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Tian J, Zhang F, Zhang G, Li X, Wen C, Li H. A long noncoding RNA functions in pumpkin fruit development through S-adenosyl-L-methionine synthetase. PLANT PHYSIOLOGY 2024; 195:940-957. [PMID: 38417836 PMCID: PMC11142375 DOI: 10.1093/plphys/kiae099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 03/01/2024]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in various biological processes. However, the regulatory roles of lncRNAs underlying fruit development have not been extensively studied. The pumpkin (Cucurbita spp.) is a preferred model for understanding the molecular mechanisms regulating fruit development because of its variable shape and size and large inferior ovary. Here, we performed strand-specific transcriptome sequencing on pumpkin (Cucurbita maxima "Rimu") fruits at 6 developmental stages and identified 5,425 reliably expressed lncRNAs. Among the 332 lncRNAs that were differentially expressed during fruit development, the lncRNA MSTRG.44863.1 was identified as a negative regulator of pumpkin fruit development. MSTRG.44863.1 showed a relatively high expression level and an obvious period-specific expression pattern. Transient overexpression and silencing of MSTRG.44863.1 significantly increased and decreased the content of 1-aminocyclopropane carboxylic acid (a precursor of ethylene) and ethylene production, respectively. RNA pull-down and microscale thermophoresis assays further revealed that MSTRG.44863.1 can interact with S-adenosyl-L-methionine synthetase (SAMS), an enzyme in the ethylene synthesis pathway. Considering that ethylene negatively regulates fruit development, these results indicate that MSTRG.44863.1 plays an important role in the regulation of pumpkin fruit development, possibly through interacting with SAMS and affecting ethylene synthesis. Overall, our findings provide a rich resource for further study of fruit-related lncRNAs while offering insights into the regulation of fruit development in plants.
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Affiliation(s)
- Jiaxing Tian
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Fan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Guoyu Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaojie Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Haizhen Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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2
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Zhao X, Li F, Ali M, Li X, Fu X, Zhang X. Emerging roles and mechanisms of lncRNAs in fruit and vegetables. HORTICULTURE RESEARCH 2024; 11:uhae046. [PMID: 38706580 PMCID: PMC11069430 DOI: 10.1093/hr/uhae046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/07/2024] [Indexed: 05/07/2024]
Abstract
With the development of genome sequencing technologies, many long non-coding RNAs (lncRNAs) have been identified in fruit and vegetables. lncRNAs are primarily transcribed and spliced by RNA polymerase II (Pol II) or plant-specific Pol IV/V, and exhibit limited evolutionary conservation. lncRNAs intricately regulate various aspects of fruit and vegetables, including pigment accumulation, reproductive tissue development, fruit ripening, and responses to biotic and abiotic stresses, through diverse mechanisms such as gene expression modulation, interaction with hormones and transcription factors, microRNA regulation, and involvement in alternative splicing. This review presents a comprehensive overview of lncRNA classification, basic characteristics, and, most importantly, recent advances in understanding their functions and regulatory mechanisms.
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Affiliation(s)
- Xiuming Zhao
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Fujun Li
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Maratab Ali
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Xiaoan Li
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Xiaodong Fu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
| | - Xinhua Zhang
- College of Agricultural Engineering and Food Science, Shandong University of Technology, Zibo, 255000, Shandong, China
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3
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Mierziak J, Wojtasik W. Epigenetic weapons of plants against fungal pathogens. BMC PLANT BIOLOGY 2024; 24:175. [PMID: 38443788 PMCID: PMC10916060 DOI: 10.1186/s12870-024-04829-8] [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: 07/14/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In the natural environment, plants face constant exposure to biotic stress caused by fungal attacks. The plant's response to various biotic stresses relies heavily on its ability to rapidly adjust the transcriptome. External signals are transmitted to the nucleus, leading to activation of transcription factors that subsequently enhance the expression of specific defense-related genes. Epigenetic mechanisms, including histone modifications and DNA methylation, which are closely linked to chromatin states, regulate gene expression associated with defense against biotic stress. Additionally, chromatin remodelers and non-coding RNA play a significant role in plant defense against stressors. These molecular modifications enable plants to exhibit enhanced resistance and productivity under diverse environmental conditions. Epigenetic mechanisms also contribute to stress-induced environmental epigenetic memory and priming in plants, enabling them to recall past molecular experiences and utilize this stored information for adaptation to new conditions. In the arms race between fungi and plants, a significant aspect is the cross-kingdom RNAi mechanism, whereby sRNAs can traverse organismal boundaries. Fungi utilize sRNA as an effector molecule to silence plant resistance genes, while plants transport sRNA, primarily through extracellular vesicles, to pathogens in order to suppress virulence-related genes. In this review, we summarize contemporary knowledge on epigenetic mechanisms of plant defense against attack by pathogenic fungi. The role of epigenetic mechanisms during plant-fungus symbiotic interactions is also considered.
