sesame ( Sesamum indicum L.) Reveals the LncRNA and mRNA Regulatory Network Responding to Low Nitrogen Stress. Int J Mol Sci 2024; 25:5501. [PMID: 38791539 PMCID: PMC11122487 DOI: 10.3390/ijms25105501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/05/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Nitrogen is one of the important factors restricting the development of sesame planting and industry in China. Cultivating sesame varieties tolerant to low nitrogen is an effective way to solve the problem of crop nitrogen deficiency. To date, the mechanism of low nitrogen tolerance in sesame has not been elucidated at the transcriptional level. In this study, two sesame varieties Zhengzhi HL05 (ZZ, nitrogen efficient) and Burmese prolific (MD, nitrogen inefficient) in low nitrogen were used for RNA-sequencing. A total of 3964 DEGs (differentially expressed genes) and 221 DELs (differentially expressed lncRNAs) were identified in two sesame varieties at 3d and 9d after low nitrogen stress. Among them, 1227 genes related to low nitrogen tolerance are mainly located in amino acid metabolism, starch and sucrose metabolism and secondary metabolism, and participate in the process of transporter activity and antioxidant activity. In addition, a total of 209 pairs of lncRNA-mRNA were detected, including 21 pairs of trans and 188 cis. WGCNA (weighted gene co-expression network analysis) analysis divided the obtained genes into 29 modules; phenotypic association analysis identified three low-nitrogen response modules; through lncRNA-mRNA co-expression network, a number of hub genes and cis/trans-regulatory factors were identified in response to low-nitrogen stress including GS1-2 (glutamine synthetase 1-2), PAL (phenylalanine ammonia-lyase), CHS (chalcone synthase, CHS), CAB21 (chlorophyll a-b binding protein 21) and transcription factors MYB54, MYB88 and NAC75 and so on. As a trans regulator, lncRNA MSTRG.13854.1 affects the expression of some genes related to low nitrogen response by regulating the expression of MYB54, thus responding to low nitrogen stress. Our research is the first to provide a more comprehensive understanding of DEGs involved in the low nitrogen stress of sesame at the transcriptome level. These results may reveal insights into the molecular mechanisms of low nitrogen tolerance in sesame and provide diverse genetic resources involved in low nitrogen tolerance research.
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Affiliation(s)
- Pengyu Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Feng Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Yuan Tian
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Dongyong Wang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Jinzhou Fu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Yasi Rong
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Yin Wu
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
| | - Tongmei Gao
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (P.Z.); (F.L.); (Y.T.); (D.W.); (J.F.); (Y.R.); (Y.W.)
- The Shennong Laboratory, Zhengzhou 450002, China
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Guan C, Li W, Wang G, Yang R, Zhang J, Zhang J, Wu B, Gao R, Jia C. Transcriptomic analysis of ncRNAs and mRNAs interactions during drought stress in switchgrass. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 339:111930. [PMID: 38007196 DOI: 10.1016/j.plantsci.2023.111930] [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: 09/08/2023] [Revised: 11/01/2023] [Accepted: 11/21/2023] [Indexed: 11/27/2023]
Abstract
Switchgrass (Panicum virgatum L.) plays a pivotal role as a bioenergy feedstock in the production of cellulosic ethanol and contributes significantly to enhancing ecological grasslands and soil quality. The utilization of non-coding RNAs (ncRNAs) has gained momentum in deciphering the intricate genetic responses to abiotic stress in various plant species. Nevertheless, the current research landscape lacks a comprehensive exploration of the responses of diverse ncRNAs, including long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs), to drought stress in switchgrass. In this study, we employed whole transcriptome sequencing to comprehensively characterize the expression profiles of both mRNA and ncRNAs during episodes of drought stress in switchgrass. Our analysis identified a total of 12,511 mRNAs, 59 miRNAs, 38 circRNAs, and 368 lncRNAs that exhibited significant differential expression between normal and drought-treated switchgrass leaves. Notably, the majority of up-regulated mRNAs displayed pronounced enrichment within the starch and sucrose metabolism pathway, as validated through KEGG analysis. Co-expression analysis illuminated that differentially expressed (DE) lncRNAs conceivably regulated 1308 protein-coding genes in trans and 7110 protein-coding genes in cis. Furthermore, both cis- and trans-target mRNAs of DE lncRNAs exhibited enrichment in four common KEGG pathways. The intricate interplay between lncRNAs and circRNAs with miRNAs via miRNA response elements was explored within the competitive endogenous RNA (ceRNA) network framework. As a result, we constructed elaborate regulatory networks, including lncRNA-novel_miRNA480-mRNA, lncRNA-novel_miRNA304-mRNA, lncRNA/circRNA-novel_miRNA122-PvSS4, and lncRNA/circRNA-novel_miRNA14-PvSS4, and subsequently validated the functionality of the target gene, starch synthase 4 (PvSS4). Furthermore, through the overexpression of PvSS4, we ascertained its capacity to enhance drought tolerance in yeast. However, it is noteworthy that PvSS4 did not exhibit any discernible impact under salt stress conditions. These findings, as presented herein, not only contribute substantively to our understanding of ceRNA networks but also offer a basis for further investigations into their potential functions in response to drought stress in switchgrass.
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Affiliation(s)
- Cong Guan
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Wei Li
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing 100193, China
| | - Guoliang Wang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Ruimei Yang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; College of Grassland Science and Technology, China Agricultural University, No.2 Yuan Mingyuan West Road, Beijing 100193, China
| | - Jinglei Zhang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Jinhong Zhang
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Bo Wu
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Run Gao
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China
| | - Chunlin Jia
- Institute of Leisure Agriculture, Shandong Academy of Agricultural Science, Jinan 250100, China; Key Laboratory of East China Urban Agriculture, Ministry of Agriculture, Jinan 250100, China; Shandong Engineering Research Center of Ecological and Horticultural Plant Breeding, Jinan 250100, China.
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5
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Magar ND, Shah P, Barbadikar KM, Bosamia TC, Madhav MS, Mangrauthia SK, Pandey MK, Sharma S, Shanker AK, Neeraja CN, Sundaram RM. Long non-coding RNA-mediated epigenetic response for abiotic stress tolerance in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108165. [PMID: 38064899 DOI: 10.1016/j.plaphy.2023.108165] [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: 12/25/2022] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024]
Abstract
Plants perceive environmental fluctuations as stress and confront several stresses throughout their life cycle individually or in combination. Plants have evolved their sensing and signaling mechanisms to perceive and respond to a variety of stresses. Epigenetic regulation plays a critical role in the regulation of genes, spatiotemporal expression of genes under stress conditions and imparts a stress memory to encounter future stress responses. It is quintessential to integrate our understanding of genetics and epigenetics to maintain plant fitness, achieve desired genetic gains with no trade-offs, and durable long-term stress tolerance. The long non-coding RNA >200 nts having no coding potential (or very low) play several roles in epigenetic memory, contributing to the regulation of gene expression and the maintenance of cellular identity which include chromatin remodeling, imprinting (dosage compensation), stable silencing, facilitating nuclear organization, regulation of enhancer-promoter interactions, response to environmental signals and epigenetic switching. The lncRNAs are involved in a myriad of stress responses by activation or repression of target genes and hence are potential candidates for deploying in climate-resilient breeding programs. This review puts forward the significant roles of long non-coding RNA as an epigenetic response during abiotic stresses in plants and the prospects of deploying lncRNAs for designing climate-resilient plants.
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Affiliation(s)
- Nakul D Magar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India; Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Kalyani M Barbadikar
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India.
| | - Tejas C Bosamia
- Plant Omics Division, CSIR-Central Salt and Marine Chemicals Research Institute, Gujarat, 364002, India
| | - M Sheshu Madhav
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, 502324, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250004, India
| | - Arun K Shanker
- Plant Physiology, ICAR-Central Research Institute for Dryland Agriculture, Hyderabad, 500059, India
| | - C N Neeraja
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - R M Sundaram
- Biotechnology Section, ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
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6
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Jia Y, Zhao H, Niu Y, Wang Y. Long noncoding RNA from Betula platyphylla, BplncSIR1, confers salt tolerance by regulating BpNAC2 to mediate reactive oxygen species scavenging and stomatal movement. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:48-65. [PMID: 37697445 PMCID: PMC10754008 DOI: 10.1111/pbi.14164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 07/11/2023] [Accepted: 08/04/2023] [Indexed: 09/13/2023]
Abstract
Long noncoding RNAs (lncRNAs) play an important role in abiotic stress tolerance. However, their function in conferring abiotic stress tolerance is still unclear. Herein, we characterized the function of a salt-responsive nuclear lncRNA (BplncSIR1) from Betula platyphylla (birch). Birch plants overexpressing and knocking out for BplncSIR1 were generated. BplncSIR1 was found to improve salt tolerance by inducing antioxidant activity and stomatal closure, and also accelerate plant growth. Chromatin isolation by RNA purification (ChIRP) combined with RNA sequencing indicated that BplncSIR1 binds to the promoter of BpNAC2 (encoding NAC domain-containing protein 2) to activate its expression. Plants overexpressing and knocking out for BpNAC2 were generated. Consistent with that of BplncSIR1, overexpression of BpNAC2 also accelerated plant growth and conferred salt tolerance. In addition, BpNAC2 binds to different cis-acting elements, such as G-box and 'CCAAT' sequences, to regulate the genes involved in salt tolerance, resulting in reduced ROS accumulation and decreased water loss rate by stomatal closure. Taken together, BplncSIR1 serves as the regulator of BpNAC2 to induce its expression in response to salt stress, and activated BpNAC2 accelerates plant growth and improves salt tolerance. Therefore, BplncSIR1 might be a candidate gene for molecular breeding to cultivate plants with both a high growth rate and improved salt tolerance.
