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Dong B, Meng D, Song Z, Cao H, Du T, Qi M, Wang S, Xue J, Yang Q, Fu Y. CcNFYB3-CcMATE35 and LncRNA CcLTCS-CcCS modules jointly regulate the efflux and synthesis of citrate to enhance aluminium tolerance in pigeon pea. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:181-199. [PMID: 37776153 PMCID: PMC10754017 DOI: 10.1111/pbi.14179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 09/03/2023] [Accepted: 09/10/2023] [Indexed: 10/01/2023]
Abstract
Aluminium (Al) toxicity decreases crop production in acid soils in general, but many crops have evolved complex mechanisms to resist it. However, our current understanding of how plants cope with Al stress and perform Al resistance is still at the initial stage. In this study, the citrate transporter CcMATE35 was identified to be involved in Al stress response. The release of citrate was increased substantially in CcMATE35 over-expression (OE) lines under Al stress, indicating enhanced Al resistance. It was demonstrated that transcription factor CcNFYB3 regulated the expression of CcMATE35, promoting the release of citrate from roots to increase Al resistance in pigeon pea. We also found that a Long noncoding RNA Targeting Citrate Synthase (CcLTCS) is involved in Al resistance in pigeon pea. Compared with controls, overexpression of CcLTCS elevated the expression level of the Citrate Synthase gene (CcCS), leading to increases in root citrate level and citrate release, which forms another module to regulate Al resistance in pigeon pea. Simultaneous overexpression of CcNFYB3 and CcLTCS further increased Al resistance. Taken together, these findings suggest that the two modules, CcNFYB3-CcMATE35 and CcLTCS-CcCS, jointly regulate the efflux and synthesis of citrate and may play an important role in enhancing the resistance of pigeon pea under Al stress.
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Affiliation(s)
- Biying Dong
- State Key Laboratory of Efficient Production of Forest ResourcesBeijing Forestry UniversityBeijingChina
- The Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain WetlandsNational Forestry and Grassland Administration, Beijing Forestry UniversityBeijingChina
| | - Dong Meng
- State Key Laboratory of Efficient Production of Forest ResourcesBeijing Forestry UniversityBeijingChina
- The Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain WetlandsNational Forestry and Grassland Administration, Beijing Forestry UniversityBeijingChina
| | - Zhihua Song
- State Key Laboratory of Efficient Production of Forest ResourcesBeijing Forestry UniversityBeijingChina
- The Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain WetlandsNational Forestry and Grassland Administration, Beijing Forestry UniversityBeijingChina
| | - Hongyan Cao
- State Key Laboratory of Efficient Production of Forest ResourcesBeijing Forestry UniversityBeijingChina
- The Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain WetlandsNational Forestry and Grassland Administration, Beijing Forestry UniversityBeijingChina
| | - Tingting Du
- State Key Laboratory of Efficient Production of Forest ResourcesBeijing Forestry UniversityBeijingChina
- The Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain WetlandsNational Forestry and Grassland Administration, Beijing Forestry UniversityBeijingChina
| | - Meng Qi
- State Key Laboratory of Efficient Production of Forest ResourcesBeijing Forestry UniversityBeijingChina
- The Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain WetlandsNational Forestry and Grassland Administration, Beijing Forestry UniversityBeijingChina
| | - Shengjie Wang
- State Key Laboratory of Efficient Production of Forest ResourcesBeijing Forestry UniversityBeijingChina
- The Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain WetlandsNational Forestry and Grassland Administration, Beijing Forestry UniversityBeijingChina
| | - Jingyi Xue
- State Key Laboratory of Efficient Production of Forest ResourcesBeijing Forestry UniversityBeijingChina
- The Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain WetlandsNational Forestry and Grassland Administration, Beijing Forestry UniversityBeijingChina
| | - Qing Yang
- State Key Laboratory of Efficient Production of Forest ResourcesBeijing Forestry UniversityBeijingChina
- The Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain WetlandsNational Forestry and Grassland Administration, Beijing Forestry UniversityBeijingChina
| | - Yujie Fu
- State Key Laboratory of Efficient Production of Forest ResourcesBeijing Forestry UniversityBeijingChina
- The Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain WetlandsNational Forestry and Grassland Administration, Beijing Forestry UniversityBeijingChina
