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He S, Bing J, Zhong Y, Zheng X, Zhou Z, Wang Y, Hu J, Sun X. PlantCircRNA: a comprehensive database for plant circular RNAs. Nucleic Acids Res 2024:gkae709. [PMID: 39189447 DOI: 10.1093/nar/gkae709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 07/11/2024] [Accepted: 08/02/2024] [Indexed: 08/28/2024] Open
Abstract
Circular RNAs (circRNAs) represent recently discovered novel regulatory non-coding RNAs. While they are present in many eukaryotes, there has been limited research on plant circRNAs. We developed PlantCircRNA (https://plant.deepbiology.cn/PlantCircRNA/) to fill this gap. The two most important features of PlantCircRNA are (i) it incorporates circRNAs from 94 plant species based on 39 245 RNA-sequencing samples and (ii) it imports the original AtCircDB and CropCircDB databases. We manually curated all circRNAs from published articles, and imported them into the database. Furthermore, we added detailed information of tissue as well as abiotic stresses to the database. To help users understand these circRNAs, the database includes a detection score to measure their consistency and a naming system following the guidelines recently proposed for eukaryotes. Finally, we developed a comprehensive platform for users to visualize, analyze, and download data regarding specific circRNAs. This resource will serve as a home for plant circRNAs and provide the community with unprecedented insights into these mysterious molecule.
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Affiliation(s)
- Shutian He
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Jianhao Bing
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Yang Zhong
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Xiaoyang Zheng
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Ziyu Zhou
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Yifei Wang
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Jiming Hu
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
| | - Xiaoyong Sun
- Agricultural Big Data Research Center, College of Information Science and Engineering, Shandong Agricultural University, Taian 271018, China
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2
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Zhang D, Ma Y, Naz M, Ahmed N, Zhang L, Zhou JJ, Yang D, Chen Z. Advances in CircRNAs in the Past Decade: Review of CircRNAs Biogenesis, Regulatory Mechanisms, and Functions in Plants. Genes (Basel) 2024; 15:958. [PMID: 39062737 PMCID: PMC11276256 DOI: 10.3390/genes15070958] [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: 06/20/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Circular RNA (circRNA) is a type of non-coding RNA with multiple biological functions. Whole circRNA genomes in plants have been identified, and circRNAs have been demonstrated to be widely present and highly expressed in various plant tissues and organs. CircRNAs are highly stable and conserved in plants, and exhibit tissue specificity and developmental stage specificity. CircRNAs often interact with other biomolecules, such as miRNAs and proteins, thereby regulating gene expression, interfering with gene function, and affecting plant growth and development or response to environmental stress. CircRNAs are less studied in plants than in animals, and their regulatory mechanisms of biogenesis and molecular functions are not fully understood. A variety of circRNAs in plants are involved in regulating growth and development and responding to environmental stress. This review focuses on the biogenesis and regulatory mechanisms of circRNAs, as well as their biological functions during growth, development, and stress responses in plants, including a discussion of plant circRNA research prospects. Understanding the generation and regulatory mechanisms of circRNAs is a challenging but important topic in the field of circRNAs in plants, as it can provide insights into plant life activities and their response mechanisms to biotic or abiotic stresses as well as new strategies for plant molecular breeding and pest control.
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Affiliation(s)
- Dongqin Zhang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (D.Z.); (M.N.); (N.A.); (L.Z.); (J.-J.Z.); (D.Y.)
| | - Yue Ma
- College of Agriculture, Guizhou University, Guiyang 550025, China;
| | - Misbah Naz
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (D.Z.); (M.N.); (N.A.); (L.Z.); (J.-J.Z.); (D.Y.)
| | - Nazeer Ahmed
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (D.Z.); (M.N.); (N.A.); (L.Z.); (J.-J.Z.); (D.Y.)
| | - Libo Zhang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (D.Z.); (M.N.); (N.A.); (L.Z.); (J.-J.Z.); (D.Y.)
| | - Jing-Jiang Zhou
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (D.Z.); (M.N.); (N.A.); (L.Z.); (J.-J.Z.); (D.Y.)
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, UK
| | - Ding Yang
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (D.Z.); (M.N.); (N.A.); (L.Z.); (J.-J.Z.); (D.Y.)
| | - Zhuo Chen
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, China; (D.Z.); (M.N.); (N.A.); (L.Z.); (J.-J.Z.); (D.Y.)
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Li S, Wang J, Ren G. CircRNA: An emerging star in plant research: A review. Int J Biol Macromol 2024; 272:132800. [PMID: 38825271 DOI: 10.1016/j.ijbiomac.2024.132800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/04/2024]
Abstract
CircRNAs are a class of covalently closed non-coding RNA formed by linking the 5' terminus and the 3' terminus after reverse splicing. CircRNAs are widely found in eukaryotes, and they are highly conserved, with spatio-temporal expression specificity and stability. CircRNAs can act as miRNA sponges to regulate the expression of downstream target genes, regulating the transcription of parental genes and some can even be translated into peptides or proteins. Research on circRNAs in plants is still in its infancy compared to that in animals. With the deepening of research, the results of a variety of plant circRNAs suggest that they play an important role in growth and development, and tolerance towards abiotic stresses such as salt, drought, low temperature, high temperature and other adverse environments. In this review paper, we elaborated the molecular characteristics, mechanism of action, function and bioinformatics databases of plant circRNAs, combined with the progress of circRNA research in animals, discussed the potential mechanism of action of plant circRNAs, and proposed the unsolved problems and prospects for future application of plant circRNAs.
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Affiliation(s)
- Simin Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Jingyi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Guocheng Ren
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan 250014, China; Dongying Institute, Shandong Normal University, Dongying 257000, China.
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Baruah PM, Bordoloi KS, Gill SS, Agarwala N. CircRNAs responsive to winter dormancy and spring flushing conditions of tea leaf buds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111828. [PMID: 37586421 DOI: 10.1016/j.plantsci.2023.111828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/18/2023]
Abstract
Circular RNAs (circRNAs) are important regulators of diverse biological processes of plants. However, the evolution and potential functions of circRNAs during winter dormancy and spring bud flushing of tea plant is largely unknown. Using RNA-seq data, a total of 1184 circRNAs were identified in the winter dormant and spring bud flushing leaf samples of tea plants in two different cultivars exhibiting different duration of winter dormancy. A total of 156 circRNAs are found to be differentially expressed and the weighted gene co-expression network (WGCNA) analysis revealed that 22 and 20 differentially expressed-circRNAs (DE-circRNAs) positively correlated with the flushing and dormant leaf traits, respectively, in both the tea cultivars used. Some transcription factors (TFs) viz. MYB, WRKY, ERF, bHLH and several genes related to secondary metabolite biosynthetic pathways are found to co-express with circRNAs. DE-circRNAs also predicted to interact with miRNAs and can regulate phytohormone biosynthesis and various signalling pathways in tea plant. This study uncovers the potential roles of circRNAs to determine winter dormancy and spring bud flushing conditions in tea plants.
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Affiliation(s)
- Pooja Moni Baruah
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati 781014, Assam, India
| | - Kuntala Sarma Bordoloi
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati 781014, Assam, India; Mangaldai College, Upahupara, Mangaldai 784125, Assam, India
| | - Sarvajeet Singh Gill
- Centre for Biotechnology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Guwahati 781014, Assam, India.