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Affiliation(s)
- Yaqi Jia
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Huimin Zhao
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Yani Niu
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
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7
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Lu Z, Wang X, Lin X, Mostafa S, Bao H, Ren S, Cui J, Jin B. Genome-Wide Identification and Characterization of Long Non-Coding RNAs Associated with Floral Scent Formation in Jasmine ( Jasminum sambac). Biomolecules 2023; 14:45. [PMID: 38254645 PMCID: PMC10812929 DOI: 10.3390/biom14010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/19/2023] [Accepted: 12/26/2023] [Indexed: 01/24/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as curial regulators of diverse biological processes in plants. Jasmine (Jasminum sambac) is a world-renowned ornamental plant for its attractive and exceptional flower fragrance. However, to date, no systematic screening of lncRNAs and their regulatory roles in the production of the floral fragrance of jasmine flowers has been reported. In this study, we identified a total of 31,079 novel lncRNAs based on an analysis of strand-specific RNA-Seq data from J. sambac flowers at different stages. The lncRNAs identified in jasmine flowers exhibited distinct characteristics compared with protein-coding genes (PCGs), including lower expression levels, shorter transcript lengths, and fewer exons. Certain jasmine lncRNAs possess detectable sequence conservation with other species. Expression analysis identified 2752 differentially expressed lncRNAs (DE_lncRNAs) and 8002 DE_PCGs in flowers at the full-blooming stage. DE_lncRNAs could potentially cis- and trans-regulate PCGs, among which DE_lincRNAs and their targets showed significant opposite expression patterns. The flowers at the full-blooming stage are specifically enriched with abundant phenylpropanoids and terpenoids potentially contributed by DE_lncRNA cis-regulated PCGs. Notably, we found that many cis-regulated DE_lncRNAs may be involved in terpenoid and phenylpropanoid/benzenoid biosynthesis pathways, which potentially contribute to the production of jasmine floral scents. Our study reports numerous jasmine lncRNAs and identifies floral-scent-biosynthesis-related lncRNAs, which highlights their potential functions in regulating the floral scent formation of jasmine and lays the foundations for future molecular breeding.
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Affiliation(s)
- Zhaogeng Lu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Xinwen Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Xinyi Lin
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Salma Mostafa
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Hongyan Bao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Shixiong Ren
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Jiawen Cui
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
| | - Biao Jin
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (Z.L.)
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8
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Tang X, Li Q, Feng X, Yang B, Zhong X, Zhou Y, Wang Q, Mao Y, Xie W, Liu T, Tang Q, Guo W, Wu F, Feng X, Wang Q, Lu Y, Xu J. Identification and Functional Analysis of Drought-Responsive Long Noncoding RNAs in Maize Roots. Int J Mol Sci 2023; 24:15039. [PMID: 37894720 PMCID: PMC10606207 DOI: 10.3390/ijms242015039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts with lengths of more than 200 nt and limited protein-coding potential. They were found to play important roles in plant stress responses. In this study, the maize drought-tolerant inbred line AC7643 and drought-sensitive inbred line AC7729/TZSRW, as well as their recombinant inbred lines (RILs) were selected to identify drought-responsive lncRNAs in roots. Compared with non-responsive lncRNAs, drought-responsive lncRNAs had different sequence characteristics in length of genes and number of exons. The ratio of down-regulated lncRNAs induced by drought was significantly higher than that of coding genes; and lncRNAs were more widespread expressed in recombination sites in the RILs. Additionally, by integration of the modifications of DNA 5-methylcytidine (5mC), histones, and RNA N6-methyladenosine (m6A), it was found that the enrichment of histone modifications associated with transcriptional activation in the genes generated lncRNAs was lower that coding genes. The lncRNAs-mRNAs co-expression network, containing 15,340 coding genes and 953 lncRNAs, was constructed to investigate the molecular functions of lncRNAs. There are 13 modules found to be associated with survival rate under drought. We found nine SNPs located in lncRNAs among the modules associated with plant survival under drought. In conclusion, we revealed the characteristics of lncRNAs responding to drought in maize roots based on multiomics studies. These findings enrich our understanding of lncRNAs under drought and shed light on the complex regulatory networks that are orchestrated by the noncoding RNAs in response to drought stress.
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Affiliation(s)
- Xin Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qimeng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoju Feng
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiu Zhong
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Mao
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Wubin Xie
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Tianhong Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qi Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Guo
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Fengkai Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuanjun Feng
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Qingjun Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Lu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
| | - Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China; (X.T.); (Q.L.); (X.F.); (B.Y.); (X.Z.); (Y.Z.); (Q.W.); (Y.M.); (W.X.); (T.L.); (Q.T.); (W.G.); (F.W.); (X.F.); (Q.W.)
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
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9
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Zhang YC, Yuan C, Chen YQ. Noncoding RNAs and their roles in regulating the agronomic traits of crops. FUNDAMENTAL RESEARCH 2023; 3:718-726. [PMID: 38933294 PMCID: PMC11197796 DOI: 10.1016/j.fmre.2023.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/09/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023] Open
Abstract
Molecular breeding is one of the most effective methods for improving the performance of crops. Understanding the genome features of crops, especially the physiological functions of individual genes, is of great importance to molecular breeding. Evidence has shown that genomes of both animals and plants transcribe numerous non-coding RNAs, which are involved in almost every aspect of development. In crops, an increasing number of studies have proven that non-coding RNAs are new genetic resources for regulating crop traits. In this review, we summarize the current knowledge of non-coding RNAs, which are potential crop trait regulators, and focus on the functions of long non-coding RNAs (lncRNAs) in determining crop grain yield, phased small-interfering RNAs (phasiRNAs) in regulating fertility, small interfering RNAs (siRNAs) and microRNAs (miRNAs) in facilitating plant immune response and disease resistance, and miRNAs mediating nutrient and metal stress. Finally, we also discuss the next-generation method for ncRNA application in crop domestication and breeding.
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Affiliation(s)
- Yu-Chan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chao Yuan
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yue-Qin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, School of Life Science, Sun Yat-Sen University, Guangzhou 510275, China
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10
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Sun N, Bu Y, Wu X, Ma X, Yang H, Du L, Li X, Xiao J, Lin J, Jing Y. Comprehensive analysis of lncRNA-mRNA regulatory network in Populus associated with xylem development. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154055. [PMID: 37506405 DOI: 10.1016/j.jplph.2023.154055] [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: 04/19/2023] [Revised: 07/01/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
Long noncoding RNAs (lncRNAs) play essential roles in numerous biological processes in plants, such as regulating the gene expression. However, only a few studies have looked into their potential functions in xylem development. High-throughput sequencing of P. euramericana 'Zhonglin46' developing and mature xylem was performed in this study. Through sequencing analysis, 14,028 putative lncRNA transcripts were identified, including 4525 differentially expressed lncRNAs (DELs). Additional research revealed that in mature xylem, a total of 2320 DELs were upregulated and 2205 were downregulated compared to developing xylem. Meanwhile, there were a total of 8122 differentially expressed mRNAs (DEMs) that were upregulated and 16,424 that were downregulated in mature xylem compared with developing xylem. The cis- and trans-target genes of DELs were analyzed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, which indicated that these DELs participate in controlling the phenylpropanoid and lignin biosynthesis pathway as well as the starch and sucrose metabolism pathway. Among the cis-regulated DELs, LNC_006291, LNC_006292, and LNC_006532 all participate in regulating multiple HCT gene family membranes. As targets, POPTR_001G045900v3 (CCR2) and POPTR_018G063500v3 (SUS) both have only one cis-regulatory lncRNA, referred to as LNC_000057 and LNC_006212, respectively. Moreover, LNC_004484 and two DELs named LNC_008014 and LNC_010781 were revealed to be important nodes in the co-expression network of trans-lncRNAs and mRNAs associated to the lignin biosynthesis pathway and cellulose and xylan biosynthetic pathways, respectively. Finally, quantitative real-time PCR (qRT-PCR) was used to confirme 34 pairs of lncRNA-mRNA. Taken together, these findings may help to clarify the regulatory role that lncRNAs play in xylem development and wood formation.
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Affiliation(s)
- Na Sun
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Yufen Bu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xinyuan Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xiaocen Ma
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Haobo Yang
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Liang Du
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Xiaojuan Li
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Jianwei Xiao
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Jinxing Lin
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
| | - Yanping Jing
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China; The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, No. 35 Qinghua East Road, Beijing, 100083, China.
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11
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Rawal HC, Ali S, Mondal TK. Role of non-coding RNAs against salinity stress in Oryza species: Strategies and challenges in analyzing miRNAs, tRFs and circRNAs. Int J Biol Macromol 2023; 242:125172. [PMID: 37268077 DOI: 10.1016/j.ijbiomac.2023.125172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/04/2023]
Abstract
Salinity is an imbalanced concentration of mineral salts in the soil or water that causes yield loss in salt-sensitive crops. Rice plant is vulnerable to soil salinity stress at seedling and reproductive stages. Different non-coding RNAs (ncRNAs) post-transcriptionally regulate different sets of genes during different developmental stages under varying salinity tolerance levels. While microRNAs (miRNAs) are well known small endogenous ncRNAs, tRNA-derived RNA fragments (tRFs) are an emerging class of small ncRNAs derived from tRNA genes with a demonstrated regulatory role, like miRNAs, in humans but unexplored in plants. Circular RNA (circRNA), another ncRNA produced by back-splicing events, acts as target mimics by preventing miRNAs from binding with their target mRNAs, thereby reducing the miRNA's action upon its target. Same may hold true between circRNAs and tRFs. Hence, the work done on these ncRNAs was reviewed and no reports were found for circRNAs and tRFs under salinity stress in rice, either at seedling or reproductive stages. Even the reports on miRNAs are restricted to seedling stage only, in spite of severe effects on rice crop production due to salt stress during reproductive stage. Moreover, this review sheds light on strategies to predict and analyze these ncRNAs in an effective manner.
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Affiliation(s)
- Hukam Chand Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India; School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Shakir Ali
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India; Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard (Hamdard University), Hamdard Nagar, New Delhi 110062, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Centre, Pusa, New Delhi 110012, India.
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12
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Hu S, Hu Y, Mei H, Li J, Xuan W, Jeyaraj A, Zhao Z, Zhao Y, Han R, Chen X, Li X. Genome-wide analysis of long non-coding RNAs (lncRNAs) in tea plants ( Camellia sinensis) lateral roots in response to nitrogen application. FRONTIERS IN PLANT SCIENCE 2023; 14:1080427. [PMID: 36909382 PMCID: PMC9998519 DOI: 10.3389/fpls.2023.1080427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Tea (Camellia sinensis) is one of the significant cash crops in China. As a leaf crop, nitrogen supply can not only increase the number of new shoots and leaves but also improve the tenderness of the former. However, a conundrum remains in science, which is the molecular mechanism of nitrogen use efficiency, especially long non-coding RNA (lncRNA). In this study, a total of 16,452 lncRNAs were identified through high-throughput sequencing analysis of lateral roots under nitrogen stress and control conditions, of which 9,451 were differentially expressed lncRNAs (DE-lncRNAs). To figure out the potential function of nitrogen-responsive lncRNAs, co-expression clustering was employed between lncRNAs and coding genes. KEGG enrichment analysis revealed nitrogen-responsive lncRNAs may involve in many biological processes such as plant hormone signal transduction, nitrogen metabolism and protein processing in endoplasmic reticulum. The expression abundance of 12 DE-lncRNAs were further verified by RT-PCR, and their expression trends were consistent with the results of RNA-seq. This study expands the research on lncRNAs in tea plants, provides a novel perspective for the potential regulation of lncRNAs on nitrogen stress, and valuable resources for further improving the nitrogen use efficiency of tea plants.
