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Zhang A, Pi W, Wang Y, Li Y, Wang J, Liu S, Cui X, Liu H, Yao D, Zhao R. Update on functional analysis of long non-coding RNAs in common crops. FRONTIERS IN PLANT SCIENCE 2024; 15:1389154. [PMID: 38872885 PMCID: PMC11169716 DOI: 10.3389/fpls.2024.1389154] [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: 02/21/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024]
Abstract
With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional RNAs comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes have been extensively investigated in animals, there has been considerably less research on plant lncRNAs. Nevertheless, multiple studies on major crops showed lncRNAs are involved in crucial processes, including growth and development, reproduction, and stress responses. This review summarizes the progress in the research on lncRNA roles in several major crops, presents key strategies for exploring lncRNAs in crops, and discusses current challenges and future prospects. The insights provided in this review will enhance our comprehension of lncRNA functions in crops, with potential implications for improving crop genetics and breeding.
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Affiliation(s)
- Aijing Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
- College of Agronomy, Jilin Agricultural University, Changchun, China
| | - Wenxuan Pi
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yashuo Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yuxin Li
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Jiaxin Wang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Shuying Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiyan Cui
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Huijing Liu
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Rengui Zhao
- College of Agronomy, Jilin Agricultural University, Changchun, China
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Weng M, Zhang D, Wang H, Yang C, Lin H, Pan Y, Lin Y. Long non-coding RNAs and their potential function in response to postharvest senescence of Sparassis latifolia during cold storage. Sci Rep 2024; 14:747. [PMID: 38185662 PMCID: PMC10772075 DOI: 10.1038/s41598-023-46744-2] [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: 05/15/2023] [Accepted: 11/04/2023] [Indexed: 01/09/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) have been shown to play crucial roles in response to aging processes. However, how lncRNAs regulate postharvest senescence of Sparassis latifolia (S. latifolia) with oriented polypropylene (OPP) film packing during cold storage remains unclear. In this study, we performed RNA-seq using the fruiting bodies of S. latifolia stored at 4 ℃ for 0, 8, 16 and 24 days after harvest, and profiled the lncRNA and mRNA transcriptome, respectively. In total, 1003 putative lncRNAs were identified, and there were 495, 483 and 162 differentially expressed (DE) lncRNAs, and 3680, 3941 and 1870 differentially expressed mRNAs after 8, 16 and 24 days of storage, respectively, compared to 0 day of storage. Target genes of differentially expressed lncRNAs were found to significantly associate with carbon and energy metabolism, response to abiotic stimulus, amino acid biosynthesis and metabolism, and protein synthesis and transcription. In addition, DE-lncRNA-mRNA co-expression networks in response to aging stress were also constructed. Taken together, these results confirm the regulatory role of lncRNAs in postharvest senescence of S. latifolia and will facilitate for improving preservation method.
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Affiliation(s)
- Mengting Weng
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Di Zhang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Hongyu Wang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Chi Yang
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Hongyi Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China
| | - Yanfang Pan
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Yanquan Lin
- Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China.
- National and Local Joint Engineering Research Center for Breeding & Cultivation of Featured Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou, 350014, China.
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Huang J, Liu M, Chen H, Zhang J, Xie X, Jiang L, Zhang S, Jiang C, Zhang J, Zhang Q, Yang G, Chi H, Tian G. Elucidating the Influence of MPT-driven necrosis-linked LncRNAs on immunotherapy outcomes, sensitivity to chemotherapy, and mechanisms of cell death in clear cell renal carcinoma. Front Oncol 2023; 13:1276715. [PMID: 38162499 PMCID: PMC10757362 DOI: 10.3389/fonc.2023.1276715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 11/26/2023] [Indexed: 01/03/2024] Open
Abstract
Background Clear cell renal carcinoma (ccRCC) stands as the prevailing subtype among kidney cancers, making it one of the most prevalent malignancies characterized by significant mortality rates. Notably,mitochondrial permeability transition drives necrosis (MPT-Driven Necrosis) emerges as a form of cell death triggered by alterations in the intracellular microenvironment. MPT-Driven Necrosis, recognized as a distinctive type of programmed cell death. Despite the association of MPT-Driven Necrosis programmed-cell-death-related lncRNAs (MPTDNLs) with ccRCC, their precise functions within the tumor microenvironment and prognostic implications remain poorly understood. Therefore, this study aimed to develop a novel prognostic model that enhances prognostic predictions for ccRCC. Methods Employing both univariate Cox proportional hazards and Lasso regression methodologies, this investigation distinguished genes with differential expression that are intimately linked to prognosis.Furthermore, a comprehensive prognostic risk assessment model was established using multiple Cox proportional hazards regression. Additionally, a thorough evaluation was conducted to explore the associations between the characteristics of MPTDNLs and clinicopathological features, tumor microenvironment, and chemotherapy sensitivity, thereby providing insights into their interconnectedness.The model constructed based on the signatures of MPTDNLs was verified to exhibit excellent prediction performance by Cell Culture and Transient Transfection, Transwell and other experiments. Results By analyzing relevant studies, we identified risk scores derived from MPTDNLs as an independent prognostic determinant for ccRCC, and subsequently we developed a Nomogram prediction model that combines clinical features and associated risk assessment. Finally, the application of experimental techniques such as qRT-PCR helped to compare the expression of MPTDNLs in healthy tissues and tumor samples, as well as their role in the proliferation and migration of renal clear cell carcinoma cells. It was found that there was a significant correlation between CDK6-AS1 and ccRCC results, and CDK6-AS1 plays a key role in the proliferation and migration of ccRCC cells. Impressive predictive results were generated using marker constructs based on these MPTDNLs. Conclusions In this research, we formulated a new prognostic framework for ccRCC, integrating mitochondrial permeability transition-induced necrosis. This model holds significant potential for enhancing prognostic predictions in ccRCC patients and establishing a foundation for optimizing therapeutic strategies.