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Das P, Grover M, Mishra DC, Guha Majumdar S, Shree B, Kumar S, Mir ZA, Chaturvedi KK, Bhardwaj SC, Singh AK, Rai A. Genome-wide identification and characterization of Puccinia striiformis-responsive lncRNAs in Triticum aestivum. FRONTIERS IN PLANT SCIENCE 2023; 14:1120898. [PMID: 37650000 PMCID: PMC10465180 DOI: 10.3389/fpls.2023.1120898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/10/2023] [Indexed: 09/01/2023]
Abstract
Wheat stripe rust (yellow rust) caused by Puccinia striiformis f. sp. tritici (Pst) is a serious biotic stress factor limiting wheat production worldwide. Emerging evidence demonstrates that long non-coding RNAs (lncRNAs) participate in various developmental processes in plants via post-transcription regulation. In this study, RNA sequencing (RNA-seq) was performed on a pair of near-isogenic lines-rust resistance line FLW29 and rust susceptible line PBW343-which differed only in the rust susceptibility trait. A total of 6,807 lncRNA transcripts were identified using bioinformatics analyses, among which 10 lncRNAs were found to be differentially expressed between resistance and susceptible lines. In order to find the target genes of the identified lncRNAs, their interactions with wheat microRNA (miRNAs) were predicted. A total of 199 lncRNAs showed interactions with 65 miRNAs, which further target 757 distinct mRNA transcripts. Moreover, detailed functional annotations of the target genes were used to identify the candidate genes, pathways, domains, families, and transcription factors that may be related to stripe rust resistance response in wheat plants. The NAC domain protein, disease resistance proteins RPP13 and RPM1, At1g58400, monodehydroascorbate reductase, NBS-LRR-like protein, rust resistance kinase Lr10-like, LRR receptor, serine/threonine-protein kinase, and cysteine proteinase are among the identified targets that are crucial for wheat stripe rust resistance. Semiquantitative PCR analysis of some of the differentially expressed lncRNAs revealed variations in expression profiles of two lncRNAs between the Pst-resistant and Pst-susceptible genotypes at least under one condition. Additionally, simple sequence repeats (SSRs) were also identified from wheat lncRNA sequences, which may be very useful for conducting targeted gene mapping studies of stripe rust resistance in wheat. These findings improved our understanding of the molecular mechanism responsible for the stripe rust disease that can be further utilized to develop wheat varieties with durable resistance to this disease.
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Affiliation(s)
- Parinita Das
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Monendra Grover
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | | | - Bharti Shree
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Zahoor Ahmad Mir
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | | | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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6
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Liu R, Ma Y, Guo T, Li G. Identification, biogenesis, function, and mechanism of action of circular RNAs in plants. PLANT COMMUNICATIONS 2023; 4:100430. [PMID: 36081344 PMCID: PMC9860190 DOI: 10.1016/j.xplc.2022.100430] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/11/2022] [Accepted: 09/05/2022] [Indexed: 06/15/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded, closed RNA molecules with unique functions that are ubiquitously expressed in all eukaryotes. The biogenesis of circRNAs is regulated by specific cis-acting elements and trans-acting factors in humans and animals. circRNAs mainly exert their biological functions by acting as microRNA sponges, forming R-loops, interacting with RNA-binding proteins, or being translated into polypeptides or proteins in human and animal cells. Genome-wide identification of circRNAs has been performed in multiple plant species, and the results suggest that circRNAs are abundant and ubiquitously expressed in plants. There is emerging compelling evidence to suggest that circRNAs play essential roles during plant growth and development as well as in the responses to biotic and abiotic stress. However, compared with recent advances in human and animal systems, the roles of most circRNAs in plants are unclear at present. Here we review the identification, biogenesis, function, and mechanism of action of plant circRNAs, which will provide a fundamental understanding of the characteristics and complexity of circRNAs in plants.
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Affiliation(s)
- Ruiqi Liu
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Yu Ma
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Tao Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas and Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Guanglin Li
- Key Laboratory of Ministry of Education for Medicinal Plant Resource and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, China.
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7
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Zhang P, Dai M. CircRNA: a rising star in plant biology. J Genet Genomics 2022; 49:1081-1092. [PMID: 35644325 DOI: 10.1016/j.jgg.2022.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 01/14/2023]
Abstract
Circular RNAs (circRNAs) are covalently closed single-stranded RNA molecules, which are widespread in eukaryotic cells. As regulatory molecules, circRNAs have various functions, such as regulating gene expression, binding miRNAs or proteins, and being translated into proteins, which are important for cell proliferation and cell differentiation, individual growth and development, as well as many other biological processes. However, compared with that in animal models, studies of circRNAs in plants lags behind and, particularly, the regulatory mechanisms of biogenesis and molecular functions of plant circRNAs remain elusive. Recent studies have shown that circRNAs are wide spread in plants with tissue- or development-specific expression patterns and are responsive to a variety of environmental stresses. In this review, we summarize these advances, focusing on the regulatory mechanisms of biogenesis, molecular and biological functions of circRNAs, and the methods for investigating circRNAs. We also discuss the challenges and the prospects of plant circRNA studies.
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Affiliation(s)
- Pei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Mingqiu Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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8
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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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Chen X, Xu X, Zhang S, Munir N, Zhu C, Zhang Z, Chen Y, Xuhan X, Lin Y, Lai Z. Genome-wide circular RNA profiling and competing endogenous RNA regulatory network analysis provide new insights into the molecular mechanisms underlying early somatic embryogenesis in Dimocarpus longan Lour. TREE PHYSIOLOGY 2022; 42:1876-1898. [PMID: 35313353 DOI: 10.1093/treephys/tpac032] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Circular RNAs (circRNAs) are widely involved in plant growth and development. However, the function of circRNAs in plant somatic embryogenesis (SE) remains elusive. Here, by using high-throughput sequencing, a total of 5029 circRNAs were identified in the three stages of longan (Dimocarpus longan Lour.) early SE. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that differentially expressed (DE) circRNA host genes were enriched in the 'non-homologous end-joining' (NHEJ) and 'butanoate metabolism' pathways. In addition, the reactive oxygen species (ROS) content during longan early SE was determined. The results indicated that ROS-induced DNA double-strand breaks may not depend on the NHEJ repair pathway. Correlation analyses of the levels of related metabolites (glutamate, γ-aminobutyrate and pyruvate) and the expression levels of circRNAs and their host genes involved in butanoate metabolism were performed. The results suggested that circRNAs may act as regulators of the expression of cognate mRNAs, thereby affecting the accumulation of related compounds. A competing endogenous RNA (ceRNA) network of DE circRNAs, DE mRNAs, DE long noncoding RNAs (lncRNAs) and DE microRNAs (miRNAs) was constructed. The results showed that the putative targets of the noncoding RNA (ncRNAs) were significantly enriched in the KEGG pathways 'mitogen-activated protein kinase signaling' and 'nitrogen metabolism'. Furthermore, the expression patterns of the candidate circRNAs, lncRNAs, miRNAs and mRNAs confirmed the negative correlation between miRNAs and ceRNAs. In addition, two circRNA overexpression vectors were constructed to further verify the ceRNA network correlations in longan early SE. Our study revealed the potential role of circRNAs in longan early SE, providing new insights into the intricate regulatory mechanism underlying plant SE.
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Affiliation(s)
- Xiaohui Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Xiaoping Xu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Shuting Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Nigarish Munir
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Chen Zhu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Zihao Zhang
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Yukun Chen
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Xu Xuhan
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
- Institut de la Recherche Interdisciplinaire de Toulouse, IRIT-ARI, 31300 Toulouse, France
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, No. 15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian 350002, China
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Li Y, Liu X, Xiao Y, Wen Y, Li K, Ma Z, Yang L, Zhu Y, Yin J. Genome-wide characterization and function analysis uncovered roles of wheat LIMs in responding to adverse stresses and TaLIM8-4D function as a susceptible gene. THE PLANT GENOME 2022; 15:e20246. [PMID: 35894660 DOI: 10.1002/tpg2.20246] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/14/2022] [Indexed: 05/27/2023]
Abstract
The Lin-11, Isl-1, and Mec-3 domains (LIM) transcription factors play essential roles in regulating plant biological processes. Despite that, there is a lack of a full understanding of LIMs in wheat (Triticum aestivum L.). In this study, 28 wheat LIM s (TaLIMs) were identified and designated as TaLIM1-1A to TaLIM12-7D. The cis-regulatory element analysis showed that TaLIMs were rich in elements related to biological and abiotic stresses. Expression profiling analysis showed that certain members of TaLIMs were responsive to biotic and abiotic stresses, such as TaLIM1-1A, TaLIM3-2B, TaLIM8-4D, and TaLIM10-5D, were significantly induced by heat, drought, sodium chloride (NaCl), abscisic acid (ABA) and Fusarium graminearum stresses. Furthermore, the biological function of TaLIM8-4D was analyzed and results showed that it was subcellular localization in the nucleus and could induce weak cell death in Nicotiana benthamiana leaves. Additionally, overexpression of TaLIM8-4D could upregulate plant pathogenesis-related (PR) genes, promoting the infection of hemibiotrophic pathogen, implying that TaLIM8-4D could function as susceptible gene in the nucleus by upregulating PR genes and inducing cell death to promote the colonization of hemibiotrophic agent F. graminearum. Overall, the systematic identification, characterization, expression profiling, evolutionary, and function analyses provided the ability to understand TaLIMs and laid a foundation for the further function study of LIM family members in wheat.