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Affiliation(s)
- Shunkai Hu
- International Institute of Tea Industry Innovation for “One Belt, One Road”, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yimeng Hu
- International Institute of Tea Industry Innovation for “One Belt, One Road”, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Huiling Mei
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jianjie Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Wei Xuan
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Anburaj Jeyaraj
- International Institute of Tea Industry Innovation for “One Belt, One Road”, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Zhen Zhao
- International Institute of Tea Industry Innovation for “One Belt, One Road”, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yuxin Zhao
- International Institute of Tea Industry Innovation for “One Belt, One Road”, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Rui Han
- International Institute of Tea Industry Innovation for “One Belt, One Road”, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xuan Chen
- International Institute of Tea Industry Innovation for “One Belt, One Road”, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xinghui Li
- International Institute of Tea Industry Innovation for “One Belt, One Road”, Nanjing Agricultural University, Nanjing, Jiangsu, China
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13
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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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14
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Tian R, Sun X, Liu C, Chu J, Zhao M, Zhang WH. A Medicago truncatula lncRNA MtCIR1 negatively regulates response to salt stress. PLANTA 2023; 257:32. [PMID: 36602592 DOI: 10.1007/s00425-022-04064-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
A lncRNA MtCIR1 negatively regulates the response to salt stress in Medicago truncatula seed germination by modulating seedling growth and ABA metabolism and signaling by enhancing Na+ accumulation. Increasing evidence suggests that long non-coding RNAs (lncRNAs) are involved in the regulation of plant tolerance to varying abiotic stresses. A large number of lncRNAs that are responsive to abiotic stress have been identified in plants; however, the mechanisms underlying the regulation of plant responses to abiotic stress by lncRNAs are largely unclear. Here, we functionally characterized a salt stress-responsive lncRNA derived from the leguminous model plant M. truncatula, referred to as MtCIR1, by expressing MtCIR1 in Arabidopsis thaliana in which no such homologous sequence was observed. Expression of MtCIR1 rendered seed germination more sensitive to salt stress by enhanced accumulation of abscisic acid (ABA) due to suppressing the expression of the ABA catabolic enzyme CYP707A2. Expression of MtCIR1 also suppressed the expression of genes associated with ABA receptors and signaling. The ABA-responsive gene AtPGIP2 that was involved in degradation of cell wall during seed germination was up-regulated by expressing MtCIR1. On the other hand, expression of MtCIR1 in Arabidopsis thaliana enhanced foliar Na+ accumulation by down-regulating genes encoding Na+ transporters, thus rendering the transgenic plants more sensitive to salt stress. These results demonstrate that the M. truncatula lncRNA MtCIR1 negatively regulates salt stress response by targeting ABA metabolism and signaling during seed germination and foliar Na+ accumulation by affecting Na+ transport under salt stress during seedling growth. These novel findings would advance our knowledge on the regulatory roles of lncRNAs in response of plants to salt stress.
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Affiliation(s)
- Rui Tian
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Xiaohan Sun
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, People's Republic of China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Cuimei Liu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Mingui Zhao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
| | - Wen-Hao Zhang
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, People's Republic of China.
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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15
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Govindasamy P, Muthusamy SK, Bagavathiannan M, Mowrer J, Jagannadham PTK, Maity A, Halli HM, G. K. S, Vadivel R, T. K. D, Raj R, Pooniya V, Babu S, Rathore SS, L. M, Tiwari G. Nitrogen use efficiency-a key to enhance crop productivity under a changing climate. FRONTIERS IN PLANT SCIENCE 2023; 14:1121073. [PMID: 37143873 PMCID: PMC10151540 DOI: 10.3389/fpls.2023.1121073] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 03/20/2023] [Indexed: 05/06/2023]
Abstract
Nitrogen (N) is an essential element required for the growth and development of all plants. On a global scale, N is agriculture's most widely used fertilizer nutrient. Studies have shown that crops use only 50% of the applied N effectively, while the rest is lost through various pathways to the surrounding environment. Furthermore, lost N negatively impacts the farmer's return on investment and pollutes the water, soil, and air. Therefore, enhancing nitrogen use efficiency (NUE) is critical in crop improvement programs and agronomic management systems. The major processes responsible for low N use are the volatilization, surface runoff, leaching, and denitrification of N. Improving NUE through agronomic management practices and high-throughput technologies would reduce the need for intensive N application and minimize the negative impact of N on the environment. The harmonization of agronomic, genetic, and biotechnological tools will improve the efficiency of N assimilation in crops and align agricultural systems with global needs to protect environmental functions and resources. Therefore, this review summarizes the literature on nitrogen loss, factors affecting NUE, and agronomic and genetic approaches for improving NUE in various crops and proposes a pathway to bring together agronomic and environmental needs.
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Affiliation(s)
- Prabhu Govindasamy
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Muthukumar Bagavathiannan, ; Prabhu Govindasamy,
| | - Senthilkumar K. Muthusamy
- Division of Crop Improvement, Indian Council of Agricultural Research (ICAR)-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - Muthukumar Bagavathiannan
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Muthukumar Bagavathiannan, ; Prabhu Govindasamy,
| | - Jake Mowrer
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | | | - Aniruddha Maity
- Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Hanamant M. Halli
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Pune, India
| | - Sujayananad G. K.
- Crop Protection, Indian Council of Agricultural Research (ICAR)-Indian Institute of Pulse Research, Kanpur, India
| | - Rajagopal Vadivel
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Pune, India
| | - Das T. K.
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rishi Raj
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Vijay Pooniya
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Subhash Babu
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sanjay Singh Rathore
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Muralikrishnan L.
- Division of Agricultural Extension, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Gopal Tiwari
- Division of Agronomy, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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16
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Patra GK, Gupta D, Rout GR, Panda SK. Role of long non coding RNA in plants under abiotic and biotic stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 194:96-110. [PMID: 36399914 DOI: 10.1016/j.plaphy.2022.10.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Evolutionary processes have evolved plants to cope with several different natural stresses. Basic physiological activities of crop plants are significantly harmed by these stresses, reducing productivity and eventually leading to death. The recent advancements in high-throughput sequencing of transcriptome and expression profiling with NGS techniques lead to the innovation of various RNAs which do not code for proteins, more specifically long non-coding RNAs (lncRNAs), undergirding regulate growth, development, and the plant defence mechanism transcriptionally under stress situations. LncRNAs are a diverse set of RNAs that play key roles in various biological processes at the level of transcription, post-transcription, and epigenetics. These are thought to serve crucial functions in plant immunity and response to changes in the environment. In plants, however, just a few lncRNAs have been functionally identified. In this review, we will address recent advancements in comprehending lncRNA regulatory functions, focusing on the expanding involvement of lncRNAs in modulating environmental stress responsiveness in plants.
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Affiliation(s)
- Gyanendra K Patra
- Department of Agriculture Biotechnology, Orissa University of Agriculture and Technology, Bhubaneswar, 751 003, Odisha, India
| | - Divya Gupta
- School of Life Sciences, Central University of Rajasthan, NH 8, Bandarsindri, Ajmer, 305817, Rajasthan, India
| | - Gyana Ranjan Rout
- Department of Agriculture Biotechnology, Orissa University of Agriculture and Technology, Bhubaneswar, 751 003, Odisha, India
| | - Sanjib Kumar Panda
- School of Life Sciences, Central University of Rajasthan, NH 8, Bandarsindri, Ajmer, 305817, Rajasthan, India.
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17
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Zheng K, Wang Z, Pang L, Song Z, Zhao H, Wang Y, Wang B, Han S. Systematic Identification of Methyl Jasmonate-Responsive Long Noncoding RNAs and Their Nearby Coding Genes Unveils Their Potential Defence Roles in Tobacco BY-2 Cells. Int J Mol Sci 2022; 23:ijms232415568. [PMID: 36555209 PMCID: PMC9778826 DOI: 10.3390/ijms232415568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/27/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are distributed in various species and play critical roles in plant growth, development, and defence against stimuli. However, the lncRNA response to methyl jasmonate (MeJA) treatment has not been well characterized in Nicotiana tabacum Bright Yellow-2 (BY-2) cells, and their roles in plant defence remain elusive. Here, 7848 reliably expressed lncRNAs were identified in BY-2 cells, of which 629 differentially expressed (DE) lncRNAs were characterized as MeJA-responsive lncRNAs. The lncRNAs in BY-2 cells had a strong genus specificity in Nicotiana. The combined analysis of the cis-regulated lncRNAs and their target genes revealed the potential up- and downregulated target genes that are responsible for different biological functions and metabolic patterns. In addition, some lncRNAs for response-associated target genes might be involved in plant defence and stress resistance via their MeJA- and defence-related cis-regulatory elements. Moreover, some MeJA-responsive lncRNA target genes were related to quinolinate phosphoribosyltransferase, lipoxygenases, and endopeptidase inhibitors, which may contribute to nicotine synthesis and disease and insect resistance, indicating that MeJA-responsive lncRNAs regulate nicotine biosynthesis and disease resistance by regulating their potential target genes in BY-2 cells. Therefore, our results provide more targets for genetically engineering the nicotine content and plant defence in tobacco plants.
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Affiliation(s)
- Kaifeng Zheng
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Zitao Wang
- College of Life Sciences, Qinghai Normal University, Xining 810008, China
- Academy of Plateau Science and Sustainability of the People’s Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Xining 810008, China
| | - Lu Pang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Zhongbang Song
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China
| | - Heping Zhao
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yingdian Wang
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Academy of Plateau Science and Sustainability of the People’s Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Xining 810008, China
| | - Bingwu Wang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China
- Correspondence: (B.W.); (S.H.)
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resources and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing 100875, China
- Academy of Plateau Science and Sustainability of the People’s Government of Qinghai Province & Beijing Normal University, Qinghai Normal University, Xining 810008, China
- Correspondence: (B.W.); (S.H.)
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18
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Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
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Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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19
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Samarfard S, Ghorbani A, Karbanowicz TP, Lim ZX, Saedi M, Fariborzi N, McTaggart AR, Izadpanah K. Regulatory non-coding RNA: The core defense mechanism against plant pathogens. J Biotechnol 2022; 359:82-94. [PMID: 36174794 DOI: 10.1016/j.jbiotec.2022.09.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 12/13/2022]
Abstract
Plant pathogens damage crops and threaten global food security. Plants have evolved complex defense networks against pathogens, using crosstalk among various signaling pathways. Key regulators conferring plant immunity through signaling pathways include protein-coding genes and non-coding RNAs (ncRNAs). The discovery of ncRNAs in plant transcriptomes was first considered "transcriptional noise". Recent reviews have highlighted the importance of non-coding RNAs. However, understanding interactions among different types of noncoding RNAs requires additional research. This review attempts to consider how long-ncRNAs, small-ncRNAs and circular RNAs interact in response to pathogenic diseases within different plant species. Developments within genomics and bioinformatics could lead to the further discovery of plant ncRNAs, knowledge of their biological roles, as well as an understanding of their importance in exploiting the recent molecular-based technologies for crop protection.