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Affiliation(s)
- Justyna Mierziak
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, Wroclaw, 51-148, Poland
| | - Wioleta Wojtasik
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63, Wroclaw, 51-148, Poland.
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Riyazuddin R, Singh K, Iqbal N, Labhane N, Ramteke P, Singh VP, Gupta R. Unveiling the biosynthesis, mechanisms, and impacts of miRNAs in drought stress resilience in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107978. [PMID: 37660607 DOI: 10.1016/j.plaphy.2023.107978] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/13/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Drought stress is one of the most serious threats to sustainable agriculture and is predicted to be further intensified in the coming decades. Therefore, understanding the mechanism of drought stress tolerance and the development of drought-resilient crops are the major goals at present. In recent years, noncoding microRNAs (miRNAs) have emerged as key regulators of gene expressions under drought stress conditions and are turning out to be the potential candidates that can be targeted to develop drought-resilient crops in the future. miRNAs are known to target and decrease the expression of various genes to govern the drought stress response in plants. In addition, emerging evidence also suggests a regulatory role of long non-coding RNAs (lncRNAs) in the regulation of miRNAs and the expression of their target genes by a process referred as miRNA sponging. In this review, we present the regulatory roles of miRNAs in the modulation of drought-responsive genes along with discussing their biosynthesis and action mechanisms. Additionally, the interactive roles of miRNAs with phytohormone signaling components have also been highlighted to present the global view of miRNA functioning under drought-stress conditions.
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Affiliation(s)
- Riyazuddin Riyazuddin
- Institute of Plant Biology, Biological Research Centre, Temesvári krt. 62, H-6726, Szeged, Hungary.
| | - Kalpita Singh
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary; Department of Biological Resources, Agricultural Institute, Centre for Agricultural Research, ELKH, Brunszvik u. 2, H-2462, Martonvásár, Hungary.
| | - Nadeem Iqbal
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, 6726, Szeged, Hungary; Doctoral School of Environmental Sciences, University of Szeged, Szeged, Hungary.
| | - Nitin Labhane
- Department of Botany, Bhavan's College Andheri West, Mumbai, 400058, India.
| | - Pramod Ramteke
- Department of Biotechnology, Dr. Ambedkar College, Nagpur, India.
| | - Vijay Pratap Singh
- Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj, 211002, India
| | - Ravi Gupta
- College of General Education, Kookmin University, 02707, Seoul, Republic of Korea.
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5
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Zhang W, Yang Y, Zhu X, Yang S, Liao X, Li H, Li Z, Liao Q, Tang J, Zhao G, Wu L. Integrated analyses of metabolomics and transcriptomics reveal the potential regulatory roles of long non-coding RNAs in gingerol biosynthesis. BMC Genomics 2023; 24:490. [PMID: 37633894 PMCID: PMC10464350 DOI: 10.1186/s12864-023-09553-5] [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: 01/05/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
BACKGROUND As the characteristic functional component in ginger, gingerols possess several health-promoting properties. Long non-coding RNAs (lncRNAs) act as crucial regulators of diverse biological processes. However, lncRNAs in ginger are not yet identified so far, and their potential roles in gingerol biosynthesis are still unknown. In this study, metabolomic and transcriptomic analyses were performed in three main ginger cultivars (leshanhuangjiang, tonglingbaijiang, and yujiang 1 hao) in China to understand the potential roles of the specific lncRNAs in gingerol accumulation. RESULTS A total of 744 metabolites were monitored by metabolomics analysis, which were divided into eleven categories. Among them, the largest group phenolic acid category contained 143 metabolites, including 21 gingerol derivatives. Of which, three gingerol analogs, [8]-shogaol, [10]-gingerol, and [12]-shogaol, accumulated significantly. Moreover, 16,346 lncRNAs, including 2,513, 1,225, and 2,884 differentially expressed (DE) lncRNA genes (DELs), were identified in all three comparisons by transcriptomic analysis. Gene ontology enrichment (GO) analysis showed that the DELs mainly enriched in the secondary metabolite biosynthetic process, response to plant hormones, and phenol-containing compound metabolic process. Correlation analysis revealed that the expression levels of 11 DE gingerol biosynthesis enzyme genes (GBEGs) and 190 transcription factor genes (TF genes), such as MYB1, ERF100, WRKY40, etc. were strongly correlation coefficient with the contents of the three gingerol analogs. Furthermore, 7 and 111 upstream cis-acting lncRNAs, 1,200 and 2,225 upstream trans-acting lncRNAs corresponding to the GBEGs and TF genes were identified, respectively. Interestingly, 1,184 DELs might function as common upstream regulators to these GBEGs and TFs genes, such as LNC_008452, LNC_006109, LNC_004340, etc. Furthermore, protein-protein interaction networks (PPI) analysis indicated that three TF proteins, MYB4, MYB43, and WRKY70 might interact with four GBEG proteins (PAL1, PAL2, PAL3, and 4CL-4). CONCLUSION Based on these findings, we for the first time worldwide proposed a putative regulatory cascade of lncRNAs, TFs genes, and GBEGs involved in controlling of gingerol biosynthesis. These results not only provide novel insights into the lncRNAs involved in gingerol metabolism, but also lay a foundation for future in-depth studies of the related molecular mechanism.