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Sun X, Tang M, Xu L, Luo X, Shang Y, Duan W, Huang Z, Jin C, Chen G. Genome-wide identification of long non-coding RNAs and their potential functions in radish response to salt stress. Front Genet 2023; 14:1232363. [PMID: 38028592 PMCID: PMC10656690 DOI: 10.3389/fgene.2023.1232363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are increasingly recognized as cis- and trans-acting regulators of protein-coding genes in plants, particularly in response to abiotic stressors. Among these stressors, high soil salinity poses a significant challenge to crop productivity. Radish (Raphanus sativus L.) is a prominent root vegetable crop that exhibits moderate susceptibility to salt stress, particularly during the seedling stage. Nevertheless, the precise regulatory mechanisms through which lncRNAs contribute to salt response in radish remain largely unexplored. In this study, we performed genome-wide identification of lncRNAs using strand-specific RNA sequencing on radish fleshy root samples subjected to varying time points of salinity treatment. A total of 7,709 novel lncRNAs were identified, with 363 of them displaying significant differential expression in response to salt application. Furthermore, through target gene prediction, 5,006 cis- and 5,983 trans-target genes were obtained for the differentially expressed lncRNAs. The predicted target genes of these salt-responsive lncRNAs exhibited strong associations with various plant defense mechanisms, including signal perception and transduction, transcription regulation, ion homeostasis, osmoregulation, reactive oxygen species scavenging, photosynthesis, phytohormone regulation, and kinase activity. Notably, this study represents the first comprehensive genome-wide analysis of salt-responsive lncRNAs in radish, to the best of our knowledge. These findings provide a basis for future functional analysis of lncRNAs implicated in the defense response of radish against high salinity, which will aid in further understanding the regulatory mechanisms underlying radish response to salt stress.
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Affiliation(s)
- Xiaochuan Sun
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Mingjia Tang
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | - Liang Xu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xiaobo Luo
- Guizhou Institute of Biotechnology, Guizhou Province Academy of Agricultural Sciences, Guiyang, China
| | - Yutong Shang
- Guizhou Institute of Biotechnology, Guizhou Province Academy of Agricultural Sciences, Guiyang, China
| | - Weike Duan
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Zhinan Huang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Cong Jin
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Guodong Chen
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
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Pinky, Jain R, Yadav A, Sharma R, Dhaka N. Emerging roles of long non-coding RNAs in regulating agriculturally important seed traits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108019. [PMID: 37714026 DOI: 10.1016/j.plaphy.2023.108019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/26/2023] [Accepted: 09/06/2023] [Indexed: 09/17/2023]
Abstract
Seeds have enormous economic importance as source of calories, nutrition, edible oil, and biofuels. Therefore, seed traits like seed size and shape, weight, micronutrient content, oil content, quality, post-harvest sprouting, etc., are some of the main targets in crop improvement. Designing the strategies for their improvement benefits heavily from understanding the regulatory aspects of seed development. Recent studies indicate that long non-coding RNAs (lncRNAs) are one of the important regulators of seed development. They played a significant role in crop domestication by influencing seed traits. LncRNAs are conventionally defined as non-coding RNAs greater than 200 bp in length but lacking protein coding potential. Here we highlight the emerging pieces of evidence of lncRNA-mediated regulation of seed development through diverse mechanisms, for instance, by acting as target mimics or precursors of regulatory small RNAs or through chromatin remodeling and post-transcriptional repression. We also enumerate the insights from high-throughput transcriptomic studies from developing seeds of cereal, oilseed, biofuel, and pulse crops. We highlight the lncRNA candidates and lncRNA-mediated regulatory networks regulating seed development and related agronomic traits. Further, we discuss the potential of lncRNAs for improvement of agriculturally important seed traits through marker-assisted breeding and/or transgenic approaches.
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Affiliation(s)
- Pinky
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rubi Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Abhinandan Yadav
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India
| | - Rita Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani, Rajasthan, India
| | - Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana, India.