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Affiliation(s)
- Samira Samarfard
- Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia
| | - Abozar Ghorbani
- Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, the Islamic Republic of Iran.
| | | | - Zhi Xian Lim
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Mahshid Saedi
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, Sanandaj, the Islamic Republic of Iran
| | - Niloofar Fariborzi
- Department of Medical Entomology and Vector Control, School of Health, Shiraz University of Medical Sciences, Shiraz, the Islamic Republic of Iran
| | - Alistair R McTaggart
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Keramatollah Izadpanah
- Plant Virology Research Center, College of Agriculture, Shiraz University, Shiraz, the Islamic Republic of Iran
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20
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Zhao Z, Zang S, Zou W, Pan YB, Yao W, You C, Que Y. Long Non-Coding RNAs: New Players in Plants. Int J Mol Sci 2022; 23:ijms23169301. [PMID: 36012566 PMCID: PMC9409372 DOI: 10.3390/ijms23169301] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
During the process of growth and development, plants are prone to various biotic and abiotic stresses. They have evolved a variety of strategies to resist the adverse effects of these stresses. lncRNAs (long non-coding RNAs) are a type of less conserved RNA molecules of more than 200 nt (nucleotides) in length. lncRNAs do not code for any protein, but interact with DNA, RNA, and protein to affect transcriptional, posttranscriptional, and epigenetic modulation events. As a new regulatory element, lncRNAs play a critical role in coping with environmental pressure during plant growth and development. This article presents a comprehensive review on the types of plant lncRNAs, the role and mechanism of lncRNAs at different molecular levels, the coordination between lncRNA and miRNA (microRNA) in plant immune responses, the latest research progress of lncRNAs in plant growth and development, and their response to biotic and abiotic stresses. We conclude with a discussion on future direction for the elaboration of the function and mechanism of lncRNAs.
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Affiliation(s)
- Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong-Bao Pan
- Sugarcane Research Unit, USDA-ARS, Houma, LA 70360, USA
| | - Wei Yao
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China
| | - Cuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
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21
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Aslam MM, Waseem M, Xu W, Ying L, Zhang J, Yuan W. Global Identification of White Lupin lncRNAs Reveals Their Role in Cluster Roots under Phosphorus Deficiency. Int J Mol Sci 2022; 23:ijms23169012. [PMID: 36012274 PMCID: PMC9409226 DOI: 10.3390/ijms23169012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/05/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
Phosphorus (P) deficiency heterogeneously affected plant nutritional status and physiological performance, ultimately leading to a severe yield reduction. A few putative long non-coding RNAs (lncRNAs) responding to P-starvation in the model crops Arabidopsis thaliana and Oryza sativa have been characterized. White lupin (Lupinus albus) is of prime importance, and is a legume with increasing agronomic value as a protein crop as it exhibits extreme tolerance to nutrient deficiency, particularly P deficiency. Despite its adapted nature to P deficiency, nothing is known about low P-induced lncRNAs in white lupin roots. To address this issue, we identified 39,840 mRNA and 2028 lncRNAs in the eight developmental stages of white lupin root (S0–S7 and lateral root, LR) grown under P deficiency. From these 2028 lncRNAs, 1564 were intergenic and 464 natural antisense intergenic transcript (NAT) lncRNAs. We further predicted six potential targets of miRNAs with twelve lncRNAs, which may regulate P-deficiency-related processes. Moreover, the weighted gene co-expression network analysis (WGCNA) revealed seven modules that were correlated with the expression pattern of lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed 606 GO terms and 27 different pathways including signal transduction, energy synthesis, detoxification, and Pi transport. In addition, we screened 13 putative lncRNAs that showed a distinct expression pattern in each root, indicating their role in the P deficiency regulatory network. Therefore, white lupin may be a reference legume to characterize P-deficiency-responsive novel lncRNAs, which would highlight the role of lncRNAs in the regulation of plant responses to P deficiency.
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Affiliation(s)
- Mehtab Muhammad Aslam
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong
- Joint International Research Laboratory of Water and Nutrient in Crop, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Muhammad Waseem
- Department of Botany, University of Narowal, Narowal 51601, Pakistan
| | - Weifeng Xu
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Water and Nutrient in Crop, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Li Ying
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Jianhua Zhang
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong
- Correspondence: (J.Z.); (W.Y.)
| | - Wei Yuan
- Joint International Research Laboratory of Water and Nutrient in Crop, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (J.Z.); (W.Y.)
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22
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Guo Y, Xu H, Chen B, Grünhofer P, Schreiber L, Lin J, Zhao Y. Genome-wide analysis of long non-coding RNAs in shoot apical meristem and vascular cambium in Populus tomentosa. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153759. [PMID: 35820347 DOI: 10.1016/j.jplph.2022.153759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/14/2022] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Shoot apical and lateral meristems play essential roles in the formation and development of primary and secondary growth in plants. A delicate regulatory mechanism is needed to maintain homeostatic balance between the primary and secondary growth, as well as the self-renewal of meristems with the rate of cell division and differentiation of new meristems. However, little is known about the roles of long non-coding RNAs (lncRNAs) in the regulation of maintenance and differentiation of primary and secondary growth in Populus, especially in the cambium division and differentiation into secondary xylem. Here, 1298 lncRNAs were identified both in the apical meristem and vascular cambium, with 80 lncRNAs being expressed only in shoot apical meristem and 45 only in vascular cambium. There are 410 differentially expressed lncRNAs in shoot apical meristem and vascular cambium, among which 271 lncRNAs were up-regulated and 139 were down-regulated in cambium. The GO enrichment analysis revealed that differentially expressed lncRNAs mainly influenced the expression of lncRNAs related to the ribosome pathway, plant hormone signal pathway and photosynthesis pathway. The differentially expressed lncRNAs mainly target mRNA through cis-regulation in the vascular cambium. In addition, six key lncRNAs and also their significantly upregulated target genes were identified. Theses target genes are involved in plant secondary metabolites, cellulose and lignin synthesis, hormone and signal transduction. In addition, six key lncRNAs were identified, their significantly upregulated target genes are related to plant secondary metabolites, cellulose and lignin synthesis, hormone and signal transduction. Investigating lncRNA-mRNA interactions, we further found some genes that may be related to the development of vascular cambium, such as domain-containing transcription factors, cellulose synthesis genes, calcium dependent protein kinase 2, cytokinin receptor 1, glycosyl transferase and polyphenol oxidase. Our findings provide new insights into the lncRNA-mRNA networks in the development of vascular cambium of secondary growth in Populus.
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Affiliation(s)
- Yayu Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Bo Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Paul Grünhofer
- Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Lukas Schreiber
- Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, D-53115, Bonn, Germany.
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
| | - Yuanyuan Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Science and Technology, Beijing Forestry University, Beijing, 100083, China.
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23
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Wang Y, Gui C, Wu J, Gao X, Huang T, Cui F, Liu H, Sethupathy S. Spatio-Temporal Modification of Lignin Biosynthesis in Plants: A Promising Strategy for Lignocellulose Improvement and Lignin Valorization. Front Bioeng Biotechnol 2022; 10:917459. [PMID: 35845403 PMCID: PMC9283729 DOI: 10.3389/fbioe.2022.917459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Lignin is essential for plant growth, structural integrity, biotic/abiotic stress resistance, and water transport. Besides, lignin constitutes 10–30% of lignocellulosic biomass and is difficult to utilize for biofuel production. Over the past few decades, extensive research has uncovered numerous metabolic pathways and genes involved in lignin biosynthesis, several of which have been highlighted as the primary targets for genetic manipulation. However, direct manipulation of lignin biosynthesis is often associated with unexpected abnormalities in plant growth and development for unknown causes, thus limiting the usefulness of genetic engineering for biomass production and utilization. Recent advances in understanding the complex regulatory mechanisms of lignin biosynthesis have revealed new avenues for spatial and temporal modification of lignin in lignocellulosic plants that avoid growth abnormalities. This review explores recent work on utilizing specific transcriptional regulators to modify lignin biosynthesis at both tissue and cellular levels, focusing on using specific promoters paired with functional or regulatory genes to precisely control lignin synthesis and achieve biomass production with desired properties. Further advances in designing more appropriate promoters and other regulators will increase our capacity to modulate lignin content and structure in plants, thus setting the stage for high-value utilization of lignin in the future.
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Affiliation(s)
- Yongli Wang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- *Correspondence: Yongli Wang, ; Sivasamy Sethupathy,
| | - Cunjin Gui
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Jiangyan Wu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Xing Gao
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Ting Huang
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Fengjie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Huan Liu
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
| | - Sivasamy Sethupathy
- Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China
- *Correspondence: Yongli Wang, ; Sivasamy Sethupathy,
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24
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The Intersection of Non-Coding RNAs Contributes to Forest Trees' Response to Abiotic Stress. Int J Mol Sci 2022; 23:ijms23126365. [PMID: 35742808 PMCID: PMC9223653 DOI: 10.3390/ijms23126365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/15/2022] [Accepted: 06/01/2022] [Indexed: 12/10/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play essential roles in plants by modulating the expression of genes at the transcriptional or post-transcriptional level. In recent years, ncRNAs have been recognized as crucial regulators for growth and development in forest trees, and ncRNAs that respond to various abiotic stresses are now under intense study. In this review, we summarized recent advances in the understanding of abiotic stress-responsive microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in forest trees. Furthermore, we analyzed the intersection of miRNAs, and epigenetic modified ncRNAs of forest trees in response to abiotic stress. In particular, the abiotic stress-related lncRNA/circRNA-miRNA-mRNA regulatory network of forest trees was explored.