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Affiliation(s)
- Wenlin Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
- College of Food Science, Southwest University, Beibei, 400715, China
| | - Yang Yang
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China
| | - Xuedong Zhu
- Southeast Chongqing Academy of Agricultural Sciences, Fuling, 408000, China
| | - Suyu Yang
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China
| | - Ximei Liao
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China
| | - Honglei Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
| | - Zhexin Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
| | - Qinhong Liao
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China
| | - Jianmin Tang
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, 402160, China.
| | - Guohua Zhao
- College of Food Science, Southwest University, Beibei, 400715, China.
| | - Lin Wu
- Chongqing Key Laboratory of Biology and Genetic Breeding for Tuber and Root Crops, College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, China.
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Yue Z, Pan X, Li J, Si F, Yin L, Hou Y, Chen X, Li X, Zhang Y, Ma J, Yang J, Li H, Luan F, Huang W, Zhang X, Yuan L, Zhang R, Wei C. Whole-transcriptome analyses identify key differentially expressed mRNAs, lncRNAs, and miRNAs associated with male sterility in watermelon. FRONTIERS IN PLANT SCIENCE 2023; 14:1138415. [PMID: 36938061 PMCID: PMC10019506 DOI: 10.3389/fpls.2023.1138415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Male sterility is a valuable trait for watermelon breeding, as watermelon hybrids exhibit obvious heterosis. However, the underlying regulatory mechanism is still largely unknown, especially regarding the related non-coding genes. In the present study, approximately 1035 differentially expressed genes (DEGs), as well as 80 DE-lncRNAs and 10 DE-miRNAs, were identified, with the overwhelming majority down-regulated in male-sterile floral buds. Enrichment analyses revealed that the general phenylpropanoid pathway as well as its related metabolisms was predicted to be altered in a mutant compared to its fertile progenitor. Meanwhile, the conserved genetic pathway DYT1-TDF1-AMS-MS188-MS1, as well as the causal gene ClAMT1 for the male-sterile mutant Se18, was substantially disrupted during male reproductive development. In addition, some targets of the key regulators AMS and MS188 in tapetum development were also down-regulated at a transcriptional level, such as ABCG26 (Cla004479), ACOS5 (Cla022956), CYP703A2 (Cla021151), PKSA (Cla021099), and TKPR1 (Cla002563). Considering lncRNAs may act as functional endogenous target mimics of miRNAs, competitive endogenous RNA networks were subsequently constructed, with the most complex one containing three DE-miRNAs, two DE-lncRNAs, and 21 DEGs. Collectively, these findings not only contribute to a better understanding of genetic regulatory networks underlying male sterility in watermelon, but also provide valuable candidates for future research.