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Madhawan A, Bhunia RK, Kumar P, Sharma V, Sinha K, Fandade V, Rahim MS, Parveen A, Mishra A, Roy J. Interaction between long noncoding RNA (lnc663) and microRNA (miR1128) regulates PDAT-like gene activity in bread wheat (Triticum aestivum L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108040. [PMID: 37738867 DOI: 10.1016/j.plaphy.2023.108040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/21/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023]
Abstract
Amylose, a starch subcomponent, can bind lipids within its helical groove and form an amylose-lipid complex, known as resistant starch type 5 (RS-5). RS contributes to lower glycaemic index of grain with health benefits. Unfortunately, genes involved in lipid biosynthesis in wheat grain remain elusive. Our study aims to characterize the lipid biosynthesis gene and its post-transcriptional regulation using the parent bread wheat variety 'C 306' and its EMS-induced mutant line 'TAC 75' varying in amylose content. Quantitative analyses of starch-bound lipids showed that 'TAC 75' has significantly higher lipid content in grains than 'C 306' variety. Furthermore, expression analyses revealed the higher expression of wheat phospholipid: diacylglycerol acyltransferase-like (PDAT-like) in the 'TAC 75' compared to the 'C 306'. Overexpression and ectopic expression of TaPDAT in yeast and tobacco leaf confirmed its ability to accumulate lipids in vivo. Enzyme activity assay showed that TaPDAT catalyzes the triacylglycerol synthesis by acylating 1,2-diacylglycerol. Interestingly, the long non-coding RNA, lnc663, was upregulated with the TaPDAT gene, while the miRNA, miR1128, downregulated in the 'TAC 75', indicating a regulatory relationship. The GFP reporter assay confirmed that the lnc663 acts as a positive regulator, and the miR1128 as a negative regulator of the TaPDAT gene, which controls lipid accumulation in wheat grain. Our findings outline TaPDAT-mediated biosynthesis of lipid accumulation and reveal the molecular mechanism of the lnc663 and miR1128 mediated regulation of the TaPDAT gene in wheat grain.
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Affiliation(s)
- Akansha Madhawan
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India; Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
| | - Rupam Kumar Bhunia
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India; Plant Biotechnology Department, Gujarat Biotechnology University, Near Gujarat International Finance Tec (GIFT)-City, Gandhinagar, Gujarat, India.
| | - Prashant Kumar
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India; Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
| | - Vinita Sharma
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
| | - Kshitija Sinha
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
| | - Vikas Fandade
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India; Regional Centre for Biotechnology (RCB), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana, 121001, India.
| | - Mohammed Saba Rahim
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
| | - Afsana Parveen
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
| | - Ankita Mishra
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
| | - Joy Roy
- Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
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Zhang Y, Chen G, Deng L, Gao B, Yang J, Ding C, Zhang Q, Ouyang W, Guo M, Wang W, Liu B, Zhang Q, Sung WK, Yan J, Li G, Li X. Integrated 3D genome, epigenome and transcriptome analyses reveal transcriptional coordination of circadian rhythm in rice. Nucleic Acids Res 2023; 51:9001-9018. [PMID: 37572350 PMCID: PMC10516653 DOI: 10.1093/nar/gkad658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 07/11/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023] Open
Abstract
Photoperiods integrate with the circadian clock to coordinate gene expression rhythms and thus ensure plant fitness to the environment. Genome-wide characterization and comparison of rhythmic genes under different light conditions revealed delayed phase under constant darkness (DD) and reduced amplitude under constant light (LL) in rice. Interestingly, ChIP-seq and RNA-seq profiling of rhythmic genes exhibit synchronous circadian oscillation in H3K9ac modifications at their loci and long non-coding RNAs (lncRNAs) expression at proximal loci. To investigate how gene expression rhythm is regulated in rice, we profiled the open chromatin regions and transcription factor (TF) footprints by time-series ATAC-seq. Although open chromatin regions did not show circadian change, a significant number of TFs were identified to rhythmically associate with chromatin and drive gene expression in a time-dependent manner. Further transcriptional regulatory networks mapping uncovered significant correlation between core clock genes and transcription factors involved in light/temperature signaling. In situ Hi-C of ZT8-specific expressed genes displayed highly connected chromatin association at the same time, whereas this ZT8 chromatin connection network dissociates at ZT20, suggesting the circadian control of gene expression by dynamic spatial chromatin conformation. These findings together implicate the existence of a synchronization mechanism between circadian H3K9ac modifications, chromatin association of TF and gene expression, and provides insights into circadian dynamics of spatial chromatin conformation that associate with gene expression rhythms.