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25
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Yuan T, Zhu C, Li G, Liu Y, Yang K, Li Z, Song X, Gao Z. An Integrated Regulatory Network of mRNAs, microRNAs, and lncRNAs Involved in Nitrogen Metabolism of Moso Bamboo. Front Genet 2022; 13:854346. [PMID: 35651936 PMCID: PMC9149284 DOI: 10.3389/fgene.2022.854346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/14/2022] [Indexed: 11/18/2022] Open
Abstract
Nitrogen is a key macronutrient essential for plant growth and development, and its availability has a strong influence on biological processes. Nitrogen fertilizer has been widely applied in bamboo forests in recent decades; however, the mechanism of nitrogen metabolism in bamboo is not fully elucidated. Here, we characterized the morphological, physiological, and transcriptome changes of moso bamboo in response to different schemes for nitrogen addition to illuminate the regulation mechanism of nitrogen metabolism. The appropriate addition of nitrogen improved the chlorophyll content and Pn (net photosynthetic rate) of leaves, the nitrogen and ammonium contents of the seedling roots, the biomass of the whole seedling, the number of lateral roots, and the activity of enzymes involved in nitrogen metabolism in the roots. Based on the whole transcriptome data of the roots, a total of 8,632 differentially expressed mRNAs (DEGs) were identified under different nitrogen additions, such as 52 nitrate transporter genes, 6 nitrate reductase genes, 2 nitrite reductase genes, 2 glutamine synthase genes, 2 glutamate synthase genes (GOGAT), 3 glutamate dehydrogenase genes, and 431 TFs belonging to 23 families. Meanwhile, 123 differentially expressed miRNAs (DEMs) and 396 differentially expressed lncRNAs (DELs) were characterized as nitrogen responsive, respectively. Furthermore, 94 DEM-DEG pairs and 23 DEL-DEG pairs involved in nitrogen metabolism were identified. Finally, a predicted regulatory network of nitrogen metabolism was initially constructed, which included 17 nitrogen metabolic pathway genes, 15 TFs, 4 miRNAs, and 10 lncRNAs by conjoint analysis of DEGs, DEMs, and DELs and their regulatory relationships, which was supported by RNA-seq data and qPCR results. The lncRNA-miRNA-mRNA network provides new insights into the regulation mechanism of nitrogen metabolism in bamboo, which facilitates further genetic improvement for bamboo to adapt to the fluctuating nitrogen environment.
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Affiliation(s)
- Tingting Yuan
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Chenglei Zhu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Guangzhu Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Yan Liu
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Kebin Yang
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Zhen Li
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
| | - Xinzhang Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Hangzhou, China
| | - Zhimin Gao
- Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo and Rattan Science and Technology, Beijing, China.,International Center for Bamboo and Rattan, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, Beijing, China
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26
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Ye X, Wang S, Zhao X, Gao N, Wang Y, Yang Y, Wu E, Jiang C, Cheng Y, Wu W, Liu S. Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:978-993. [PMID: 35218100 DOI: 10.1111/tpj.15714] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 06/05/2023]
Abstract
Long non-coding RNAs (lncRNAs) are emerging as versatile regulators in diverse biological processes. However, little is known about their cis- and trans-regulatory contributions in gene expression under salt stress. Using 27 RNA-seq data sets from Populus trichocarpa leaves, stems and roots, we identified 2988 high-confidence lncRNAs, including 1183 salt-induced differentially expressed lncRNAs. Among them, 301 lncRNAs have potential for positively affecting their neighboring genes, predominantly in a cis-regulatory manner rather than by co-transcription. Additionally, a co-expression network identified six striking salt-associated modules with a total of 5639 genes, including 426 lncRNAs, and in these lncRNA sequences, the DNA/RNA binding motifs are enriched. This suggests that lncRNAs might contribute to distant gene expression of the salt-associated modules in a trans-regulatory manner. Moreover, we found 30 lncRNAs that have potential to simultaneously cis- and trans-regulate salt-responsive homologous genes, and Ptlinc-NAC72, significantly induced under long-term salt stress, was selected for validating its regulation of the expression and functional roles of the homologs PtNAC72.A and PtNAC72.B (PtNAC72.A/B). The transient transformation of Ptlinc-NAC72 and a dual-luciferase assay of Ptlinc-NAC72 and PtNAC72.A/B promoters confirmed that Ptlinc-NAC72 can directly upregulate PtNAC72.A/B expression, and a presence/absence assay was further conducted to show that the regulation is probably mediated by Ptlinc-NAC72 recognizing the tandem elements (GAAAAA) in the PtNAC72.A/B 5' untranslated region (5'-UTR). Finally, the overexpression of Ptlinc-NAC72 produces a hypersensitive phenotype under salt stress. Altogether, our results shed light on the cis- and trans-regulation of gene expression by lncRNAs in Populus and provides an example of long-term salt-induced Ptlinc-NAC72 that could be used to mitigate growth costs by conferring plant resilience to salt stress.
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Affiliation(s)
- Xiaoxue Ye
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Ni Gao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yao Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin, 150040, China
| | - Yanmei Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Ernest Wu
- Department of Forest & Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cheng Jiang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yuxiang Cheng
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), School of Forestry, Northeast Forestry University, Harbin, 150040, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
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Unravelling lncRNA mediated gene expression as potential mechanism for regulating secondary metabolism in Citrus limon. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2021.101448] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Hu X, Wei Q, Wu H, Huang Y, Peng X, Han G, Ma Q, Zhao Y. Identification and characterization of heat-responsive lncRNAs in maize inbred line CM1. BMC Genomics 2022; 23:208. [PMID: 35291949 PMCID: PMC8925227 DOI: 10.1186/s12864-022-08448-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 03/07/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Frequent occurrence of extreme high temperature is a major threat to crop production. Increasing evidence demonstrates that long non-coding RNAs (lncRNAs) have important biological functions in the regulation of the response to heat stress. However, the regulatory mechanism of lncRNAs involved in heat response requires further exploration and the regulatory network remains poorly understood in maize. RESULTS In this research, high-throughput sequencing was adopted to systematically identify lncRNAs in maize inbred line CM1. In total, 53,249 lncRNAs (259 known lncRNAs and 52,990 novel lncRNAs) were detected, of which 993 lncRNAs showed significantly differential expression (DElncRNAs) under heat stress. By predicting the target genes, 953 common targets shared by cis- and trans-regulation of the DElncRNAs were identified, which exhibited differential expression between the control and the heat stress treatments. Functional annotation indicated that a number of important biological processes and pathways, including photosynthesis, metabolism, translation, stress response, hormone signal transduction, and spliceosome, were enriched for the common targets, suggesting that they play important roles in heat response. A lncRNA-mediated regulatory network was constructed to visualize the molecular response mechanism in response to heat stress, which represented the direct regulatory relationships of DElncRNAs, differentially expressed miRNAs, target genes, and functional annotations. CONCLUSIONS This study lays a foundation for further elucidation of the regulatory mechanism for the response to heat stress in the maize inbred line CM1. The findings provide important information for identification of heat-responsive genes, which will be beneficial for the molecular breeding in the cultivation of heat-tolerant maize germplasm.
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Affiliation(s)
- Xiaolin Hu
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 203036, China
| | - Qiye Wei
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 203036, China
| | - Hongying Wu
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 203036, China
| | - Yuanxiang Huang
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 203036, China
| | - Xiaojian Peng
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 203036, China
| | - Guomin Han
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 203036, China
| | - Qing Ma
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 203036, China
| | - Yang Zhao
- The National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 203036, China.
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Shi F, Pang Z, Liu C, Zhou L, Tan C, Ren J, Ye X, Feng H, Liu Z. Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis). Sci Rep 2022; 12:2667. [PMID: 35177672 PMCID: PMC8854722 DOI: 10.1038/s41598-022-06556-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 01/24/2022] [Indexed: 01/17/2023] Open
Abstract
Anther development is precisely regulated by a complex gene network, which is of great significance to plant breeding. However, the molecular mechanism of anther development in Chinese cabbage is unclear. Here, we identified microRNAs (miRNAs), mRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to anther development in Chinese cabbage (Brassica campestris L. ssp. pekinensis) to construct competitive endogenous RNA (ceRNA) regulatory networks and provide valuable knowledge on anther development. Using whole-transcriptome sequencing, 9055, 585, 1344, and 165 differentially expressed mRNAs (DEmRNAs), miRNAs (DEmiRNAs), lncRNAs (DElncRNAs), and circRNAs (DEcircRNAs) were identified, respectively, in the anthers of Chinese cabbage compared with those in samples of the vegetative mass of four true leaves. An anther-related ceRNA regulatory network was constructed using miRNA targeting relationships, and 450 pairs of ceRNA relationships, including 97 DEmiRNA-DEmRNA, 281 DEmiRNA-DElncRNA, and 23 DEmiRNA-DEcircRNA interactions, were obtained. We identified important genes and their interactions with lncRNAs, circRNAs, and miRNAs involved in microsporogenesis, tapetum and callose layer development, pollen wall formation, and anther dehiscence. We analyzed the promoter activity of six predominant anther expression genes, which were expressed specifically in the anthers of Arabidopsis thaliana, indicating that they may play an important role in anther development of Chinese cabbage. This study lays the foundation for further research on the molecular mechanisms of anther growth and development in Chinese cabbage.
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Affiliation(s)
- Fengyan Shi
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Zhijin Pang
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Chuanhong Liu
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Li Zhou
- Integrated Technical Service Center, Bayuquan Customs, Yingkou, 115007, China
| | - Chong Tan
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Jie Ren
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Xueling Ye
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Hui Feng
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Zhiyong Liu
- Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, 120 Dongling Road, Shenhe District, Shenyang, 110866, China.
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Xu H, Chen B, Zhao Y, Guo Y, Liu G, Li R, Zeisler-Diehl VV, Chen Y, He X, Schreiber L, Lin J. Non-Coding RNA Analyses of Seasonal Cambium Activity in Populus tomentosa. Cells 2022; 11:cells11040640. [PMID: 35203291 PMCID: PMC8869787 DOI: 10.3390/cells11040640] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/06/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
Non-coding RNA, known as long non-coding RNA (lncRNA), circular RNA (circRNA) and microRNA (miRNA), are taking part in the multiple developmental processes in plants. However, the roles of which played during the cambium activity periodicity of woody plants remain poorly understood. Here, lncRNA/circRNA-miRNA-mRNA regulatory networks of the cambium activity periodicity in Populus tomentosa was constructed, combined with morphologic observation and transcriptome profiling. Light microscopy and Periodic Acid Schiff (PAS) staining revealed that cell walls were much thicker and number of cell layers was increased during the active-dormant stage, accompanied by abundant change of polysaccharides. The novel lncRNAs and circRNAs were investigated, and we found that 2037 lncRNAs and 299 circRNAs were differentially expression during the vascular cambium period, respectively. Moreover, 1046 genes were identified as a target gene of 2037 novel lncRNAs, and 89 of which were the miRNA precursors or targets. By aligning miRNA precursors to the 7655 lncRNAs, 21 lncRNAs were identified as precursors tof 19 known miRNAs. Furthermore, the target mRNA of lncRNA/circRNA-miRNA network mainly participated in phytohormone, cell wall alteration and chlorophyll metabolism were analyzed by GO enrichment and KEGG pathway. Especially, circRNA33 and circRNA190 taking part in the phytohormone signal pathway were down-regulated during the active-dormant transition. Xyloglucan endotransglucosylase/hydrolase protein 24-like and UDP-glycosyltransferase 85A1 involved in the cell wall modification were the targets of lncRNA MSTRG.11198.1 and MSTRG.1050.1. Notably, circRNA103 and MSTRG.10851.1 regulate the cambium periodicity may interact with the miR482. These results give a new light into activity–dormancy regulation, associated with transcriptional dynamics and non-coding RNA networks of potential targets identification.