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Affiliation(s)
- Zhen Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaona Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jiayue Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Fengfei Si
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Lijuan Yin
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yinjie Hou
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaoyao Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Xin Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Yong Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianxiang Ma
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Jianqiang Yang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Hao Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Feishi Luan
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Wenfeng Huang
- Vegetable Research Institute of Hainan Academy of Agricultural Sciences, Haikou, Hainan, China
| | - Xian Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin, China
| | - Li Yuan
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Ruimin Zhang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an, Shandong, China
| | - Chunhua Wei
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
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Zhuo X, Yu Q, Russo R, Zhang Y, Wei X, Wang YZ, Holden PM, Gmitter FG. Role of long non-coding RNA in regulatory network response to Candidatus Liberibacter asiaticus in citrus. FRONTIERS IN PLANT SCIENCE 2023; 14:1090711. [PMID: 36890903 PMCID: PMC9986497 DOI: 10.3389/fpls.2023.1090711] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Long non-coding RNAs (lncRNAs) serve as crucial regulators in plant response to various diseases, while none have been systematically identified and characterized in response to citrus Huanglongbing (HLB) caused by Candidatus Liberibacter asiaticus (CLas) bacteria. Here, we comprehensively investigated the transcriptional and regulatory dynamics of the lncRNAs in response to CLas. Samples were collected from leaf midribs of CLas- and mock-inoculated HLB-tolerant rough lemon (Citrus jambhiri) and HLB-sensitive sweet orange (C. sinensis) at week 0, 7, 17, and 34 following inoculation using CLas+ budwood of three biological replicates in the greenhouse. A total of 8,742 lncRNAs, including 2,529 novel lncRNAs, were identified from RNA-seq data with rRNA-removed from strand-specific libraries. Genomic variation analyses of conserved lncRNAs from 38 citrus accessions showed that 26 single nucleotide polymorphisms (SNPs) were significantly correlated with HLB. In addition, lncRNA-mRNA weighted gene co-expression network analysis (WGCNA) showed a significant module correlated with CLas-inoculation in rough lemon. Notably, the most significant LNC_28805 and multiple co-expressed genes related to plant defense in the module were targeted by miRNA5021, suggesting that LNC28805 might compete with endogenous miR5021 to maintain the homeostasis of immune gene expression levels. Candidate WRKY33 and SYP121 genes targeted by miRNA5021 were identified as two key hub genes interacting with bacteria pathogen response genes based on the prediction of protein-protein interaction (PPI) network. These two genes were also found within HLB-associated QTL in linkage group 6. Overall, our findings provide a reference for a better understanding of the role of lncRNAs involved in citrus HLB regulation.
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Affiliation(s)
| | | | | | | | | | | | | | - Fred G. Gmitter
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, United States
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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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9
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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: 19] [Impact Index Per Article: 9.5] [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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10
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Dey SS, Sharma PK, Munshi AD, Jaiswal S, Behera TK, Kumari K, G. B, Iquebal MA, Bhattacharya RC, Rai A, Kumar D. Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber ( Cucumis sativus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:884476. [PMID: 35991462 PMCID: PMC9383263 DOI: 10.3389/fpls.2022.884476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Cucumber is an extremely perishable vegetable; however, under room conditions, the fruits become unfit for consumption 2-3 days after harvesting. One natural variant, DC-48 with an extended shelf-life was identified, fruits of which can be stored up to 10-15 days under room temperature. The genes involved in this economically important trait are regulated by non-coding RNAs. The study aims to identify the long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) by taking two contrasting genotypes, DC-48 and DC-83, at two different fruit developmental stages. The upper epidermis of the fruits was collected at 5 days and 10 days after pollination (DAP) for high throughput RNA sequencing. The differential expression analysis was performed to identify differentially expressed (DE) lncRNAs and circRNAs along with the network analysis of lncRNA, miRNA, circRNA, and mRNA interactions. A total of 97 DElncRNAs were identified where 18 were common under both the developmental stages (8 down regulated and 10 upregulated). Based on the back-spliced reads, 238 circRNAs were found to be distributed uniformly throughout the cucumber genomes with the highest numbers (71) in chromosome 4. The majority of the circRNAs (49%) were exonic in origin followed by inter-genic (47%) and intronic (4%) origin. The genes related to fruit firmness, namely, polygalacturonase, expansin, pectate lyase, and xyloglucan glycosyltransferase were present in the target sites and co-localized networks indicating the role of the lncRNA and circRNAs in their regulation. Genes related to fruit ripening, namely, trehalose-6-phosphate synthase, squamosa promoter binding protein, WRKY domain transcription factors, MADS box proteins, abscisic stress ripening inhibitors, and different classes of heat shock proteins (HSPs) were also found to be regulated by the identified lncRNA and circRNAs. Besides, ethylene biosynthesis and chlorophyll metabolisms were also found to be regulated by DElncRNAs and circRNAs. A total of 17 transcripts were also successfully validated through RT PCR data. These results would help the breeders to identify the complex molecular network and regulatory role of the lncRNAs and circRNAs in determining the shelf-life of cucumbers.
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Affiliation(s)
- Shyam S. Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Parva Kumar Sharma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A. D. Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - T. K. Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Khushboo Kumari
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Boopalakrishnan G.