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Affiliation(s)
- Yiting Li
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Xi Liu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Yongxin Xiao
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Yong Wen
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Keke Li
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Zhaolan Ma
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Lijun Yang
- Key Laboratory of Integrated Pest Management of Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds Control, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Yongxing Zhu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Junliang Yin
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
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11
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Transcriptome Profiles of Circular RNAs in Common Wheat during Fusarium Head Blight Disease. DATA 2022. [DOI: 10.3390/data7090121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed RNA molecules, and have been identified in many crops. However, there are few datasets for circRNA junctions from common wheat during Fusarium head blight disease. In the present study, we used RNA-seq to determine the changes in circRNAs among the control (CK) and 1, 3, and 5 days post-Fusarium graminearum inoculation (dpi) samples. More than one billion reads were produced from 12 libraries, and 99.99% of the reads were successfully mapped to a wheat reference genome. In total, 2091 high-confidence circRNAs—which had two or more junction reads and were supported by at least two circRNA identification algorithms—were detected. The completed expression profiling revealed a distinct expression pattern of circRNAs among the CK, 1dpi, 3dpi and 5dpi samples. This study provides a valuable resource for identifying F. graminearum infection-responsive circRNAs in wheat and for further functional characterization of circRNAs that participated in the Fusarium head blight disease response of wheat.
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Liu H, Nwafor CC, Piao Y, Li X, Zhan Z, Piao Z. Identification and Characterization of Circular RNAs in Brassica rapa in Response to Plasmodiophora brassicae. Int J Mol Sci 2022; 23:5369. [PMID: 35628175 PMCID: PMC9141718 DOI: 10.3390/ijms23105369] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 02/01/2023] Open
Abstract
Plasmodiophora brassicae is a soil-borne pathogen that attacks the roots of cruciferous plants and causes clubroot disease. CircRNAs are noncoding RNAs, widely existing in plant and animal species. Although knowledge of circRNAs has been updated continuously and rapidly, information about circRNAs in the regulation of clubroot disease resistance is extremely limited in Brassica rapa. Here, Chinese cabbage (BJN 222) containing clubroot resistance genes (CRa) against P. brassicae Pb4 was susceptible to PbE. To investigate the mechanism of cicRNAs responsible for clubroot disease resistance in B. rapa, circRNA-seq was performed with roots of 'BJN 222' at 0, 8, and 23 days post-inoculated (dpi) with Pb4 and PbE. A total of 231 differentially expressed circRNAs were identified between the groups. Based on the differentially expressed circRNAs, the circRNA-miRNA-mRNA network was constructed using the target genes directly or indirectly related to plant resistance. Upregulated novel_circ_000495 suppressed the expression of miR5656-y, leading to the upregulation of Bra026508, which might cause plant resistance. Our results provide new insights into clubroot resistance mechanisms and lay a foundation for further studies exploring complex gene regulation networks in B. rapa.
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Affiliation(s)
- Huishan Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (H.L.); (Y.P.); (X.L.)
| | - Chinedu Charles Nwafor
- Center for Plant Science Innovation and Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Yinglan Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (H.L.); (Y.P.); (X.L.)
| | - Xiaonan Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (H.L.); (Y.P.); (X.L.)
| | - Zongxiang Zhan
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (H.L.); (Y.P.); (X.L.)
| | - Zhongyun Piao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China; (H.L.); (Y.P.); (X.L.)
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Wang P, Wang S, Wu Y, Nie W, Yiming A, Huang J, Ahmad I, Zhu B, Chen G. Identification and Characterization of Rice Circular RNAs Responding to Xanthomonas oryzae pv. oryzae Invasion. PHYTOPATHOLOGY 2022; 112:492-500. [PMID: 34420356 DOI: 10.1094/phyto-06-21-0235-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Emerging roles of circular RNAs (circRNAs) in various biological processes have advanced our knowledge of transcriptional and posttranscriptional gene regulation. To date, no research has been conducted to explore their roles in the rice-Xanthomonas oryzae pv. oryzae interaction. Therefore, we identified 3,517 circRNAs from rice leaves infected with the highly virulent X. oryzae pv. oryzae strain PXO99A by using rRNA depleted RNA sequencing technique coupled with the CIRI2 and CIRCexplorer2 pipeline. Characterization analyses showed that these circRNAs were distributed across the whole genome of rice, and most circRNAs arose from exons (85.13%), ranged from 200 to 1,000 bp, and were with a noncanonical GT/AG (including CT/AC equivalent) splicing signal. Functional annotation and enrichment analysis of the host genes that produced the differentially expressed circRNAs (DEcircRNAs) suggested that these identified circRNAs might play an important role in reprogramming rice responses to PXO99A invasion, mainly by mediating photorespiration and chloroplast, peroxisome, and diterpenoid biosynthesis. Moreover, 31 DEcircRNAs were predicted to act as microRNA decoys in rice. The expression profile of four DEcircRNAs were validated by quantitative real-time PCR with divergent primers, and the back-splicing sites of seven DEcircRNAs were verified by PCR analysis and Sanger sequencing. Collectively, these results inferred a potential functional role of circRNAs in the regulation of rice immunity and provide novel clues about the molecular mechanisms of rice-PXO99A interaction.
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Affiliation(s)
- Peihong Wang
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Sai Wang
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Wu
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenhan Nie
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ayizekeranmu Yiming
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Huang
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Iftikhar Ahmad
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Department of Environmental Sciences, COMSATS University Islamabad, Vehari Campus, Vehari 61100, Pakistan
| | - Bo Zhu
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Gongyou Chen
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Yin J, Yan J, Hou L, Jiang L, Xian W, Guo Q. Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici. BMC Genomics 2021; 22:868. [PMID: 34856924 PMCID: PMC8638555 DOI: 10.1186/s12864-021-08183-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. RESULTS In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. CONCLUSIONS This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.
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Affiliation(s)
- Junliang Yin
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, College of Agriculture, Yangtze University, 434000 Jingzhou, Hubei China
| | - Jiahui Yan
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Lu Hou
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Liling Jiang
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Wenrong Xian
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
| | - Qingyun Guo
- Qinghai Academy of Agriculture and Forestry Science, Key Laboratory of Agricultural Integrated Pest Management, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai University, 810016 Xining, Qinghai Province China
- Qinghai Academy of Agriculture and Forestry Science, Qinghai University, 810016 Xining, China
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Wang G, Sun Q, Wang H, Liu H. Identification and characterization of circRNAs in the liver of blunt snout bream (Megalobrama amblycephala) infected with Aeromonas hydrophila. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 124:104185. [PMID: 34174243 DOI: 10.1016/j.dci.2021.104185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Circular RNAs (circRNAs), a class of non-coding RNAs, play an important role in regulating various biological processes. In the present study, circRNAs from the Megalobrama amblycephala liver were identified at five different time points post Aeromonas hydrophila using RNA-seq technology. A total of 250 circRNAs were identified, of which 106 were differentially expressed (DE) in ten pairwise comparisons. GO and KEGG analyses showed that the parental genes of DE circRNAs were enriched in phagocytosis, complement and coagulation cascades, and Fc gamma R-mediated phagocytosis pathways. According to ceRNA hypothesis, the interaction network of circRNAs, miRNAs and mRNAs was constructed. Moreover, WGCNA was conducted, and five specific modules significantly related to bacterial infection were identified. All the above results reveal the important role of circRNAs in immune response, which enriches the information of circRNAs in teleost, and helps to understand the immune response mechanism of M. amblycephala to A. hydrophila.