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Affiliation(s)
- Huimin Xu
- College of Biological Sciences, China Agricultural University, Beijing 100193, China; (H.X.); (Y.C.)
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (B.C.); (Y.Z.); (Y.G.); (R.L.)
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
- College of Life Sciences, Peking University, Beijing 100871, China;
| | - Bo Chen
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (B.C.); (Y.Z.); (Y.G.); (R.L.)
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Yuanyuan Zhao
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (B.C.); (Y.Z.); (Y.G.); (R.L.)
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Yayu Guo
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (B.C.); (Y.Z.); (Y.G.); (R.L.)
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
| | - Guijun Liu
- Institute of Radiation Technology, Beijing Academy of Science and Technology, Beijing 100875, China;
| | - Ruili Li
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (B.C.); (Y.Z.); (Y.G.); (R.L.)
| | - Viktoria V. Zeisler-Diehl
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115 Bonn, Germany; (V.V.Z.-D.); (L.S.)
| | - Yanmei Chen
- College of Biological Sciences, China Agricultural University, Beijing 100193, China; (H.X.); (Y.C.)
| | - Xinqiang He
- College of Life Sciences, Peking University, Beijing 100871, China;
| | - Lukas Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115 Bonn, Germany; (V.V.Z.-D.); (L.S.)
| | - Jinxing Lin
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; (B.C.); (Y.Z.); (Y.G.); (R.L.)
- Institute of Tree Development and Genome Editing, Beijing Forestry University, Beijing 100083, China
- Correspondence:
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Zhou J, Yang LY, Chen X, Shi WG, Deng SR, Luo ZB. Genome-Wide Identification and Characterization of Long Noncoding RNAs in Populus × canescens Roots Treated With Different Nitrogen Fertilizers. FRONTIERS IN PLANT SCIENCE 2022; 13:890453. [PMID: 35646010 PMCID: PMC9135444 DOI: 10.3389/fpls.2022.890453] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/19/2022] [Indexed: 05/14/2023]
Abstract
Nitrate (NO3 -) and ammonium (NH4 +) are the primary forms of inorganic nitrogen acquired by plant roots. LncRNAs, as key regulators of gene expression, are a class of non-coding RNAs larger than 200 bp. However, knowledge about the regulatory role of lncRNAs in response to different nitrogen forms remains limited, particularly in woody plants. Here, we performed strand-specific RNA-sequencing of P. × canescens roots under three different nitrogen fertilization treatments. In total, 324 lncRNAs and 6,112 mRNAs were identified as showing significantly differential expression between the NO3 - and NH4NO3 treatments. Moreover, 333 lncRNAs and 6,007 mRNAs showed significantly differential expression between the NH4 + and NH4NO3 treatments. Further analysis suggested that these lncRNAs and mRNAs have different response mechanisms for different nitrogen forms. In addition, functional annotation of cis and trans target mRNAs of differentially expressed lncRNAs indicated that 60 lncRNAs corresponding to 49 differentially expressed cis and trans target mRNAs were involved in plant nitrogen metabolism and amino acid biosynthesis and metabolism. Furthermore, 42 lncRNAs were identified as putative precursors of 63 miRNAs, and 28 differentially expressed lncRNAs were potential endogenous target mimics targeted by 96 miRNAs. Moreover, ceRNA regulation networks were constructed. MSTRG.6097.1, MSTRG.13550.1, MSTRG.2693.1, and MSTRG.12899.1, as hub lncRNAs in the ceRNA networks, are potential candidate lncRNAs for studying the regulatory mechanism in poplar roots under different nitrogen fertilization treatments. The results provide a basis for obtaining insight into the molecular mechanisms of lncRNA responses to different nitrogen forms in woody plants.
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32
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Regulatory long non-coding RNAs in root growth and development. Biochem Soc Trans 2021; 50:403-412. [PMID: 34940811 DOI: 10.1042/bst20210743] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022]
Abstract
As sessile organisms, plants have evolved sophisticated mechanisms of gene regulation to cope with changing environments. Among them, long non-coding RNAs (lncRNAs) are a class of RNAs regulating gene expression at both transcriptional and post-transcriptional levels. They are highly responsive to environmental cues or developmental processes and are generally involved in fine-tuning plant responses to these signals. Roots, in addition to anchoring the plant to the soil, allow it to absorb the major part of its mineral nutrients and water. Furthermore, roots directly sense environmental constraints such as mineral nutrient availability and abiotic or biotic stresses and dynamically adapt their growth and architecture. Here, we review the role of lncRNAs in the control of root growth and development. In particular, we highlight their action in fine-tuning primary root growth and the development of root lateral organs, such as lateral roots and symbiotic nodules. Lastly, we report their involvement in plant response to stresses and the regulation of nutrient assimilation and homeostasis, two processes leading to the modification of root architecture. LncRNAs could become interesting targets in plant breeding programs to subtly acclimate crops to coming environmental changes.
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Chen M, Yin Y, Zhang L, Yang X, Fu T, Huo X, Wang Y. Metabolomics and Transcriptomics Integration of Early Response of Populus tomentosa to Reduced Nitrogen Availability. FRONTIERS IN PLANT SCIENCE 2021; 12:769748. [PMID: 34956269 PMCID: PMC8692568 DOI: 10.3389/fpls.2021.769748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/09/2021] [Indexed: 06/14/2023]
Abstract
Nitrogen (N) is one of the most crucial elements for plant growth and development. However, little is known about the metabolic regulation of trees under conditions of N deficiency. In this investigation, gas chromatography-mass spectrometry (GC-MS) was used to determine global changes in metabolites and regulatory pathways in Populus tomentosa. Thirty metabolites were found to be changed significantly under conditions of low-N stress. N deficiency resulted in increased levels of carbohydrates and decreases in amino acids and some alcohols, as well as some secondary metabolites. Furthermore, an RNA-sequencing (RNA-Seq) analysis was performed to characterize the transcriptomic profiles, and 1,662 differentially expressed genes were identified in P. tomentosa. Intriguingly, four pathways related to carbohydrate metabolism were enriched. Genes involved in the gibberellic acid and indole-3-acetic acid pathways were found to be responsive to low-N stress, and the contents of hormones were then validated by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS). Coordinated metabolomics and transcriptomics analysis revealed a pattern of co-expression of five pairs of metabolites and unigenes. Overall, our investigation showed that metabolism directly related to N deficiency was depressed, while some components of energy metabolism were increased. These observations provided insights into the metabolic and molecular mechanisms underlying the interactions of N and carbon in poplar.
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Affiliation(s)
- Min Chen
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yiyi Yin
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Lichun Zhang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Xiaoqian Yang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Tiantian Fu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Xiaowei Huo
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Yanwei Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
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Zhang L, Ge X, Du J, Cheng X, Peng X, Hu J. Genome-Wide Identification of Long Non-Coding RNAs and Their Potential Functions in Poplar Growth and Phenylalanine Biosynthesis. Front Genet 2021; 12:762678. [PMID: 34868243 PMCID: PMC8634849 DOI: 10.3389/fgene.2021.762678] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
Poplar is an important bioenergy tree species. lncRNAs play important roles in various biological regulatory processes, and their expression pattern is more tissue-specific than mRNAs. In this study, P. deltoides “Danhong” (Pd) and P. simonii “Tongliao1” (Ps) with different growth rates and wood quality were used as experimental materials, and the transcriptomes of their shoot apical meristem, xylem, and phloem were sequenced. Furthermore, high-throughput RNA sequencing analysis revealed that the expression patterns of genes and lncRNAs are different between the two genotypes. 6,355 lncRNAs were identified. Based on target prediction, lncRNAs and target genes were involved in ADP binding, oxidoreductase activity, phenylpropanoid biosynthesis, and cyanoamino acid metabolism. The DElncRNAs in two poplars were co-expressed with transcription factors and structural genes of lignin and flavonoid pathways. In addition, we found the potential target lncRNAs of miRNA. This result provides basic evidence for a better understanding of the regulatory role of lncRNAs in regulating phenylalanine molecular pathways and wood formation.
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Affiliation(s)
- Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaolan Ge
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jiujun Du
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xingqi Cheng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaopeng Peng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianjun Hu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis). BMC Genomics 2021; 22:819. [PMID: 34773977 PMCID: PMC8590779 DOI: 10.1186/s12864-021-08110-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The transition from vegetative growth to reproductive growth involves various pathways. Vernalization is a crucial process for floral organ formation and regulation of flowering time that is widely utilized in plant breeding. In this study, we aimed to identify the global landscape of mRNAs, microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) related to vernalization in Chinese cabbage. These data were then used to construct a competitive endogenous RNA (ceRNA) network that provides valuable information to better understand the vernalization response. RESULTS In this study, seeds sampled from the Chinese cabbage doubled haploid (DH) line 'FT' with or without vernalization treatment were used for whole-transcriptome sequencing. A total of 2702 differentially expressed (DE) mRNAs, 151 DE lncRNAs, 16 DE circRNAs, and 233 DE miRNAs were identified in the vernalization-treated seeds. Various transcription factors, such as WRKY, MYB, NAC, bHLH, MADS-box, zinc finger protein CONSTANS-like gene, and B3 domain protein, and regulatory proteins that play important roles in the vernalization pathway were identified. Additionally, we constructed a vernalization-related ceRNA-miRNA-target gene network and obtained 199 pairs of ceRNA relationships, including 108 DEmiRNA‒DEmRNA, 67 DEmiRNA‒DElncRNA, and 12 DEmiRNA‒DEcircRNA interactions, in Chinese cabbage. Furthermore, several important vernalization-related genes and their interacting lncRNAs, circRNAs, and miRNAs, which are involved in the regulation of flowering time, floral organ formation, bolting, and flowering, were identified. CONCLUSIONS Our results reveal the potential mRNA and non-coding RNAs involved in vernalization, providing a foundation for further studies on the molecular mechanisms underlying vernalization in Chinese cabbage.
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The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation. Int J Mol Sci 2021; 22:ijms222111387. [PMID: 34768817 PMCID: PMC8583499 DOI: 10.3390/ijms222111387] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/13/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.