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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11
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Tian J, Zhang G, Zhang F, Ma J, Wen C, Li H. Genome-Wide Identification of Powdery Mildew Responsive Long Non-Coding RNAs in Cucurbita pepo. Front Genet 2022; 13:933022. [PMID: 35846119 PMCID: PMC9283782 DOI: 10.3389/fgene.2022.933022] [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: 04/30/2022] [Accepted: 05/23/2022] [Indexed: 12/05/2022] Open
Abstract
Cucurbita pepo L. is an essential economic vegetable crop worldwide, and its production is severely affected by powdery mildew (PM). However, our understanding of the molecular mechanism of PM resistance in C. pepo is very limited. Long non-coding RNAs (lncRNAs) play an important role in regulating plant responses to biotic stress. Here, we systematically identified 2,363 reliably expressed lncRNAs from the leaves of PM-susceptible (PS) and PM-resistant (PR) C. pepo. The C. pepo lncRNAs are shorter in length and expressed at a lower level than the protein-coding transcripts. Among the 2,363 lncRNAs, a total of 113 and 146 PM-responsive lncRNAs were identified in PS and PR, respectively. Six PM-responsive lncRNAs were predicted as potential precursors of microRNAs (miRNAs). In addition, 58 PM-responsive lncRNAs were predicted as targets of miRNAs and one PM-responsive lncRNA was predicted as an endogenous target mimic (eTM). Furthermore, a total of 5,200 potential cis target genes and 5,625 potential trans target genes were predicted for PM-responsive lncRNAs. Functional enrichment analysis showed that these potential target genes are involved in different biological processes, such as the plant-pathogen interaction pathway, MAPK signaling pathway, and plant hormone signal transduction pathway. Taken together, this study provides a comprehensive view of C. pepo lncRNAs and explores the putative functions of PM-responsive lncRNAs, thus laying the foundation for further study of the regulatory mechanisms of lncRNAs responding to PM.
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Affiliation(s)
- Jiaxing Tian
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Guoyu Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Fan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Jian Ma
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
| | - Haizhen Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
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12
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Sui N, Zhang R, Jiang Y, Yu H, Xu G, Wang J, Zhu Y, Xie Z, Hu J, Jiang S. Long Noncoding RNA Expression Rofiles Elucidate the Potential Roles of lncRNA- XR_003496198 in Duck Hepatitis A Virus Type 1 Infection. Front Cell Infect Microbiol 2022; 12:858537. [PMID: 35531338 PMCID: PMC9074814 DOI: 10.3389/fcimb.2022.858537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/24/2022] [Indexed: 12/11/2022] Open
Abstract
Duck hepatitis A virus type 1 (DHAV-1) is a highly lethal virus that severely affects the duck industry worldwide. Long noncoding RNAs (lncRNAs) exert crucial roles in pathogen attacks. Here, we conducted deep transcriptome analysis to investigate the dynamic changes of host lncRNAs profiles in DHAV-1-infected duck embryo fibroblasts. We identified 16,589 lncRNAs in total and characterized their genomic features. Moreover, 772 and 616 differentially expressed lncRNAs (DELs) were screened at 12 and 24 h post-infection. Additionally, we predicted the DELs' cis- and trans-target genes and constructed lncRNA-target genes regulatory networks. Functional annotation analyses indicated that the putative target genes of DELs participated in diverse vital biological processed, including immune responses, cellular metabolism, and autophagy. For example, we confirmed the dysregulation of pattern recognition receptors (TLR3, RIG-I, MDA5, LGP2, cGAS), signal transducers (STAT1), transcription factors (IRF7), immune response mediators (IL6, IL10, TRIM25, TRIM35, TRIM60, IFITM1, IFITM3, IFITM5), and autophagy-related genes (ULK1, ULK2, EIF4EBP2) using RT-qPCR. Finally, we confirmed that one DHAV-1 induced lncRNA-XR_003496198 is likely to inhibit DHAV-1 replication in DEFs. Our study comprehensively analyzed the lncRNA profiles upon DHAV-1 infection and screened the target genes involved in the innate immune response and autophagy signaling pathway, thereby revealing the essential roles of duck lncRNAs and broadening our understanding of host-virus interactions.