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Affiliation(s)
- Guowen Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Qianhui Sun
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Huanling Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China
| | - Hong Liu
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture and Rural Affair/ Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China; Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan, 430070, China.
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NGS Methodologies and Computational Algorithms for the Prediction and Analysis of Plant Circular RNAs. Methods Mol Biol 2021; 2362:119-145. [PMID: 34195961 DOI: 10.1007/978-1-0716-1645-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Circular RNAs (circRNAs) are a class of single-stranded RNAs derived from exonic, intronic, and intergenic regions from precursor messenger RNAs (pre-mRNA), where a noncanonical back-splicing event occurs, in which the 5' and 3' ends are attached by covalent bond. CircRNAs participate in the regulation of gene expression at the transcriptional and posttranscriptional level primarily as miRNA and RNA-binding protein (RBP) sponges, but also involved in the regulation of alternative RNA splicing and transcription. CircRNAs are widespread and abundant in plants where they have been involved in stress responses and development. Through the analysis of all publications in this field in the last five years, we can summarize that the identification of these molecules is carried out through next generation sequencing studies, where samples have been previously treated to eliminate DNA, rRNA, and linear RNAs as a means to enrich circRNAs. Once libraries are prepared, they are sequenced and subsequently studied from a bioinformatics point of view. Among the different tools for identifying circRNAs, we can highlight CIRI as the most used (in 60% of the published studies), as well as CIRCExplorer (20%) and find_circ (20%). Although it is recommended to use more than one program in combination, and preferably developed specifically to treat with plant samples, this is not always the case. It should also be noted that after identifying these circular RNAs, most of the authors validate their findings in the laboratory in order to obtain bona fide results.
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Sarwar R, Jiang T, Ding P, Gao Y, Tan X, Zhu K. Genome-wide analysis and functional characterization of the DELLA gene family associated with stress tolerance in B. napus. BMC PLANT BIOLOGY 2021; 21:286. [PMID: 34157966 PMCID: PMC8220683 DOI: 10.1186/s12870-021-03054-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/13/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Brassica napus is an essential crop for oil and livestock feed. Eventually, this crop's economic interest is at the most risk due to anthropogenic climate change. DELLA proteins constitute a significant repressor of plant growth to facilitate survival under constant stress conditions. DELLA proteins lack DNA binding domain but can interact with various transcription factors or transcription regulators of different hormonal families. Significant progress has been made on Arabidopsis and cereal plants. However, no comprehensive study regarding DELLA proteins has been delineated in rapeseed. RESULTS In our study, we have identified 10 BnaDELLA genes. All of the BnaDELLA genes are closely related to five AtDELLA genes, suggesting a relative function and structure. Gene duplication and synteny relationship among Brassica. napus, Arabidopsis. thaliana, Brassica rapa, Brassica oleracea, and Brassica nigra genomes were also predicted to provide valuable insights into the BnaDELLA gene family evolutionary characteristics. Chromosomal mapping revealed the uneven distribution of BnaDELLA genes on eight chromosomes, and site-specific selection assessment proposes BnaDELLA genes purifying selection. The motifs composition in all BnaDELLA genes is inconsistent; however, every BnaDELLA gene contains 12 highly conserved motifs, encoding DELLA and GRAS domains. The two known miRNAs (bna-miR6029 and bna-miR603) targets BnaC07RGA and BnaA09GAI, were also predicted. Furthermore, quantitative real-time PCR (qRT-PCR) analysis has exhibited the BnaDELLA genes diverse expression patterns in the root, mature-silique, leaf, flower, flower-bud, stem, shoot-apex, and seed. Additionally, cis-acting element prediction shows that all BnaDELLA genes contain light, stress, and hormone-responsive elements on their promoters. The gene ontology (GO) enrichment report indicated that the BnaDELLA gene family might regulate stress responses. Combine with transcriptomic data used in this study, we detected the distinct expression patterns of BnaDELLA genes under biotic and abiotic stresses. CONCLUSION In this study, we investigate evolution feature, genomic structure, miRNAs targets, and expression pattern of the BnaDELLA gene family in B. napus, which enrich our understanding of BnaDELLA genes in B. napus and suggests modulating individual BnaDELLA expression is a promising way to intensify rapeseed stress tolerance and harvest index.
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Affiliation(s)
- Rehman Sarwar
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ting Jiang
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Peng Ding
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yue Gao
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiaoli Tan
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Keming Zhu
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China.
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Bhogireddy S, Mangrauthia SK, Kumar R, Pandey AK, Singh S, Jain A, Budak H, Varshney RK, Kudapa H. Regulatory non-coding RNAs: a new frontier in regulation of plant biology. Funct Integr Genomics 2021; 21:313-330. [PMID: 34013486 PMCID: PMC8298231 DOI: 10.1007/s10142-021-00787-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/21/2021] [Accepted: 04/26/2021] [Indexed: 11/27/2022]
Abstract
Beyond the most crucial roles of RNA molecules as a messenger, ribosomal, and transfer RNAs, the regulatory role of many non-coding RNAs (ncRNAs) in plant biology has been recognized. ncRNAs act as riboregulators by recognizing specific nucleic acid targets through homologous sequence interactions to regulate plant growth, development, and stress responses. Regulatory ncRNAs, ranging from small to long ncRNAs (lncRNAs), exert their control over a vast array of biological processes. Based on the mode of biogenesis and their function, ncRNAs evolved into different forms that include microRNAs (miRNAs), small interfering RNAs (siRNAs), miRNA variants (isomiRs), lncRNAs, circular RNAs (circRNAs), and derived ncRNAs. This article explains the different classes of ncRNAs and their role in plant development and stress responses. Furthermore, the applications of regulatory ncRNAs in crop improvement, targeting agriculturally important traits, have been discussed.
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Affiliation(s)
- Sailaja Bhogireddy
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | | | - Rakesh Kumar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Life Sciences, Central University of Karnataka, Karnataka, India
| | - Arun K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Sadhana Singh
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ankit Jain
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, Western Australia, Australia
| | - Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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Song F, Cai A, Ye Q, Chen X, Lin L, Hao X. MiR-34b-3p Impaired HUVECs Viability and Migration via Targeting PDK1 in an In Vitro Model of Gestational Diabetes Mellitus. Biochem Genet 2021; 59:1381-1395. [PMID: 33856598 DOI: 10.1007/s10528-021-10064-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 03/25/2021] [Indexed: 12/28/2022]
Abstract
Gestational diabetes mellitus (GDM) leads to poor pregnancy outcomes. The methods for GDM early diagnosis and treatment are still unknown. This study aimed to investigate the expression and diagnostic potential of miR-34b-3p in GDM patients and further analyzed the effects of miR-34b-3p on HUVECs viability and migration. The expression of miR-34b-3p was detected in HUVECs of GDM and normal pregnant women by qRT-PCR. Then the HUVECs were isolated from normal pregnant women. High glucose (HG) was used to treat the HUVECs to mimic the GDM in vitro. The cell viability and migration were determined by MTT, wound healing assay, and transwell assay. The interaction between miR-34b-3p and PDK1 was evaluated by luciferase activity assay. Our results showed that miR-34b-3p was up-regulated in HUVECs of GDM patients. Then the HUVECs were isolated from normal pregnant women and they were treated with HG to mimic the GDM in vitro. Interestingly, knockdown of miR-34b-3p restored the impairment of HG treatment-induced effects in HUVECs. More importantly, PDK1 was proved to be a potential target of miR-34b-3p. Finally, the rescue experiments confirmed that miR-34b-3p impaired cell viability and migration ability in HUVECs by targeting PDK1. These findings concluded that miR-34b-3p impaired HUVECs viability and migration in GDM by targeting PDK1, which might provide a novel perspective for the pathogenesis and underlying therapeutic target for GDM.