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Noncoding-RNA-Mediated Regulation in Response to Macronutrient Stress in Plants. Int J Mol Sci 2021; 22:ijms222011205. [PMID: 34681864 PMCID: PMC8539900 DOI: 10.3390/ijms222011205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/13/2021] [Accepted: 10/16/2021] [Indexed: 01/09/2023] Open
Abstract
Macronutrient elements including nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), and sulfur (S) are required in relatively large and steady amounts for plant growth and development. Deficient or excessive supply of macronutrients from external environments may trigger a series of plant responses at phenotypic and molecular levels during the entire life cycle. Among the intertwined molecular networks underlying plant responses to macronutrient stress, noncoding RNAs (ncRNAs), mainly microRNAs (miRNAs) and long ncRNAs (lncRNAs), may serve as pivotal regulators for the coordination between nutrient supply and plant demand, while the responsive ncRNA-target module and the interactive mechanism vary among elements and species. Towards a comprehensive identification and functional characterization of nutrient-responsive ncRNAs and their downstream molecules, high-throughput sequencing has produced massive omics data for comparative expression profiling as a first step. In this review, we highlight the recent findings of ncRNA-mediated regulation in response to macronutrient stress, with special emphasis on the large-scale sequencing efforts for screening out candidate nutrient-responsive ncRNAs in plants, and discuss potential improvements in theoretical study to provide better guidance for crop breeding practices.
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Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber ( Cucumis sativus L.). Int J Mol Sci 2021; 22:ijms22158197. [PMID: 34360961 PMCID: PMC8348067 DOI: 10.3390/ijms22158197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Low oxygen level is a phenomenon often occurring during the cucumber cultivation period. Genes involved in adaptations to stress can be regulated by non-coding RNA. The aim was the identification of long non-coding RNAs (lncRNAs) involved in the response to long-term waterlogging stress in two cucumber haploid lines, i.e., DH2 (waterlogging tolerant—WL-T) and DH4 (waterlogging sensitive—WL-S). Plants, at the juvenile stage, were waterlogged for 7 days (non-primed, 1xH), and after a 14-day recovery period, plants were stressed again for another 7 days (primed, 2xH). Roots were collected for high-throughput RNA sequencing. Implementation of the bioinformatic pipeline made it possible to determine specific lncRNAs for non-primed and primed plants of both accessions, highlighting differential responses to hypoxia stress. In total, 3738 lncRNA molecules were identified. The highest number (1476) of unique lncRNAs was determined for non-primed WL-S plants. Seventy-one lncRNAs were depicted as potentially being involved in acquiring tolerance to hypoxia in cucumber. Understanding the mechanism of gene regulation under long-term waterlogging by lncRNAs and their interactions with miRNAs provides sufficient information in terms of adaptation to the oxygen deprivation in cucumber. To the best of our knowledge, this is the first report concerning the role of lncRNAs in the regulation of long-term waterlogging tolerance by priming application in cucumber.
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Chen Q, Liu K, Yu R, Zhou B, Huang P, Cao Z, Zhou Y, Wang J. From "Dark Matter" to "Star": Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs. FRONTIERS IN PLANT SCIENCE 2021; 12:650926. [PMID: 34163498 PMCID: PMC8215657 DOI: 10.3389/fpls.2021.650926] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/05/2021] [Indexed: 05/27/2023]
Abstract
Long non-coding RNAs (lncRNAs) play a vital role in a variety of biological functions in plant growth and development. In this study, we provided an overview of the molecular mechanisms of lncRNAs in interacting with other biomolecules with an emphasis on those lncRNAs validated only by low-throughput experiments. LncRNAs function through playing multiple roles, including sponger for sequestering RNA or DNA, guider or decoy for recruiting or hijacking transcription factors or peptides, and scaffold for binding with chromatin modification complexes, as well as precursor of microRNAs or small interfering RNAs. These regulatory roles have been validated in several plant species with a comprehensive list of 73 lncRNA-molecule interaction pairs in 16 plant species found so far, suggesting their commonality in the plant kingdom. Such initial findings of a small number of functional plant lncRNAs represent the beginning of what is to come as lncRNAs with unknown functions were found in orders of magnitude more than proteins.
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Affiliation(s)
- Qingshuai Chen
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Kui Liu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Ru Yu
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Bailing Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Pingping Huang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
| | - Yaoqi Zhou
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
- Institute for Glycomics and School of Information and Communication Technology, Griffith University, Gold Coast, QLD, Australia
- Institute for Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jihua Wang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, China
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Baruah PM, Krishnatreya DB, Bordoloi KS, Gill SS, Agarwala N. Genome wide identification and characterization of abiotic stress responsive lncRNAs in Capsicum annuum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 162:221-236. [PMID: 33706183 DOI: 10.1016/j.plaphy.2021.02.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/22/2021] [Indexed: 05/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a type of non-coding transcripts having length of more than 200 nucleotides lacking protein-coding ability. In the present study, 12807 lncRNAs were identified in Capsicum annuum tissues exposed to abiotic stress conditions viz. heat, cold, osmotic and salinity stress. Expression analysis of lncRNAs in different treatment conditions demonstrates their stress-specific expression. Thirty lncRNAs were found to act as precursors for 10 microRNAs (miRNAs) of C. annuum. Additionally, a total of 1807 lncRNAs were found to interact with 194 miRNAs which targeted 621 mRNAs of C. annuum. Among these, 344 lncRNAs were found to act as target mimics for 621 genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that out of those 621 gene sequences, 546 were tagged with GO terms, 105 Enzyme Code (EC) numbers were assigned to 246 genes and 223 genes are found to be involved in 63 biological pathways. In this report, we have highlighted the prospective role of lncRNAs in different abiotic stress conditions by interacting with miRNAs and regulating stress responsive transcription factors (TFs) such as DoF, WRKY, MYB, bZIP and ERF in C. annuum.
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Affiliation(s)
- Pooja Moni Baruah
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam, 781014, India
| | | | | | - Sarvajeet Singh Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, 124 001, India
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Jalukbari, Guwahati, Assam, 781014, India.
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Ma B, Zhang A, Zhao Q, Li Z, Lamboro A, He H, Li Y, Jiao S, Guan S, Liu S, Yao D, Zhang J. Genome-wide identification and analysis of long non-coding RNAs involved in fatty acid biosynthesis in young soybean pods. Sci Rep 2021; 11:7603. [PMID: 33828134 PMCID: PMC8027399 DOI: 10.1038/s41598-021-87048-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs of more than 200 nucleotides. To date, the roles of lncRNAs in soybean fatty acid synthesis have not been fully studied. Here, the low-linolenic acid mutant 'MT72' and the wild-type control 'JN18' were used as materials. The lncRNAs in young pods at 30 and 40 days (d) after flowering were systematically identified and analyzed using transcriptome sequencing technology combined with bioinformatics tools. A total of 39,324 lncRNAs and 561 differentially expressed lncRNAs were identified. A lncRNAs-miRNAs-protein-coding genes (mRNAs) network was constructed, and 46 lncRNAs, 46 miRNAs and 137 mRNAs were found to be correlated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 12 targeted mRNAs in the competing endogenous RNA network showed that these lncRNAs may be involved in the biological processes of fatty acid transport, lipid synthesis and cell division. Finally, the expression levels of differentially expressed lncRNAs, miRNAs and mRNAs were verified using qRT-PCR. The expression patterns of most genes were consistent with the sequencing results. In conclusion, new information was provided for the study of fatty acid synthesis by lncRNAs in young soybean pods.
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Affiliation(s)
- Bohan Ma
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Aijing Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Qiuzhu Zhao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Zeyuan Li
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Abraham Lamboro
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Haobo He
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yue Li
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Suqi Jiao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Shuyan Guan
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Siyan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, China.
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Zheng W, Hu H, Lu Q, Jin P, Cai L, Hu C, Yang J, Dai L, Chen J. Genome-Wide Identification and Characterization of Long Noncoding RNAs Involved in Chinese Wheat Mosaic Virus Infection of Nicotiana benthamiana. BIOLOGY 2021; 10:biology10030232. [PMID: 33802832 PMCID: PMC8002735 DOI: 10.3390/biology10030232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/23/2021] [Accepted: 03/11/2021] [Indexed: 12/30/2022]
Abstract
Simple Summary Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. However, the roles of long non-coding RNAs (lncRNAs) in the interaction between plants and viruses is unclear, particularly for the Chinese wheat mosaic virus (CWMV) interaction. In this study, we used a deep RNA sequencing strategy to profile lncRNAs involved in the response to CWMV infection in Nicotiana benthamiana and analyzed differentially expressed lncRNAs that responded to CWMV infection, using a bioinformatics method. We identified 1175 new lncRNAs in N. benthamiana infected with CWMV, with 65 lncRNAs showing differential expression. These lncRNAs were mainly enriched in plant hormone signal transduction and other pathways according to GO and KEGG pathway enrichment analyses. In addition, differential expression of XLOC_006393 after CWMV infection may be the precursor of NbmiR168c, which can respond to CWMV infection by modulating the expression of its target gene NbAGO1. We believe that our study makes a significant contribution to the literature because these results provide a valuable resource for studying lncRNAs involved in CWMV infection and improving the understanding of the molecular mechanism of CWMV infection. Abstract Recent studies have shown that a large number of long noncoding RNAs (lncRNAs) can regulate various biological processes in animals and plants. Although lncRNAs have been identified in many plants, they have not been reported in the model plant Nicotiana benthamiana. Particularly, the role of lncRNAs in plant virus infection remains unknown. In this study, we identified lncRNAs in N. benthamiana response to Chinese wheat mosaic virus (CWMV) infection by RNA sequencing. A total of 1175 lncRNAs, including 65 differentially expressed lncRNAs, were identified during CWMV infection. We then analyzed the functions of some of these differentially expressed lncRNAs. Interestingly, one differentially expressed lncRNA, XLOC_006393, was found to participate in CWMV infection as a precursor to microRNAs in N. benthamiana. These results suggest that lncRNAs play an important role in the regulatory network of N. benthamiana in response to CWMV infection.
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Affiliation(s)
- Weiran Zheng
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
| | - Haichao Hu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Qisen Lu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Peng Jin
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Linna Cai
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Cailin Hu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
| | - Liangying Dai
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- Correspondence: (L.D.); (J.C.)
| | - Jianping Chen
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (W.Z.); (H.H.); (Q.L.); (P.J.); (L.C.); (C.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China;
- Correspondence: (L.D.); (J.C.)
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Urquiaga MCDO, Thiebaut F, Hemerly AS, Ferreira PCG. From Trash to Luxury: The Potential Role of Plant LncRNA in DNA Methylation During Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2021; 11:603246. [PMID: 33488652 PMCID: PMC7815527 DOI: 10.3389/fpls.2020.603246] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/07/2020] [Indexed: 05/27/2023]
Abstract
Remarkable progress has been made in elucidating important roles of plant non-coding RNAs. Among these RNAs, long noncoding RNAs (lncRNAs) have gained widespread attention, especially their role in plant environmental stress responses. LncRNAs act at different levels of gene expression regulation, and one of these mechanisms is by recruitment of DNA methyltransferases or demethylases to regulate the target gene transcription. In this mini-review, we highlight the function of lncRNAs, including their potential role in RNA-directed DNA Methylation (RdDM) silencing pathway and their potential function under abiotic stresses conditions. Moreover, we also present and discuss studies of lncRNAs in crops. Finally, we propose a path outlook for future research that may be important for plant breeding.