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Affiliation(s)
- Ying Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoting Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Li Deng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Baibai Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Jing Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Cheng Ding
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Minrong Guo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wenxia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Beibei Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Qinghua Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Wing-Kin Sung
- Department of Chemical Pathology, Chinese University of Hong Kong, Hong Kong, China
| | - Jiapei Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Laboratory of Agricultural Bioinformatics, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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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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7
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Pronozin AY, Afonnikov DA. ICAnnoLncRNA: A Snakemake Pipeline for a Long Non-Coding-RNA Search and Annotation in Transcriptomic Sequences. Genes (Basel) 2023; 14:1331. [PMID: 37510236 PMCID: PMC10379598 DOI: 10.3390/genes14071331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are RNA molecules longer than 200 nucleotides that do not encode proteins. Experimental studies have shown the diversity and importance of lncRNA functions in plants. To expand knowledge about lncRNAs in other species, computational pipelines that allow for standardised data-processing steps in a mode that does not require user control up until the final result were actively developed recently. These advancements enable wider functionality for lncRNA data identification and analysis. In the present work, we propose the ICAnnoLncRNA pipeline for the automatic identification, classification and annotation of plant lncRNAs in assembled transcriptomic sequences. It uses the LncFinder software for the identification of lncRNAs and allows the adjustment of recognition parameters using genomic data for which lncRNA annotation is available. The pipeline allows the prediction of lncRNA candidates, alignment of lncRNA sequences to the reference genome, filtering of erroneous/noise transcripts and probable transposable elements, lncRNA classification by genome location, comparison with sequences from external databases and analysis of lncRNA structural features and expression. We used transcriptomic sequences from 15 maize libraries assembled by Trinity and Hisat2/StringTie to demonstrate the application of the ICAnnoLncRNA pipeline.
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Affiliation(s)
- Artem Yu Pronozin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Dmitry A Afonnikov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Center for Genome Research, Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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8
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Singh A, AT V, Gupta K, Sharma S, Kumar S. Long non-coding RNA and microRNA landscape of two major domesticated cotton species. Comput Struct Biotechnol J 2023; 21:3032-3044. [PMID: 37266406 PMCID: PMC10229759 DOI: 10.1016/j.csbj.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/11/2023] [Accepted: 05/11/2023] [Indexed: 06/03/2023] Open
Abstract
Allotetraploid cotton plants Gossypium hirsutum and Gossypium barbadense have been widely cultivated for their natural, renewable textile fibres. Even though ncRNAs in domesticated cotton species have been extensively studied, systematic identification and annotation of lncRNAs and miRNAs expressed in various tissues and developmental stages under various biological contexts are limited. This influences the comprehension of their functions and future research on these cotton species. Here, we report high confidence lncRNAs and miRNA collection from G. hirsutum accession and G. barbadense accession using large-scale RNA-seq and small RNA-seq datasets incorporated into a user-friendly database, CoNCRAtlas. This database provides a wide range and depth of lncRNA and miRNA annotation based on the systematic integration of extensive annotations such as expression patterns derived from transcriptome data analysis in thousands of samples, as well as multi-omics annotations. We assume this comprehensive resource will accelerate evolutionary and functional studies in ncRNAs and inform future breeding programs for cotton improvement. CoNCRAtlas is accessible at http://www.nipgr.ac.in/CoNCRAtlas/.
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Affiliation(s)
- Ajeet Singh
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
- Postdoctoral Associate, Ophthalmology, Baylor College of Medicine, Houston, TX, USA
| | - Vivek AT
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Kanika Gupta
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Shruti Sharma
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
| | - Shailesh Kumar
- Bioinformatics Lab, National Institute of Plant Genome Research, New Delhi 110067, India
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Saxena S, Das A, Kaila T, Ramakrishna G, Sharma S, Gaikwad K. Genomic survey of high-throughput RNA-Seq data implicates involvement of long intergenic non-coding RNAs (lincRNAs) in cytoplasmic male-sterility and fertility restoration in pigeon pea. Genes Genomics 2023; 45:783-811. [PMID: 37115379 DOI: 10.1007/s13258-023-01383-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/21/2022] [Indexed: 04/29/2023]
Abstract
BACKGROUND Long-intergenic non-coding RNAs (lincRNAs) originate from intergenic regions and have no coding potential. LincRNAs have emerged as key players in the regulation of various biological processes in plant development. Cytoplasmic male-sterility (CMS) in association with restorer-of-fertility (Rf) systems makes it a highly reliable tool for exploring heterosis for producing commercial hybrid seeds. To date, there have been no reports of lincRNAs during pollen development in CMS and fertility restorer lines in pigeon pea. OBJECTIVE Identification of lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines. METHODS We employed a computational approach to identify lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines using RNA-Seq data. RESULTS We predicted a total of 2145 potential lincRNAs of which 966 were observed to be differentially expressed between the sterile and fertile pollen. We identified, 927 cis-regulated and 383 trans-regulated target genes of the lincRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the target genes revealed that these genes were specifically enriched in pathways like pollen and pollen tube development, oxidative phosphorylation, etc. We detected 23 lincRNAs that were co-expressed with 17 pollen-related genes with known functions. Fifty-nine lincRNAs were predicted to be endogenous target mimics (eTMs) for 25 miRNAs, and found to be associated with pollen development. The, lincRNA regulatory networks revealed that different lincRNA-miRNA-mRNA networks might be associated with CMS and fertility restoration. CONCLUSION Thus, this study provides valuable information by highlighting the functions of lincRNAs as regulators during pollen development in pigeon pea and utilization in hybrid seed production.