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Affiliation(s)
- Feiluan Song
- Department of Obstetrics and Gynecology, Ruian People's Hospital, No. 108 Wansong Road, Yuhai Street, Ruian City, Wenzhou City, 325200, Zhejiang Province, China
| | - Anli Cai
- Department of Obstetrics and Gynecology, Ruian People's Hospital, No. 108 Wansong Road, Yuhai Street, Ruian City, Wenzhou City, 325200, Zhejiang Province, China.
| | - Qianwen Ye
- Department of Obstetrics and Gynecology, Ruian People's Hospital, No. 108 Wansong Road, Yuhai Street, Ruian City, Wenzhou City, 325200, Zhejiang Province, China
| | - Xiang Chen
- Department of Obstetrics and Gynecology, Ruian People's Hospital, No. 108 Wansong Road, Yuhai Street, Ruian City, Wenzhou City, 325200, Zhejiang Province, China
| | - Lin Lin
- Department of Obstetrics and Gynecology, Ruian People's Hospital, No. 108 Wansong Road, Yuhai Street, Ruian City, Wenzhou City, 325200, Zhejiang Province, China
| | - Xi Hao
- Department of Obstetrics and Gynecology, Ruian People's Hospital, No. 108 Wansong Road, Yuhai Street, Ruian City, Wenzhou City, 325200, Zhejiang Province, China
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Huang X, Zhang H, Guo R, Wang Q, Liu X, Kuang W, Song H, Liao J, Huang Y, Wang Z. Systematic identification and characterization of circular RNAs involved in flag leaf senescence of rice. PLANTA 2021; 253:26. [PMID: 33410920 PMCID: PMC7790769 DOI: 10.1007/s00425-020-03544-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 12/19/2020] [Indexed: 05/30/2023]
Abstract
Circular RNAs (circRNAs) identification, expression profiles, and construction of circRNA-parental gene relationships and circRNA-miRNA-mRNA ceRNA networks indicate that circRNAs are involved in flag leaf senescence of rice. Circular RNAs (circRNAs) are a class of 3'-5' head-to-tail covalently closed non-coding RNAs which have been proved to play important roles in various biological processes. However, no systematic identification of circRNAs associated with leaf senescence in rice has been studied. In this study, a genome-wide high-throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. Here, a total of 6612 circRNAs were identified, among which, 113 circRNAs were differentially expressed (DE) during the leaf senescence process. Moreover, 4601 (69.59%) circRNAs were derived from the exons or introns of their parental genes, while 2110 (71%) of the parental genes produced only one circRNA. The sequence alignment analysis showed that hundreds of rice circRNAs were conserved among different plant species. Gene Ontology (GO) enrichment analysis revealed that parental genes of DE circRNAs were enriched in many biological processes closely related to leaf senescence. Through weighted gene co-expression network analysis (WGCNA), six continuously down-expressed circRNAs, 18 continuously up-expressed circRNAs and 15 turn-point high-expressed circRNAs were considered to be highly associated with leaf senescence. Additionally, a total of 17 senescence-associated circRNAs were predicted to have parental genes, in which, regulations of three circRNAs to their parental genes were validated by qRT-PCR. The competing endogenous RNA (ceRNA) networks were also constructed. And a total of 11 senescence-associated circRNAs were predicted to act as miRNA sponges to regulate mRNAs, in which, regulation of two circRNAs to eight mRNAs was validated by qRT-PCR. It is discussed that senescence-associated circRNAs were involved in flag leaf senescence probably through mediating their parental genes and ceRNA networks, to participate in several well-studied senescence-associated processes, mainly including the processes of transcription, translation, and posttranslational modification (especially protein glycosylation), oxidation-reduction process, involvement of senescence-associated genes, hormone signaling pathway, proteolysis, and DNA damage repair. This study not only showed the systematic identification of circRNAs involved in leaf senescence of rice, but also laid a foundation for functional research on candidate circRNAs.
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Affiliation(s)
- Xiaoping Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Hongyu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Rong Guo
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Qiang Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Xuanzhi Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Weigang Kuang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Haiyan Song
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Jianglin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China
| | - Yingjin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China.
| | - Zhaohai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education of the P.R. China, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi Province, China.
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21
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Yang X, Liu Y, Zhang H, Wang J, Zinta G, Xie S, Zhu W, Nie WF. Genome-Wide Identification of Circular RNAs in Response to Low-Temperature Stress in Tomato Leaves. Front Genet 2020; 11:591806. [PMID: 33250924 PMCID: PMC7674948 DOI: 10.3389/fgene.2020.591806] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/06/2020] [Indexed: 11/13/2022] Open
Abstract
Abiotic stress adversely inhibits the growth and development of plants, by changing the expression of multiple genes. Circular RNAs (circRNAs), as a class of non-coding RNAs, function in transcriptional and posttranscriptional regulation. Yet, the involvement of circRNAs in abiotic stress response is rarely reported. In this study, the participation and function of circRNAs in low-temperature (LT)-induced stress response were investigated in tomato leaves. We generated genome-wide profiles of circRNAs and mRNAs in tomato leaves grown at 25°C room temperature (RT) and 12°C LT. Our results show that 1,830 circRNAs were identified in tomato leaves in both RT and LT treatments, among which 1,759 were differentially induced by the LT treatment. We find that the identified circRNAs are mainly located at exons of genes, but less distributed at introns of genes or intergenic regions. Our results suggest that there are 383 differentially expressed circRNAs predicted to function as putative sponges of 266 miRNAs to target 4,476 mRNAs in total. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis assays indicate that multiple pathways were enriched in both differentially expressed genes induced by LT and parental genes of differentially expressed circRNAs induced by LT, revealing the key functions of circRNAs and the corresponding targeted genes in response to LT stress. Our results suggest that circRNAs may be involved in regulating metabolism (i.e., carbohydrate, amino acid, lipid, and energy), signal transduction, and environmental adaptation-related pathways and that these circRNAs were predicted to regulate the expression of transcription factors, genes in signal transduction pathways, and genes related to the Ca2+ channel through targeting the corresponding proteins, such as WRKY, NAC, cytochrome P450, and calmodulin binding protein. Taken together, our study uncovers that multiple circRNAs are isolated and differently regulated in response to LT stress and provides the resource and potential networks of circRNA–miRNA–mRNA under LT stress for further investigations in tomato leaves.
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Affiliation(s)
- Xuedong Yang
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Yahui Liu
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hui Zhang
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Jinyu Wang
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Gaurav Zinta
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | | | - Weimin Zhu
- Shanghai Key Laboratory of Protected Horticulture Technology, The Protected Horticulture Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wen-Feng Nie
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
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22
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CircPlant: An Integrated Tool for circRNA Detection and Functional Prediction in Plants. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:352-358. [PMID: 33157302 PMCID: PMC7801249 DOI: 10.1016/j.gpb.2020.10.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 01/26/2019] [Accepted: 02/15/2019] [Indexed: 12/22/2022]
Abstract
The recent discovery of circular RNAs (circRNAs) and characterization of their functional roles have opened a new avenue for understanding the biology of genomes. circRNAs have been implicated to play important roles in a variety of biological processes, but their precise functions remain largely elusive. Currently, a few approaches are available for novel circRNA prediction, but almost all these methods are intended for animal genomes. Considering that the major differences between the organization of plant and mammal genomes cannot be neglected, a plant-specific method is needed to enhance the validity of plant circRNA identification. In this study, we present CircPlant, an integrated tool for the exploration of plant circRNAs, potentially acting as competing endogenous RNAs (ceRNAs), and their potential functions. With the incorporation of several unique plant-specific criteria, CircPlant can accurately detect plant circRNAs from high-throughput RNA-seq data. Based on comparison tests on simulated and real RNA-seq datasets from Arabidopsis thaliana and Oryza sativa, we show that CircPlant outperforms all evaluated competing tools in both accuracy and efficiency. CircPlant is freely available at http://bis.zju.edu.cn/circplant.