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Affiliation(s)
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants. Int J Mol Sci 2020; 22:ijms22010086. [PMID: 33374835 PMCID: PMC7795044 DOI: 10.3390/ijms22010086] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Advances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. Given the pivotal role of lncRNAs in various biological processes, their functional characterization in agriculturally essential crop plants is crucial for bridging the gap between phenotype and genotype.
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Zhou X, Cui J, Meng J, Luan Y. Interactions and links among the noncoding RNAs in plants under stresses. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3235-3248. [PMID: 33025081 DOI: 10.1007/s00122-020-03690-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/16/2020] [Indexed: 05/11/2023]
Abstract
The complex interplay among sRNAs, lncRNAs and circRNAs has been implicated in plants under biotic and abiotic stresses. Here, we review current advances in our understanding of ncRNA interactions and links, which have considerable potential for improving the agronomic traits and the environmental adaptability of plants. Plants can respond to biotic or abiotic stresses. To cope with various conditions, numerous intricate molecular regulatory mechanisms have evolved in plants. Noncoding RNAs (ncRNAs) can be divided into small noncoding RNAs (sRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). Emerging evidence has demonstrated that interplay among the ncRNAs acts as a novel layer in the regulatory mechanisms, which has attracted substantial interest. Links between sRNAs can affect plant immune responses and development in synergistic or antagonistic manners. Additionally, multiple interactions between lncRNAs and sRNAs are involved in crop breeding, disease resistance and high tolerance to environmental stresses. Here, we summarize current knowledge of the interactions and links among the ncRNAs in plant responses to stresses and the methods for identifying ncRNA interactions. Furthermore, challenges and prospects for further progress in elucidating ncRNA interactions and links are highlighted.
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Affiliation(s)
- Xiaoxu Zhou
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Cui
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.
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Fukuda M, Fujiwara T, Nishida S. Roles of Non-Coding RNAs in Response to Nitrogen Availability in Plants. Int J Mol Sci 2020; 21:ijms21228508. [PMID: 33198163 PMCID: PMC7696010 DOI: 10.3390/ijms21228508] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 01/06/2023] Open
Abstract
Nitrogen (N) is an essential nutrient for plant growth and development; therefore, N deficiency is a major limiting factor in crop production. Plants have evolved mechanisms to cope with N deficiency, and the role of protein-coding genes in these mechanisms has been well studied. In the last decades, regulatory non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and long ncRNAs (lncRNAs), have emerged as important regulators of gene expression in diverse biological processes. Recent advances in technologies for transcriptome analysis have enabled identification of N-responsive ncRNAs on a genome-wide scale. Characterization of these ncRNAs is expected to improve our understanding of the gene regulatory mechanisms of N response. In this review, we highlight recent progress in identification and characterization of N-responsive ncRNAs in Arabidopsis thaliana and several other plant species including maize, rice, and Populus.
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Affiliation(s)
- Makiha Fukuda
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA;
| | - Toru Fujiwara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan;
| | - Sho Nishida
- Department of Bioresource Science, Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
- Correspondence: ; Tel.: +81-952-28-8720
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Waititu JK, Zhang C, Liu J, Wang H. Plant Non-Coding RNAs: Origin, Biogenesis, Mode of Action and Their Roles in Abiotic Stress. Int J Mol Sci 2020; 21:E8401. [PMID: 33182372 PMCID: PMC7664903 DOI: 10.3390/ijms21218401] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 01/21/2023] Open
Abstract
As sessile species, plants have to deal with the rapidly changing environment. In response to these environmental conditions, plants employ a plethora of response mechanisms that provide broad phenotypic plasticity to allow the fine-tuning of the external cues related reactions. Molecular biology has been transformed by the major breakthroughs in high-throughput transcriptome sequencing and expression analysis using next-generation sequencing (NGS) technologies. These innovations have provided substantial progress in the identification of genomic regions as well as underlying basis influencing transcriptional and post-transcriptional regulation of abiotic stress response. Non-coding RNAs (ncRNAs), particularly microRNAs (miRNAs), short interfering RNAs (siRNAs), and long non-coding RNAs (lncRNAs), have emerged as essential regulators of plants abiotic stress response. However, shared traits in the biogenesis of ncRNAs and the coordinated cross-talk among ncRNAs mechanisms contribute to the complexity of these molecules and might play an essential part in regulating stress responses. Herein, we highlight the current knowledge of plant microRNAs, siRNAs, and lncRNAs, focusing on their origin, biogenesis, modes of action, and fundamental roles in plant response to abiotic stresses.
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Affiliation(s)
- Joram Kiriga Waititu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.K.W.); (C.Z.)
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.K.W.); (C.Z.)
| | - Jun Liu
- National Key Facility for Crop Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.K.W.); (C.Z.)
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Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana. Funct Integr Genomics 2020; 21:17-30. [PMID: 33130916 DOI: 10.1007/s10142-020-00758-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/19/2020] [Accepted: 10/25/2020] [Indexed: 01/23/2023]
Abstract
Nutrient stress is the most important environmental stress that limits plant growth and development. Although recent evidence highlights the vital functions of long non-coding RNAs (lncRNA) in response to single nutrient stress in some model plants, a comprehensive investigation of the effect of lncRNAs in response to nutrient stress has not been performed in Arabidopsis thaliana. Here, we presented the identification and characterization of lncRNAs under seven nutrient stress conditions. The expression pattern analysis revealed that aberrant expression of lncRNAs is a stress-specific manner under nutrient stress conditions and that lncRNAs are more sensitive to nutrient stress than protein-coding genes (PCGs). Moreover, competing endogenous RNA (ceRNA) network and lncRNA-mRNA co-expression network (CEN) were constructed to explore the potential function of these lncRNAs under nutrient stress conditions. We further combined different expressed lncRNAs with ceRNA network and CEN to select key lncRNAs in response to nutrient stress. Together, our study provides important information for further insights into the role of lncRNAs in response to stress in plants.
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Jha UC, Nayyar H, Jha R, Khurshid M, Zhou M, Mantri N, Siddique KHM. Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation. BMC PLANT BIOLOGY 2020; 20:466. [PMID: 33046001 PMCID: PMC7549229 DOI: 10.1186/s12870-020-02595-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/12/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The immobile nature of plants means that they can be frequently confronted by various biotic and abiotic stresses during their lifecycle. Among the various abiotic stresses, water stress, temperature extremities, salinity, and heavy metal toxicity are the major abiotic stresses challenging overall plant growth. Plants have evolved complex molecular mechanisms to adapt under the given abiotic stresses. Long non-coding RNAs (lncRNAs)-a diverse class of RNAs that contain > 200 nucleotides(nt)-play an essential role in plant adaptation to various abiotic stresses. RESULTS LncRNAs play a significant role as 'biological regulators' for various developmental processes and biotic and abiotic stress responses in animals and plants at the transcription, post-transcription, and epigenetic level, targeting various stress-responsive mRNAs, regulatory gene(s) encoding transcription factors, and numerous microRNAs (miRNAs) that regulate the expression of different genes. However, the mechanistic role of lncRNAs at the molecular level, and possible target gene(s) contributing to plant abiotic stress response and adaptation, remain largely unknown. Here, we review various types of lncRNAs found in different plant species, with a focus on understanding the complex molecular mechanisms that contribute to abiotic stress tolerance in plants. We start by discussing the biogenesis, type and function, phylogenetic relationships, and sequence conservation of lncRNAs. Next, we review the role of lncRNAs controlling various abiotic stresses, including drought, heat, cold, heavy metal toxicity, and nutrient deficiency, with relevant examples from various plant species. Lastly, we briefly discuss the various lncRNA databases and the role of bioinformatics for predicting the structural and functional annotation of novel lncRNAs. CONCLUSIONS Understanding the intricate molecular mechanisms of stress-responsive lncRNAs is in its infancy. The availability of a comprehensive atlas of lncRNAs across whole genomes in crop plants, coupled with a comprehensive understanding of the complex molecular mechanisms that regulate various abiotic stress responses, will enable us to use lncRNAs as potential biomarkers for tailoring abiotic stress-tolerant plants in the future.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Rintu Jha
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Khurshid
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nitin Mantri
- School of Science, RMIT University, Plenty Road, Bundoora. Victoria. 3083., Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia.
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Third-generation sequencing found LncRNA associated with heat shock protein response to heat stress in Populus qiongdaoensis seedlings. BMC Genomics 2020; 21:572. [PMID: 32831021 PMCID: PMC7444055 DOI: 10.1186/s12864-020-06979-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/11/2020] [Indexed: 01/23/2023] Open
Abstract
Background As air temperatures increase globally, more and more plants are exposed to heat-stress conditions. Although many studies have explored regulation networks in plants with the aim of improving their heat-stress tolerance, only few have revealed them in trees. Here, individuals of Populus qiongdaoensis seedlings, which grows naturally in tropical areas, exposed to heat at 40 °C and the non-coding regulation networks were explored using the PacBio RSII and the Illumina sequencing platform. Results In total, we obtained 88,161 full-length transcripts representing 39,343 genes using 5,498,988 long reads and 350,026,252 clean reads, and also 216 microRNAs (miRNAs) via 95,794,107 reads. We then identified 928 putative long non-coding RNAs (lncRNAs), consisting of 828 sense lncRNAs (89.22%), 34 long intergenic non-coding RNAs (3.66%), 16 antisense (1.72%), and 50 sense intronic lncRNAs (5.39%). Under the dual criteria of |log2fold-change| ≥ 1 and P-value < 0.05, 1690 genes, 25 lncRNAs, and 15 miRNAs were found differentially expressed under the heat stress treatment. Furthermore, 563 and 595 mRNAs were detected as target genes of 14 differently expressed miRNAs and 26 differentially expressed lncRNAs. Functional annotation analysis of these target genes demonstrated they were related to cell membrane stability, plant hormone signal transduction, antioxidation, and aldarate metabolism. Lastly, we uncovered a key interaction network of lncRNAs, miRNAs and mRNAs that consisted of miR1444d, miR482a.1, miR530a, lncHSP18.2, HSP18.1, and HSP18.2. Expression level analysis showed that miRNAs in the network were up-regulated, while mRNAs and lncRNA were down-regulated, and also found that lncHSP18.2 may cis-regulate HSP18.2. Conclusions Functional enrichment analysis of target genes of miRNAs and lncRNAs indicated that miRNAs and lncRNAs play an important role in the response to heat stress P. qiongdaoensis. Lastly, by investigating the miRNA–lncRNA–mRNA network of this species, we revealed that miRNAs may negatively regulate both lncRNAs and mRNAs in tree responses to heat stress, and found that lncHSP18.2 may cis-regulate HSP18.2.
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