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Affiliation(s)
- Swati Saxena
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Antara Das
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Tanvi Kaila
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - G Ramakrishna
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi, 110012, India.
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Kumar B, Saha B, Jaiswal S, Angadi UB, Rai A, Iquebal MA. Genome-wide identification and characterization of tissue-specific non-coding RNAs in black pepper ( Piper nigrum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1079221. [PMID: 37008483 PMCID: PMC10060637 DOI: 10.3389/fpls.2023.1079221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/08/2023] [Indexed: 06/19/2023]
Abstract
Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are the two classes of non-coding RNAs (ncRNAs) present predominantly in plant cells and have various gene regulatory functions at pre- and post-transcriptional levels. Previously deemed as "junk", these ncRNAs have now been reported to be an important player in gene expression regulation, especially in stress conditions in many plant species. Black pepper, scientifically known as Piper nigrum L., despite being one of the most economically important spice crops, lacks studies related to these ncRNAs. From a panel of 53 RNA-Seq datasets of black pepper from six tissues, namely, flower, fruit, leaf, panicle, root, and stem of six black pepper cultivars, covering eight BioProjects across four countries, we identified and characterized a total of 6406 lncRNAs. Further downstream analysis inferred that these lncRNAs regulated 781 black pepper genes/gene products via miRNA-lncRNA-mRNA network interactions, thus working as competitive endogenous RNAs (ceRNAs). The interactions may be various mechanisms like miRNA-mediated gene silencing or lncRNAs acting as endogenous target mimics (eTMs) of the miRNAs. A total of 35 lncRNAs were also identified to be potential precursors of 94 miRNAs after being acted upon by endonucleases like Drosha and Dicer. Tissue-wise transcriptome analysis revealed 4621 circRNAs. Further, miRNA-circRNA-mRNA network analysis showed 432 circRNAs combining with 619 miRNAs and competing for the binding sites on 744 mRNAs in different black pepper tissues. These findings can help researchers to get a better insight to the yield regulation and responses to stress in black pepper in endeavor of higher production and improved breeding programs in black pepper varieties.
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Soorni A, Karimi M, Al Sharif B, Habibi K. Genome-wide screening and characterization of long noncoding RNAs involved in flowering/bolting of Lactuca sativa. BMC PLANT BIOLOGY 2023; 23:3. [PMID: 36588159 PMCID: PMC9806901 DOI: 10.1186/s12870-022-04031-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Lettuce (Lactuca sativa L.) is considered the most important vegetable in the leafy vegetable group. However, bolting affects quality, gives it a bitter taste, and as a result makes it inedible. Bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although bolting/flowering responsive genes have been identified in most sensitive and non-sensitive species, non-coding RNA molecules like long non-coding RNAs (lncRNAs) have not been investigated in lettuce. Hence, in this study, potential long non-coding RNAs that regulate flowering /bolting were investigated in two lettuce strains S24 (resistant strain) and S39 (susceptible strain) in different flowering times to better understand the regulation of lettuce bolting mechanism. For this purpose, we used two RNA-seq datasets to discover the lncRNA transcriptome profile during the transition from vegetative to reproductive phase. RESULTS For identifying unannotated transcripts in these datasets, a 7-step pipeline was employed to filter out these transcripts and terminate with 293 novel lncRNAs predicted by PLncPRO and CREMA. These transcripts were then utilized to predict cis and trans flowering-associated targets and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Computational predictions of target gene function showed the involvement of putative flowering-related genes and enrichment of the floral regulators FLC, CO, FT, and SOC1 in both datasets. Finally, 17 and 18 lncRNAs were proposed as competing endogenous target mimics (eTMs) for novel and known lncRNA miRNAs, respectively. CONCLUSION Overall, this study provides new insights into lncRNAs that control the flowering time of plants known for bolting, such as lettuce, and opens new windows for further study.