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Yang Z, Yang Z, Xie Y, Liu Q, Mei Y, Wu Y. Systematic Identification and Analysis of Light-Responsive Circular RNA and Co-expression Networks in Lettuce ( Lactuca sativa). G3 (BETHESDA, MD.) 2020; 10:2397-2410. [PMID: 32398233 PMCID: PMC7341150 DOI: 10.1534/g3.120.401331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 05/09/2020] [Indexed: 11/18/2022]
Abstract
Circular RNA (circRNA) is a covalently-closed single-stranded RNA molecule that plays an important role in transcriptional regulation of gene expression in a variety of species. Light intensity is a pivotal environmental factor affecting plant growth and development. However, little is known regarding photoresponsive plant circRNAs. Here, we aimed to investigate the expression and function of circRNAs in lettuce leaves in response to different light intensity treatments. We performed RNA sequencing (RNA-Seq) on leaves of lettuce (Lactuca sativa) to determine circRNA expression profiles and reverse-transcription polymerase chain reaction (PCR) to validate the candidate circRNA molecules. We then combined bioinformatics approach to explore the function of the parental genes of circRNA, including network, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes pathway analysis. We identified 1650 circRNAs in lettuce, of which 1508 (86.40%) were derived from exons. Using real-time PCR, we characterized 10 validated differentially expressed circRNAs and their parental genes, all of which showed expression patterns consistent with RNA-Seq data. Interestingly, the expression of circRNA was, in some cases, inversely correlated with the expression of the parental gene. Furthermore, analysis of the circRNA-microRNA-mRNA network suggests that circRNAs may be involved in plant hormone signaling and chlorophyll metabolism during photoreactivity. These findings provide an essential reference basis for studying circRNAs' biological mechanisms in light-treated plants.
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Affiliation(s)
| | - Zhao Yang
- College of Life Sciences, and
- College of Science, Northwest A&F University, 712100 Yangling, Shaan Xi, China
| | - Yingge Xie
- College of Science, Northwest A&F University, 712100 Yangling, Shaan Xi, China
- College of Life Sciences, and
| | | | - Yanhao Mei
- College of Horticulture
- College of Horticulture
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24
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Jiang W, Yin J, Zhang H, He Y, Shuai S, Chen S, Cao S, Li W, Ma D, Chen H. Genome-wide identification, characterization analysis and expression profiling of auxin-responsive GH3 family genes in wheat (Triticum aestivum L.). Mol Biol Rep 2020; 47:3885-3907. [DOI: 10.1007/s11033-020-05477-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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25
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Genome-Wide Identification, Structure Characterization, and Expression Profiling of Dof Transcription Factor Gene Family in Wheat (Triticum aestivum L.). AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10020294] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA binding with one finger (Dof) proteins are plant-specific transcription factors with crucial roles in plant growth and stress response. Even so, little is known about them in wheat. In this study, 108 wheat Dof (TaDof) genes across 21 chromosomes were detected. Although variable in sequence length, molecular weight, and isoelectric point, all TaDof proteins contained conserved zinc-finger structures and were phylogenetically divided into 7 sub-groups. Exon/intron and motif analyses suggested that TaDof structures and conserved motifs were similar within sub-groups but diverse among sub-groups. Many segmental duplications were identified and Ka/Ks and inter-species synthetic analyses indicated that polyploidization was main reason for increased number of TaDofs. Prediction and experimental confirmation revealed that TaDofs functioned as transcription factors in the nucleus. Expression pattern profiling showed that TaDofs specifically affected growth and development, and biotic and abiotic stress responses. Wheat miRNAs and cis-regulator were predicted as essential players in molding TaDofs expression patterns. qRT-PCR analysis revealed that TaDofs were induced by salt and drought stresses. Customized annotation revealed that TaDofs were widely involved in phytohormone response, defense, growth and development, and metabolism. Our study provided a comprehensive understanding to wheat TaDofs.
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26
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Lv L, Yu K, Lü H, Zhang X, Liu X, Sun C, Xu H, Zhang J, He X, Zhang D. Transcriptome-wide identification of novel circular RNAs in soybean in response to low-phosphorus stress. PLoS One 2020; 15:e0227243. [PMID: 31961887 PMCID: PMC6974154 DOI: 10.1371/journal.pone.0227243] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/16/2019] [Indexed: 02/07/2023] Open
Abstract
Low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Circular RNAs (circRNAs) are novel noncoding RNAs that play a crucial role in plant responses to abiotic stress. However, how LP stress mediates the biogenesis of circRNAs in soybean remains unclear. Here, to explore the response mechanisms of circRNAs to LP stress, the roots of two representative soybean genotypes with different P-use efficiency, Bogao (a LP-sensitive genotype) and Nannong 94156 (a LP-tolerant genotype), were used for the construction of RNA sequencing (RNA-seq) libraries and circRNA identification. In total, 371 novel circRNA candidates, including 120 significantly differentially expressed (DE) circRNAs, were identified across different P levels and genotypes. More DE circRNAs were significantly regulated by LP stress in Bogao than in NN94156, suggesting that the tolerant genotype was less affected by LP stress than the sensitive genotype was; in other words, NN94156 may have a better ability to maintain P homeostasis under LP stress. Moreover, a positive correlation was observed between the expression patterns of P stress-induced circRNAs and their circRNA-host genes. Gene Ontology (GO) enrichment analysis of these circRNA-host genes and microRNA (miRNA)-targeted genes indicated that these DE circRNAs were involved mainly in defense responses, ADP binding, nucleoside binding, organic substance catabolic processes, oxidoreductase activity, and signal transduction. Together, our results revealed that LP stress can significantly alter the genome-wide profiles of circRNAs and indicated that the regulation of circRNAs was both genotype and environment specific in response to LP stress. LP-induced circRNAs might provide a rich resource for LP-responsive circRNA candidates for future studies.
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Affiliation(s)
- Lingling Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Kaiye Yu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Haiyan Lü
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiangqian Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaoqian Liu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Chongyuan Sun
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Huanqing Xu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jinyu Zhang
- Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaohui He
- Smart City Institute, Zhengzhou University, Zhengzhou, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou, China
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27
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Guria A, Sharma P, Natesan S, Pandi G. Circular RNAs-The Road Less Traveled. Front Mol Biosci 2020; 6:146. [PMID: 31998746 PMCID: PMC6965350 DOI: 10.3389/fmolb.2019.00146] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022] Open
Abstract
Circular RNAs are the most recent addition in the non-coding RNA family, which has started to gain recognition after a decade of obscurity. The first couple of reports that emerged at the beginning of this decade and the amount of evidence that has accumulated thereafter has, however, encouraged RNA researchers to navigate further in the quest for the exploration of circular RNAs. The joining of 5′ and 3′ ends of RNA molecules through backsplicing forms circular RNAs during co-transcriptional or post-transcriptional processes. These molecules are capable of effectively sponging microRNAs, thereby regulating the cellular processes, as evidenced by numerous animal and plant systems. Preliminary studies have shown that circular RNA has an imperative role in transcriptional regulation and protein translation, and it also has significant therapeutic potential. The high stability of circular RNA is rendered by its closed ends; they are nevertheless prone to degradation by circulating endonucleases in serum or exosomes or by microRNA-mediated cleavage due to their high complementarity. However, the identification of circular RNAs involves diverse methodologies and the delineation of its possible role and mechanism in the regulation of cellular and molecular architecture has provided a new direction for the continuous research into circular RNA. In this review, we discuss the possible mechanism of circular RNA biogenesis, its structure, properties, degradation, and the growing amount of evidence regarding the detection methods and its role in animal and plant systems.
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Affiliation(s)
- Ashirbad Guria
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Priyanka Sharma
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Sankar Natesan
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai, India
| | - Gopal Pandi
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Madurai, India
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28
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Vaschetto LM, Litholdo CG, Sendín LN, Terenti Romero CM, Filippone MP. Cereal Circular RNAs (circRNAs): An Overview of the Computational Resources for Identification and Analysis. Methods Mol Biol 2020; 2072:157-163. [PMID: 31541445 DOI: 10.1007/978-1-4939-9865-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Circular RNAs (circRNAs) are a widespread class of endogenous noncoding RNAs and they have been studied in the past few years, implying important biological functions in all kingdoms of life. Recently, circRNAs have been identified in many plant species, including cereal crops, showing differential expression during stress response and developmental programs, which suggests their role in these process. In the following years, it is expected that insights into the functional roles of circRNAs can be used by cereal scientists and molecular breeders with the aim to develop new strategies for crop improvement. Here, we briefly outline the current knowledge about circRNAs in plants and we also outline available computational resources for their validation and analysis in cereal species.