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Affiliation(s)
- Nana Sui
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Ruihua Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Yue Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Honglei Yu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Guige Xu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Jingyu Wang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Yanli Zhu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Zhijing Xie
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
| | - Jiaqing Hu
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
- Shandong GreenBlue Biotechnology Co. Ltd., Taian, China
| | - Shijin Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian, China
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13
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Expression Patterns and Regulation of Non-Coding RNAs during Synthesis of Cellulose in Eucalyptus grandis Hill. FORESTS 2021. [DOI: 10.3390/f12111565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cellulose, an essential structural component in the plant cell wall and a renewable biomass resource, plays a significant role in nature. Eucalyptus’s excellent timber tree species (including Eucalyptus grandis Hill) provide many raw materials for the paper and wood industries. The synthesis of cellulose is a very complex process involving multiple genes and regulated by various biological networks. However, research on regulating associated genes and non-coding RNAs during cellulose synthesis in E. grandis remains lacking. In this study, the wood anatomical characteristics and chemical indexes of E. grandis were analyzed by taking three different parts (diameter at breast height (DBH), middle and upper part of the trunk) from the main stem of E. grandis as raw materials. The role of non-coding RNAs (Long non-coding RNA, lncRNA; Micro RNA, miRNA; Circle RNA, circRNA) on regulating candidate genes was presented, and the network map of ceRNA (Competing endogenous RNA) regulation during wood cellulose biosynthesis of E. grandis was constructed. The transcriptome sequencing of nine samples obtained from the trunk of the immature xylem in E. grandis at DBH, middle and upper parts had a 95.81 G clean reading, 57,480 transcripts, 7365 lncRNAs, and 5180 circRNAs. Each sample had 172–306 known miRNAs and 1644–3508 new miRNAs. A total of 190 DE-lncRNAs (Differentially expressed long non-coding RNAs), 174 DE-miRNAs (Differentially expressed micro RNAs), and 270 DE-circRNAs (Differentially expressed circle RNAs) were obtained by comparing transcript expression levels. Four lncRNAs and nine miRNAs were screened out, and the ceRNA regulatory network was constructed. LncRNA1 and lncRNA4 regulated the genes responsible for cellulose synthesis in E. grandis, which were overexpressed in 84K (Populus Alba × Populus glandulosa) poplar. The cellulose and lignin content in lncRNA4-oe were significantly higher than wild type 84K poplar and lncRNA1-oe. The average plant height, middle and basal part of the stem diameter in lncRNA4-oe were significantly higher than the wild type. However, there was no significant difference between the growth of lncRNA1-oe and the wild type. Further studies are warranted to explore the molecular regulatory mechanism of cellulose biosynthesis in Eucalyptus species.
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14
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Ghorbani F, Abolghasemi R, Haghighi M, Etemadi N, Wang S, Karimi M, Soorni A. Global identification of long non-coding RNAs involved in the induction of spinach flowering. BMC Genomics 2021; 22:704. [PMID: 34587906 PMCID: PMC8482690 DOI: 10.1186/s12864-021-07989-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait. Results In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. Conclusions This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07989-1.
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Affiliation(s)
- Fatemeh Ghorbani
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Reza Abolghasemi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Maryam Haghighi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Nematollah Etemadi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Shui Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Marzieh Karimi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.,Department of Plant Breeding and Biotechnology, College of Agriculture, University of Shahrekord, Shahrekord, Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
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15
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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: 6] [Impact Index Per Article: 2.0] [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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16
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Shaw RK, Shen Y, Zhao Z, Sheng X, Wang J, Yu H, Gu H. Molecular Breeding Strategy and Challenges Towards Improvement of Downy Mildew Resistance in Cauliflower ( Brassica oleracea var. botrytis L.). FRONTIERS IN PLANT SCIENCE 2021; 12:667757. [PMID: 34354719 PMCID: PMC8329456 DOI: 10.3389/fpls.2021.667757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/31/2021] [Indexed: 06/13/2023]
Abstract
Cauliflower (Brassica oleracea var. botrytis L.) is one of the important, nutritious and healthy vegetable crops grown and consumed worldwide. But its production is constrained by several destructive fungal diseases and most importantly, downy mildew leading to severe yield and quality losses. For sustainable cauliflower production, developing resistant varieties/hybrids with durable resistance against broad-spectrum of pathogens is the best strategy for a long term and reliable solution. Identification of novel resistant resources, knowledge of the genetics of resistance, mapping and cloning of resistance QTLs and identification of candidate genes would facilitate molecular breeding for disease resistance in cauliflower. Advent of next-generation sequencing technologies (NGS) and publishing of draft genome sequence of cauliflower has opened the flood gate for new possibilities to develop enormous amount of genomic resources leading to mapping and cloning of resistance QTLs. In cauliflower, several molecular breeding approaches such as QTL mapping, marker-assisted backcrossing, gene pyramiding have been carried out to develop new resistant cultivars. Marker-assisted selection (MAS) would be beneficial in improving the precision in the selection of improved cultivars against multiple pathogens. This comprehensive review emphasizes the fascinating recent advances made in the application of molecular breeding approach for resistance against an important pathogen; Downy Mildew (Hyaloperonospora parasitica) affecting cauliflower and Brassica oleracea crops and highlights the QTLs identified imparting resistance against this pathogen. We have also emphasized the critical research areas as future perspectives to bridge the gap between availability of genomic resources and its utility in identifying resistance genes/QTLs to breed downy mildew resistant cultivars. Additionally, we have also discussed the challenges and the way forward to realize the full potential of molecular breeding for downy mildew resistance by integrating marker technology with conventional breeding in the post-genomics era. All this information will undoubtedly provide new insights to the researchers in formulating future breeding strategies in cauliflower to develop durable resistant cultivars against the major pathogens in general and downy mildew in particular.