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Affiliation(s)
- Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
| | | | - Batoul Al Sharif
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Khashayar Habibi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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12
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KIM EOJIN, KIM HYUNJIN, YEO MINKYUNG, KIM CHULHWAN, KIM JOOYOUNG, PARK SUNGSOO, KIM HYUNSOO, CHAE YANGSEOK. Identification of a Novel Long Non-coding RNA, lnc-ATMIN-4:2, and its Clinicopathological and Prognostic Significance in Advanced Gastric Cancer. Cancer Genomics Proteomics 2022; 19:761-772. [PMID: 36316044 PMCID: PMC9620448 DOI: 10.21873/cgp.20358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND/AIM Long non-coding RNAs (lncRNAs) are emerging as significant regulators of gene expression and a novel promising biomarker for cancer diagnosis and prognosis. This study identified a novel, differentially expressed lncRNA in advanced gastric cancer (AGC), Inc-ATMIN-4:2, and evaluated its clinicopathological and prognostic significance. PATIENTS AND METHODS Whole transcriptome sequencing was performed to identify differentially expressed lncRNAs in AGC tissue samples. We also analyzed lnc-ATMIN-4:2 expression in 317 patients with AGC using RNA in situ hybridization. RESULTS High (>30 dots) lnc-ATMIN-4:2 expression significantly correlated with younger age, poorly differentiated histology, diffuse type, deeper invasion depth, perineural invasion, lymph node metastasis, and higher stage group. In addition, high lnc-ATMIN-4:2 expression was significantly associated with worse overall survival in patients with AGC. CONCLUSION This study elucidated the significance of lncRNAs in AGC and indicated the value of lnc-ATMIN-4:2 expression as a predictive biomarker for the overall survival of patients with AGC.
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Affiliation(s)
- EOJIN KIM
- Department of Pathology, Korea University College of Medicine, Seoul, Republic of Korea
| | - HYUNJIN KIM
- Pathology Center, Seegene Medical Foundation, Seoul, Republic of Korea
| | - MIN-KYUNG YEO
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - CHUL HWAN KIM
- Department of Pathology, Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
| | - JOO YOUNG KIM
- Department of Pathology, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Republic of Korea
| | - SUNGSOO PARK
- Division of Foregut Surgery, Korea University College of Medicine, Seoul, Republic of Korea
| | - HYUN-SOO KIM
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - YANG-SEOK CHAE
- Department of Pathology, Korea University College of Medicine, Seoul, Republic of Korea,Department of Pathology, Anam Hospital, Korea University College of Medicine, Seoul, Republic of Korea
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Khemka N, Rajkumar MS, Garg R, Jain M. Genome-wide analysis suggests the potential role of lncRNAs during seed development and seed size/weight determination in chickpea. PLANTA 2022; 256:79. [PMID: 36094579 DOI: 10.1007/s00425-022-03986-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The integrated transcriptome data analyses suggested the plausible roles of lncRNAs during seed development in chickpea. The candidate lncRNAs associated with QTLs and those involved in miRNA-mediated seed size/weight determination in chickpea have been identified. Long non-coding RNAs (lncRNAs) are important regulators of various biological processes. Here, we identified lncRNAs at seven successive stages of seed development in small-seeded and large-seeded chickpea cultivars. In total, 4751 lncRNAs implicated in diverse biological processes were identified. Most of lncRNAs were conserved between the two cultivars, whereas only a few of them were conserved in other plants, suggesting their species-specificity. A large number of lncRNAs differentially expressed between the two chickpea cultivars associated with seed development-related processes were identified. The lncRNAs acting as precursors of miRNAs and those mimicking target protein-coding genes of miRNAs involved in seed size/weight determination, including HAIKU1, BIG SEEDS1, and SHB1, were also revealed. Further, lncRNAs located within seed size/weight associated quantitative trait loci were also detected. Overall, we present a comprehensive resource and identified candidate lncRNAs that may play important roles during seed development and seed size/weight determination in chickpea.