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Affiliation(s)
- Luis M Vaschetto
- Instituto de Diversidad y Ecología Animal, Consejo Nacional de Investigaciones Científicas y Técnicas (IDEA, CONICET), Córdoba, Argentina.
- Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, (FCEFyN, UNC), Córdoba, Argentina.
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, USA.
| | - Celso Gaspar Litholdo
- Centre National pour la Recherche Scientifique (CNRS)/Université de Perpignan Via Domitia (UPVD)-Laboratoire Génome et Développement des Plantes (LGDP-UMR5096), Perpignan, France
| | - Lorena Noelia Sendín
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA), Estación Experimental Agroindustrial Obispo Colombres (EEAOC)-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Tucumán, Argentina
| | - Claudia Mabel Terenti Romero
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria San Luis (INTA, EEA SAN LUIS), San Luis, Argentina
| | - María Paula Filippone
- Universidad Nacional de Tucumán, Facultad de Agronomía y Zootecnia, (UNT-FAZ), Tucumán, Argentina
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29
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Fan J, Quan W, Li GB, Hu XH, Wang Q, Wang H, Li XP, Luo X, Feng Q, Hu ZJ, Feng H, Pu M, Zhao JQ, Huang YY, Li Y, Zhang Y, Wang WM. circRNAs Are Involved in the Rice- Magnaporthe oryzae Interaction. PLANT PHYSIOLOGY 2020; 182:272-286. [PMID: 31628150 PMCID: PMC6945833 DOI: 10.1104/pp.19.00716] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 10/07/2019] [Indexed: 05/03/2023]
Abstract
Circular RNAs (circRNAs) play roles in various biological processes, but their functions in the rice (Oryza sativa) response to Magnaporthe oryzae remain elusive. Here, we demonstrate that circRNAs are involved in the rice-M. oryzae interaction using comparative circRNA-sequencing and transgenic approaches. We identified 2932 high-confidence circRNAs from young leaves of the blast-resistant accession International Rice Blast Line Pyricularia-Kanto51-m-Tsuyuake (IR25) and the blast-susceptible accession Lijiangxin Tuan Heigu (LTH) under M oryzae-infected or uninfected conditions; 636 were detected specifically upon M oryzae infection. The circRNAs in IR25 were significantly more diverse than those in LTH, especially under M. oryzae infection. Particularly, the number of circRNAs generated per parent gene was much higher in IR25 than in LTH and increased in IR25 but decreased in LTH upon M. oryzae infection. The higher diversity of circRNAs in IR25 was further associated with more frequent 3' and 5' alternative back-splicing and usage of complex splice sites. Moreover, a subset of circRNAs was differentially responsive to M oryzae in IR25 and LTH. We further confirmed that circR5g05160 promotes rice immunity against M oryzae Therefore, our data indicate that circRNA diversity is associated with different responses to M oryzae infection in rice and provide a starting point to investigate a new layer of regulation in the rice-M oryzae interaction.
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Affiliation(s)
- Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Weili Quan
- Center for Genome Analysis, ABLife Inc., Wuhan 430075, Hubei, China
| | - Guo-Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiao-Hong Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Qi Wang
- Center for Genome Analysis, ABLife Inc., Wuhan 430075, Hubei, China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xu-Pu Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiaotian Luo
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan 430075, Hubei, China
| | - Qin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Zi-Jin Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Hui Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Ji-Qun Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yan-Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yi Zhang
- Center for Genome Analysis, ABLife Inc., Wuhan 430075, Hubei, China
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
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30
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Wang W, Wang J, Wei Q, Li B, Zhong X, Hu T, Hu H, Bao C. Transcriptome-Wide Identification and Characterization of Circular RNAs in Leaves of Chinese Cabbage (Brassica rapa L. ssp. pekinensis) in Response to Calcium Deficiency-Induced Tip-burn. Sci Rep 2019; 9:14544. [PMID: 31601970 PMCID: PMC6787205 DOI: 10.1038/s41598-019-51190-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 09/26/2019] [Indexed: 12/11/2022] Open
Abstract
Circular RNA (circRNA) is a newly discovered non-coding RNA, which play significant roles in the function and transcriptional regulation of microRNA. To date, in Chinese cabbage, the functional characteristic of circRNAs in response to calcium deficiency-induced tip-burn have not been reported. In this study, 730 circRNAs were isolated from Chinese cabbage leaves, of which 23 and 22 were differentially expressed in different calcium deficiency stages compared with the control. Forty-six host genes of the differentially expressed circRNAs were identified, and one circRNA was found to act as miRNAs sponges. Based on the functional analysis of host genes and target mRNAs of the corresponding miRNAs, the identified circRNAs might participated in response to stimulus, electron carrier activity, ATPase activity, cell wall metabolism, transcription factors and plant hormone signal transduction. ABF2, a positive regulator of the abiotic stress response in the abscisic acid (ABA) pathway, may play a role in calcium deficiency tolerance through a circRNA regulatory pathway. Correspondingly, the concentration of ABA is also increased during the Ca2+ deficiency stress. Our results suggest that circRNAs participate in a broad range of biological processes and physiological functions in the response to calcium deficiency-induced tip-burn and provide a basis for further studies of the biological roles that circRNAs play in the plant stress response.
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Affiliation(s)
- Wuhong Wang
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jinglei Wang
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qingzhen Wei
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Biyuan Li
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xinmin Zhong
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Tianhua Hu
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Haijiao Hu
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Chonglai Bao
- Institute of Vegetable Research, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
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31
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Gao Z, Li J, Luo M, Li H, Chen Q, Wang L, Song S, Zhao L, Xu W, Zhang C, Wang S, Ma C. Characterization and Cloning of Grape Circular RNAs Identified the Cold Resistance-Related Vv-circATS1. PLANT PHYSIOLOGY 2019; 180:966-985. [PMID: 30962290 PMCID: PMC6548266 DOI: 10.1104/pp.18.01331] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/24/2019] [Indexed: 05/19/2023]
Abstract
Circular RNAs (circRNAs) are widely distributed and play essential roles in a series of developmental processes, although none have been identified or characterized in grapevines (Vitis vinifera). In this study, we characterized the function of grape circRNA and uncovered thousands of putative back-splicing sites by global transcriptome analysis. Our results indicated that several reported circRNA prediction algorithms should be used simultaneously to obtain comprehensive and reliable circRNA predictions in plants. Furthermore, the length of introns flanking grape circRNAs was closely related to exon circularization. Although the longer introns flanking grape circRNAs appeared to circularize more efficiently, a 20- to 50-nt region seemed large enough to drive grape circRNA biogenesis. In addition, the endogenous introns flanking circularized exon(s) in conjunction with reverse complementary sequences could support the accurate and efficient circularization of various exons in grape, which constitutes a new tool for exploring the functional consequences caused by circRNA expression. Finally, we identified 475 differentially expressed circRNAs in grape leaves under cold stress. Overexpression of Vv-circATS1, a circRNA derived from glycerol-3-P acyltransferase, improved cold tolerance in Arabidopsis (Arabidopsis thaliana), while the linear RNA derived from the same sequence cannot. These results indicate the functional difference between circRNA and linear RNA, and provide new insight into plant abiotic stress resistance.