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Affiliation(s)
| | | | | | | | | | | | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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17
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Meng X, Li A, Yu B, Li S. Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation. Comput Struct Biotechnol J 2021; 19:2567-2574. [PMID: 34025943 PMCID: PMC8114054 DOI: 10.1016/j.csbj.2021.04.062] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/24/2021] [Accepted: 04/24/2021] [Indexed: 11/28/2022] Open
Abstract
Plants employ sophisticated mechanisms to control developmental processes and to cope with environmental changes at transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs), two classes of endogenous noncoding RNAs, are key regulators of gene expression in plants. Recent studies have identified the interplay between miRNAs and lncRNAs as a novel regulatory layer of gene expression in plants. On one hand, miRNAs target lncRNAs for the production of phased small interfering RNAs (phasiRNAs). On the other hand, lncRNAs serve as origin of miRNAs or regulate the accumulation or activity of miRNAs at transcription and post-transcriptional levels. Theses lncRNA-miRNA interplays are crucial for plant development, physiology and responses to biotic and abiotic stresses. In this review, we summarize recent advances in the biological roles, interaction mechanisms and computational predication methods of the interplay between miRNAs and lncRNAs in plants.
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Affiliation(s)
- Xiangxiang Meng
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
| | - Aixia Li
- The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Bin Yu
- School of Biological Sciences & Center for Plant Science Innovation University of Nebraska-Lincoln, Lincoln, Nebraska 68588–0666, USA
| | - Shengjun Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
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18
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Li J, Li N, Zhu L, Zhang Z, Li X, Wang J, Xun H, Zhao J, Wang X, Wang T, Wang H, Liu B, Li Y, Gong L. Mutation of a major CG methylase alters genome-wide lncRNA expression in rice. G3-GENES GENOMES GENETICS 2021; 11:6146525. [PMID: 33617633 PMCID: PMC8049413 DOI: 10.1093/g3journal/jkab049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/08/2021] [Indexed: 11/14/2022]
Abstract
Plant long non-coding RNAs (lncRNAs) function in diverse biological processes, and lncRNA expression is under epigenetic regulation, including by cytosine DNA methylation. However, it remains unclear whether 5-methylcytosine (5mC) plays a similar role in different sequence contexts (CG, CHG, and CHH). In this study, we characterized and compared the profiles of genome-wide lncRNA profiles (including long intergenic non-coding RNAs [lincRNAs] and long noncoding natural antisense transcripts [lncNATs]) of a null mutant of the rice DNA methyltransferase 1, OsMET1-2 (designated OsMET1-2-/-) and its isogenic wild type (OsMET1-2+/+). The En/Spm transposable element (TE) family, which was heavily methylated in OsMET1-2+/+, was transcriptionally de-repressed in OsMET1-2-/- due to genome-wide erasure of CG methylation, and this led to abundant production of specific lncRNAs. In addition, RdDM-mediated CHH hypermethylation was increased in the 5'-upstream genomic regions of lncRNAs in OsMET1-2-/-. The positive correlation between the expression of lincRNAs and that of their proximal protein-coding genes was also analyzed. Our study shows that CG methylation negatively regulates the TE-related expression of lncRNA and demonstrates that CHH methylation is also involved in the regulation of lncRNA expression.
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Affiliation(s)
- Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ling Zhu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jinbin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongwei Xun
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xiaofei Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yu Li
- Engineering Research Center of the Ministry of Education (MOE) for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin 130118, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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Yang X, Zhang L, Yang Y, Schmid M, Wang Y. miRNA Mediated Regulation and Interaction between Plants and Pathogens. Int J Mol Sci 2021; 22:ijms22062913. [PMID: 33805611 PMCID: PMC7999934 DOI: 10.3390/ijms22062913] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 11/16/2022] Open
Abstract
Plants have evolved diverse molecular mechanisms that enable them to respond to a wide range of pathogens. It has become clear that microRNAs, a class of short single-stranded RNA molecules that regulate gene expression at the transcriptional or post-translational level, play a crucial role in coordinating plant-pathogen interactions. Specifically, miRNAs have been shown to be involved in the regulation of phytohormone signals, reactive oxygen species, and NBS-LRR gene expression, thereby modulating the arms race between hosts and pathogens. Adding another level of complexity, it has recently been shown that specific lncRNAs (ceRNAs) can act as decoys that interact with and modulate the activity of miRNAs. Here we review recent findings regarding the roles of miRNA in plant defense, with a focus on the regulatory modes of miRNAs and their possible applications in breeding pathogen-resistance plants including crops and trees. Special emphasis is placed on discussing the role of miRNA in the arms race between hosts and pathogens, and the interaction between disease-related miRNAs and lncRNAs.