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Affiliation(s)
- Niraj Khemka
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mohan Singh Rajkumar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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14
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Zhao Z, Zang S, Zou W, Pan YB, Yao W, You C, Que Y. Long Non-Coding RNAs: New Players in Plants. Int J Mol Sci 2022; 23:ijms23169301. [PMID: 36012566 PMCID: PMC9409372 DOI: 10.3390/ijms23169301] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/14/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
During the process of growth and development, plants are prone to various biotic and abiotic stresses. They have evolved a variety of strategies to resist the adverse effects of these stresses. lncRNAs (long non-coding RNAs) are a type of less conserved RNA molecules of more than 200 nt (nucleotides) in length. lncRNAs do not code for any protein, but interact with DNA, RNA, and protein to affect transcriptional, posttranscriptional, and epigenetic modulation events. As a new regulatory element, lncRNAs play a critical role in coping with environmental pressure during plant growth and development. This article presents a comprehensive review on the types of plant lncRNAs, the role and mechanism of lncRNAs at different molecular levels, the coordination between lncRNA and miRNA (microRNA) in plant immune responses, the latest research progress of lncRNAs in plant growth and development, and their response to biotic and abiotic stresses. We conclude with a discussion on future direction for the elaboration of the function and mechanism of lncRNAs.
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Affiliation(s)
- Zhennan Zhao
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shoujian Zang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenhui Zou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yong-Bao Pan
- Sugarcane Research Unit, USDA-ARS, Houma, LA 70360, USA
| | - Wei Yao
- Guangxi Key Laboratory for Sugarcane Biology & State Key Laboratory for Conservation and Utilization of Agro Bioresources, Guangxi University, Nanning 530005, China
| | - Cuihuai You
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (C.Y.); (Y.Q.); Tel.: +86-591-8385-2547 (C.Y. & Y.Q.)
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15
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Chowdhury SG, Bhattacharya D, Karmakar P. Exosomal long noncoding RNAs - the lead thespian behind the regulation, cause and cure of autophagy-related diseases. Mol Biol Rep 2022; 49:7013-7024. [PMID: 35655053 DOI: 10.1007/s11033-022-07514-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/06/2022] [Accepted: 04/25/2022] [Indexed: 11/26/2022]
Abstract
Recent advances in exosome biology have revealed significant roles of exosome and their contents in intercellular communication. Among various exosomal content, long non-coding RNAs (lncRNAs), which have a large size (˃ 200 nt) and lack protein coding potential, are known to play key roles in intercellular communication and novel biomarkers of various metabolic disorders. Moreover, long non-coding RNAs are often involved in the regulation of various cellular processes such as autophagy, apoptosis, cell proliferation. On the other hand, autophagy is the central regulating point that controls the various metabolic functions of the body. This process is known to prevent diseases and promote longevity. Therefore, the present review discusses the relationship between diseases and autophagy, and also look into the biological functions of exosome-associated lncRNAs in regulating autophagy. Furthermore, this review will summarize some of the studies that provide novel insights into the pathogenesis of autophagy-related diseases followed by the non-canonical roles played by autophagy and related proteins in the development of exosome biogenesis.
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Affiliation(s)
| | | | - Parimal Karmakar
- Department of Life Science and Biotechnology, Jadavpur University, 700032, Kolkata, India.
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16
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Wang L, Gao J, Wang C, Xu Y, Li X, Yang J, Chen K, Kang Y, Wang Y, Cao P, Xie X. Comprehensive Analysis of Long Non-coding RNA Modulates Axillary Bud Development in Tobacco ( Nicotiana tabacum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:809435. [PMID: 35237286 PMCID: PMC8884251 DOI: 10.3389/fpls.2022.809435] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Long non-coding RNAs (lncRNAs) regulate gene expression and are crucial for plant growth and development. However, the mechanisms underlying the effects of activated lncRNAs on axillary bud development remain largely unknown. By lncRNA transcriptomes of axillary buds in topped and untopped tobacco plants, we identified a total of 13,694 lncRNAs. LncRNA analysis indicated that the promoted growth of axillary bud by topping might be partially ascribed to the genes related to hormone signal transduction and glycometabolism, trans-regulated by differentially expressed lncRNAs, such as MSTRG.52498.1, MSTRG.60026.1, MSTRG.17770.1, and MSTRG.32431.1. Metabolite profiling indicated that auxin, abscisic acid and gibberellin were decreased in axillary buds of topped tobacco lines, while cytokinin was increased, consistent with the expression levels of related lncRNAs. MSTRG.52498.1, MSTRG.60026.1, MSTRG.17770.1, and MSTRG.32431.1 were shown to be influenced by hormones and sucrose treatments, and were associated with changes of axillary bud growth in the overexpression of NtCCD8 plants (with reduced axillary buds) and RNA interference of NtTB1 plants (with increased axillary buds). Moreover, MSTRG.28151.1 was identified as the antisense lncRNA of NtTB1. Silencing of MSTRG.28151.1 in tobacco significantly attenuated the expression of NtTB1 and resulted in larger axillary buds, suggesting the vital function of MSTRG.28151.1 axillary bud developmen by NtTB1. Our findings shed light on lncRNA-mRNA interactions and their functional roles in axillary bud growth, which would improve our understanding of lncRNAs as important regulators of axillary bud development and plant architecture.