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Affiliation(s)
- Zhen Gao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jing Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Meng Luo
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Hui Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Qiuju Chen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Lei Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Shiren Song
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Liping Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Wenping Xu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Shiping Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
- Institute of Agro-food Science and Technology/Key Laboratory of Agro-products Processing Technology of Shandong, Shandong Academy of Agricultural Sciences, Jinan 250100, People's Republic of China
| | - Chao Ma
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, People's Republic of China
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Zhu YX, Jia JH, Yang L, Xia YC, Zhang HL, Jia JB, Zhou R, Nie PY, Yin JL, Ma DF, Liu LC. Identification of cucumber circular RNAs responsive to salt stress. BMC PLANT BIOLOGY 2019; 19:164. [PMID: 31029105 PMCID: PMC6486992 DOI: 10.1186/s12870-019-1712-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/11/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) are 3'-5' head-to-tail covalently closed non-coding RNA that have been proved to play essential roles in many cellular and developmental processes. However, no information relate to cucumber circRNAs is available currently, especially under salt stress condition. RESULTS In this study, we sequenced circRNAs in cucumber and a total of 2787 were identified, with 1934 in root and 44 in leaf being differentially regulated under salt stress. Characteristics analysis of these circRNAs revealed following features: most of them are exon circRNAs (79.51%) and they prefer to arise from middle exon(s) of parent genes (2035/2516); moreover, most of circularization events (88.3%) use non-canonical-GT/AG splicing signals; last but not least, pairing-driven circularization is not the major way to generate cucumber circRNAs since very few circRNAs (18) contain sufficient flanking complementary sequences. Annotation and enrichment analysis of both parental genes and target mRNAs were launched to uncover the functions of differentially expressed circRNAs induced by salt stress. The results showed that circRNAs may be paly roles in salt stress response by mediating transcription, signal transcription, cell cycle, metabolism adaptation, and ion homeostasis related pathways. Moreover, circRNAs may function to regulate proline metabolisms through regulating associated biosynthesis and degradation genes. CONCLUSIONS The present study identified large number of cucumber circRNAs and function annotation revealed their possible biological roles in response to salt stress. Our findings will lay a solid foundation for further structure and function studies of cucumber circRNAs.
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Affiliation(s)
- Yong-Xing Zhu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Horticulture and Gardening/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Jian-Hua Jia
- College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Lei Yang
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Horticulture and Gardening/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Yu-Chen Xia
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Horticulture and Gardening/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Hui-Li Zhang
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Horticulture and Gardening/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Jin-Bu Jia
- Department of Biology, Southern University of Science and Technology, Shenzhen, 518055 Guangdong China
| | - Ran Zhou
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Horticulture and Gardening/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Pei-Yao Nie
- Biomarker Technologies, Beijing, 101300 China
| | - Jun-Liang Yin
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Horticulture and Gardening/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Dong-Fang Ma
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Horticulture and Gardening/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
| | - Le-Cheng Liu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Horticulture and Gardening/College of Agriculture, Yangtze University, Jingzhou, 434000 Hubei China
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Fang Z, Hou Z, Wang S, Liu Z, Wei S, Zhang Y, Song J, Yin J. Transcriptome Analysis Reveals the Accumulation Mechanism of Anthocyanins in Buckwheat ( Fagopyrum esculentum Moench) Cotyledons and Flowers. Int J Mol Sci 2019; 20:E1493. [PMID: 30934615 PMCID: PMC6471586 DOI: 10.3390/ijms20061493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 03/20/2019] [Accepted: 03/23/2019] [Indexed: 12/20/2022] Open
Abstract
Buckwheat (Fagopyrum esculentum) is a valuable crop which can produce multiple human beneficial secondary metabolites, for example, the anthocyanins in sprouts and flowers. However, as the predominant group of visible polyphenols in pigmentation, little is known about the molecular mechanisms underlying the anthocyanin biosynthesis within buckwheat. In this study, a comparative transcriptome analysis of green and red common buckwheat cultivars was carried out through RNA sequencing. Overall, 3727 and 5323 differently expressed genes (DEGs) were identified in flowers and cotyledons, respectively. Through GO and KEGG analysis, we revealed that DEGs in flowers and cotyledons are predominately involved in biosynthesis of anthocyanin. A total of 42 unigenes encoding 11 structural enzymes of the anthocyanin biosynthesis were identified as DEGs. We also identified some transcription factor families involved in the regulation of anthocyanin biosynthesis. Real-time qPCR validation of candidate genes was performed in flowers and cotyledons, and the results suggested that the high expression level of structural genes involved in anthocyanin biosynthetic pathway promotes anthocyanin accumulation. Our results provide the insight understanding for coloration of red common buckwheat.
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Affiliation(s)
- Zhengwu Fang
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
| | - Zehao Hou
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
| | - Shuping Wang
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
| | - Zhixiong Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434000, China.
| | - Shudong Wei
- College of Life Science, Yangtze University, Jingzhou 434000, China.
| | - Yingxin Zhang
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
| | - Jinghan Song
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
| | - Junliang Yin
- Hubei Collaborative Innovation Center for Grain Industry/Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture, Yangtze University, Jingzhou 434000, China.
- Forewarning and Management of Agricultural and Forestry Pests, Hubei Engineering Technology Center/Engendering Research Center of Ecology and Agricultural Use of Waterland, Ministry of Education, Yangtze University, Jingzhou 434000, China.
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Rapid identification of a stripe rust resistant gene in a space-induced wheat mutant using specific locus amplified fragment (SLAF) sequencing. Sci Rep 2018; 8:3086. [PMID: 29449594 PMCID: PMC5814476 DOI: 10.1038/s41598-018-21489-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 02/06/2018] [Indexed: 11/08/2022] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating diseases of wheat. Resistant cultivars are the preferred strategy to control the disease. Space-induced wheat mutant R39 has adult-plant resistance (APR) to Pst. Genetic analysis indicated that a single recessive gene, designated YrR39, was responsible for the APR of R39 to Pst. Bulked segregant analysis (BSA) combined with a SLAF sequencing (SLAF-seq) strategy was used to fine-map YrR39 to a 17.39 Mb segment on chromosome 4B. The region was confirmed by analysis with simple sequence repeat (SSR) markers. A total of 126 genes were annotated in the region and 21 genes with annotations associated with disease response were selected for further qRT-PCR analysis. The candidate gene Traes_4BS_C868349E1 (annotated as an F-box/LRR-repeat protein) was up-regulated after 12, 24, 48, and 96 hours post inoculation with Pst, suggesting it is likely involved in the resistance. The current study demonstrated that BSA combined with SLAF-seq for SNP discovery is an efficient approach for mapping and identifying candidate functional gene.
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Litholdo CG, da Fonseca GC. Circular RNAs and Plant Stress Responses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1087:345-353. [PMID: 30259379 DOI: 10.1007/978-981-13-1426-1_27] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Circular RNAs (circRNAs) are a novel class of noncoding RNAs that have been extensively explored in the past few years. The advent of new high-throughput sequencing technologies coupled with bioinformatics tools revealed the presence of these molecules in the transcriptome of a wide range of organisms. In animals, circRNAs can modulate gene expression and act as sponges of miRNAs to inhibit their activity. It has been demonstrated that they have the potential to be diagnostic biomarkers as their expression is closely associated to human diseases, such as Alzheimer and cancer. However, in plants their function remains elusive. Recently, the role of the circRNAs in plant stress responses has been studied. During the infection of Pseudomonas syringae in kiwifruit plants, 584 circRNAs were differentially expressed in leaf samples, and a group of them could be further associated with the stage of infection. Under phosphate deficiency conditions, 27 rice circRNAs were reported to be differentially expressed. In tomato, 163 circRNAs demonstrated chilling-responsive expression, with 102 containing miRNA-binding sites and are predicted to act as miRNA sponges. Additionally, Arabidopsis seedlings presented 1583 heat-specific circRNAs, and it was also reported that heat stress could increase the quantity, length, and alternative circularization events of circRNAs. Finally, wheat seedlings under dehydration stress had 62 circRNAs differentially expressed, with 6 being predicted as miRNA sponges. Although the role of plant circRNAs during the biotic and abiotic stresses is still poorly characterised, these molecules have the potential to expand the number of targets and tools in the biotechnology field.
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Affiliation(s)
- Celso Gaspar Litholdo
- Laboratoire Génome et Développement des Plantes, Centre National pour la Recherche Scientifique (CNRS), Perpignan, France.
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