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Affiliation(s)
- Xiaoqian Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.Y.); (L.Z.); (Y.Y.); (M.S.)
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Lichun Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.Y.); (L.Z.); (Y.Y.); (M.S.)
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Yuzhang Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.Y.); (L.Z.); (Y.Y.); (M.S.)
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Markus Schmid
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.Y.); (L.Z.); (Y.Y.); (M.S.)
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Yanwei Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China; (X.Y.); (L.Z.); (Y.Y.); (M.S.)
- National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Correspondence: ; Tel.: +86-010-62338105
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20
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Zhang B, Su T, Li P, Xin X, Cao Y, Wang W, Zhao X, Zhang D, Yu Y, Li D, Yu S, Zhang F. Identification of long noncoding RNAs involved in resistance to downy mildew in Chinese cabbage. HORTICULTURE RESEARCH 2021; 8:44. [PMID: 33642586 PMCID: PMC7917106 DOI: 10.1038/s41438-021-00479-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/14/2020] [Accepted: 12/17/2020] [Indexed: 05/07/2023]
Abstract
Brassica downy mildew, a severe disease caused by Hyaloperonospora brassicae, can cause enormous economic losses in Chinese cabbage (Brassica rapa L. ssp. pekinensis) production. Although some research has been reported recently concerning the underlying resistance to this disease, no studies have identified or characterized long noncoding RNAs involved in this defense response. In this study, using high-throughput RNA sequencing, we analyzed the disease-responding mRNAs and long noncoding RNAs in two resistant lines (T12-19 and 12-85) and one susceptible line (91-112). Clustering and Gene Ontology analysis of differentially expressed genes (DEGs) showed that more DEGs were involved in the defense response in the two resistant lines than in the susceptible line. Different expression patterns and proposed functions of differentially expressed long noncoding RNAs among T12-19, 12-85, and 91-112 indicated that each has a distinct disease response mechanism. There were significantly more cis- and trans-functional long noncoding RNAs in the resistant lines than in the susceptible line, and the genes regulated by these RNAs mostly participated in the disease defense response. Furthermore, we identified a candidate resistance-related long noncoding RNA, MSTRG.19915, which is a long noncoding natural antisense transcript of a MAPK gene, BrMAPK15. Via an agroinfiltration-mediated transient overexpression system and virus-induced gene silencing technology, BrMAPK15 was indicated to have a greater ability to defend against pathogens. MSTRG.19915-silenced seedlings showed enhanced resistance to downy mildew, probably because of the upregulated expression of BrMAPK15. This research identified and characterized long noncoding RNAs involved in resistance to downy mildew, laying a foundation for future in-depth studies of disease resistance mechanisms in Chinese cabbage.
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Affiliation(s)
- Bin Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China
| | - Tongbing Su
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China
| | - Peirong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China
| | - Xiaoyun Xin
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China
| | - Yunyun Cao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China
| | - Weihong Wang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China
| | - Xiuyun Zhao
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China
| | - Deshuang Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China
| | - Yangjun Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China
| | - Dayong Li
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China
| | - Shuancang Yu
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China.
| | - Fenglan Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Sciences (BAAFS), 100097, Beijing, China.
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, 100097, Beijing, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, 100097, Beijing, China.
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21
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The Emerging Role of Long Non-Coding RNAs in Plant Defense Against Fungal Stress. Int J Mol Sci 2020; 21:ijms21082659. [PMID: 32290420 PMCID: PMC7215362 DOI: 10.3390/ijms21082659] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/31/2022] Open
Abstract
Growing interest and recent evidence have identified long non-coding RNA (lncRNA) as the potential regulatory elements for eukaryotes. LncRNAs can activate various transcriptional and post-transcriptional events that impact cellular functions though multiple regulatory functions. Recently, a large number of lncRNAs have also been identified in higher plants, and an understanding of their functional role in plant resistance to infection is just emerging. Here, we focus on their identification in crop plant, and discuss their potential regulatory functions and lncRNA-miRNA-mRNA network in plant pathogen stress responses, referring to possible examples in a model plant. The knowledge gained from a deeper understanding of this colossal special group of plant lncRNAs will help in the biotechnological improvement of crops.
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