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Affiliation(s)
- Lin Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Junping Gao
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Chen Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Yalong Xu
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Xiaoxu Li
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Jun Yang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Kai Chen
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Yile Kang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Yaofu Wang
- China Tobacco Hunan Industrial Co., Ltd., Changsha, China
| | - Peijian Cao
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
| | - Xiaodong Xie
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of China National Tobacco Corporation (CNTC), Zhengzhou, China
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Khoei MA, Karimi M, Karamian R, Amini S, Soorni A. Identification of the Complex Interplay Between Nematode-Related lncRNAs and Their Target Genes in Glycine max L. FRONTIERS IN PLANT SCIENCE 2021; 12:779597. [PMID: 34956274 PMCID: PMC8705754 DOI: 10.3389/fpls.2021.779597] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/08/2021] [Indexed: 05/26/2023]
Abstract
Soybean (Glycine max) is a major plant protein source and oilseed crop. However, plant-parasitic nematodes (PPNs) affect its annual yield. In the current study, in order to better understand the regulation of defense mechanism against PPNs in soybean, we investigated the role of long non-coding RNAs (lncRNAs) in response to two nematode species, Heterodera glycines (SCN: soybean cyst nematode) and Rotylenchulus reniformis (reniform). To this end, two publicly available RNA-seq data sets (SCN data set and RAD: reniform-associated data set) were employed to discover the lncRNAome profile of soybean under SCN and reniform infection, respectively. Upon identification of unannotated transcripts in these data sets, a seven-step pipeline was utilized to sieve these transcripts, which ended up in 384 and 283 potential lncRNAs in SCN data set and RAD, respectively. These transcripts were then used to predict cis and trans nematode-related targets in soybean genome. Computational prediction of target genes function, some of which were also among differentially expressed genes, revealed the involvement of putative nematode-responsive genes as well as enrichment of multiple stress responses in both data sets. Finally, 15 and six lncRNAs were proposed to be involved in microRNA-mediated regulation of gene expression in soybean in response to SNC and reniform infection, respectively. Collectively, this study provides a novel insight into the signaling and regulatory network of soybean-pathogen interactions and opens a new window for further research.
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Affiliation(s)
| | | | - Roya Karamian
- Department of Biology, Faculty of Sciences, Bu-Ali Sina University, Hamedan, Iran
| | | | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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Patturaj M, Munusamy A, Kannan N, Ramasamy Y. Biologia Futura: progress and future perspectives of long non-coding RNAs in forest trees. Biol Futur 2021; 73:43-53. [PMID: 34843103 DOI: 10.1007/s42977-021-00108-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
Forest trees are affected by climate change, anthropogenic pressure, as well as abiotic and biotic stresses. Conventional tree breeding has so far been limited to enhance overall productivity, and our understanding of the genetic basis of quantitative traits is still inadequate. Quantum leaps in next-generation sequencing technologies and bioinformatics have permitted the exploration and identification of various non-coding regions of the genome other than protein coding genes. These genomic regions produce various types of non-coding RNAs and regulate myriads of biological functions at epigenetic, transcriptional and translational levels. Recently, long non-coding RNAs (lncRNAs) which act as molecular switch have been identified to be pivotal molecules in forest trees. This review focuses on progress made in regulatory mechanisms in various developmental phases like wood formation, adventitious rooting and flowering and stress responses. It was predicted that complex regulatory interactions among lncRNA, miRNA and gene exist. LncRNAs can function as a sponge for miRNAs, reducing the suppressive effect of miRNAs on target mRNAs and perhaps adding a new layer of regulatory interactions among non-coding RNA classes in trees. Furthermore, network analysis revealed the interactions of lncRNA and genes during the expression of several important genes. The insights generated about lncRNAs in forest trees would enable improvement of economically important traits including the devastating abiotic and biotic stresses. In addition, solid understanding on the wide range of regulatory functions of lncRNAs on traits influencing biomass productivity and adaptation would aid the applications of biotechnology in genetic improvement of forest trees.
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Affiliation(s)
- Maheswari Patturaj
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India
| | - Aiswarya Munusamy
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India
| | - Nithishkumar Kannan
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India
| | - Yasodha Ramasamy
- Division of Plant Biotechnology and Cytogenetics, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002, India.
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