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Affiliation(s)
- Jinbang Huang
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Mengtao Liu
- Pediatric Surgery, Guiyang Matemal and Child Health Care Hospital, Guiyang Children’s Hospital, Guiyang, China
| | - Haiqing Chen
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinhao Zhang
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Xixi Xie
- School of Stomatology, Southwest Medical University, Luzhou, China
| | - Lai Jiang
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Shengke Zhang
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chenglu Jiang
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jieying Zhang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
- National Clinical Research Center for Chinese Medicine Acupuncture and Moxibustion, Tianjin, China
| | - Qinhong Zhang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, GA, United States
| | - Hao Chi
- School of Clinical Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Gang Tian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Luzhou, China
- Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Luzhou, China
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Yang X, Liu C, Tang Q, Zhang T, Wang L, Han L, Zhang J, Pei X. Identification of LncRNAs and Functional Analysis of ceRNA Related to Fatty Acid Synthesis during Flax Seed Development. Genes (Basel) 2023; 14:genes14050967. [PMID: 37239327 DOI: 10.3390/genes14050967] [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: 02/27/2023] [Revised: 04/01/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
Flax is a flowering plant cultivated for its oil and contains various unsaturated fatty acids. Linseed oil is known as the "deep-sea fish oil" of plants, and is beneficial to brain and blood lipids, among other positive effects. Long non-coding RNAs (lncRNAs) play an important role in plant growth and development. There are not many studies assessing how lncRNAs are related to the fatty acid synthesis of flax. The relative oil contents of the seeds of the variety Heiya NO.14 (for fiber) and the variety Macbeth (for oil) were determined at 5 day, 10 day, 20 day, and 30 day after flowering. We found that 10-20 day is an important period for ALA accumulation in the Macbeth variety. The strand-specific transcriptome data were analyzed at these four time points, and a series of lncRNAs related to flax seed development were screened. A competing endogenous RNA (ceRNA) network was constructed and the accuracy of the network was verified using qRT-PCR. MSTRG.20631.1 could act with miR156 on the same target, squamosa promoter-binding-like protein (SPL), to influence fatty acid biosynthesis through a gluconeogenesis-related pathway during flax seed development. This study provides a theoretical basis for future studies assessing the potential functions of lncRNAs during seed development.
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Affiliation(s)
- Xinsen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caiyue Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiaoling Tang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tianbao Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Limin Wang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Lida Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianping Zhang
- Crop Institute, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Sun CF, Guo Y, Kataria A, Annamalai S, Malik K, Cheng JT. Comprehensive investigation of long non-coding RNAs in an endophytic fungus Calcarisporium arbuscula NRRL 3705. Arch Microbiol 2023; 205:153. [PMID: 37000333 DOI: 10.1007/s00203-023-03494-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 03/15/2023] [Accepted: 03/19/2023] [Indexed: 04/01/2023]
Abstract
Long non-coding RNAs (lncRNAs) play an important role in eukaryotic cells. However, there is no report of lncRNAs in endophytic fungi Calcarisporium arbuscula. Here, in Calcarisporium arbuscula NRRL 3705, an endophytic fungus predominantly producing mycotoxins aurovertins, the genome-wide identification of lncRNAs was carried out based on RNA-Seq. Totally, 1332 lncRNAs were identified, including 1082 long intergenic noncoding RNAs, 64 long intronic noncoding RNAs and 186 long noncoding natural antisense transcripts. The average length of lncRNA and mRNA were 254 and 1102 bp, respectively. LncRNAs were shorter, with fewer exons and lower expression levels. Moreover, there were 39 up-regulated lncRNAs and 10 down-regulated lncRNAs in the ΔaurA mutant, which lacks the aurovertin biosynthetic enzyme AurA. Interestingly, expression of genes related to the metabolism of linoleic acid and methane were significantly down regulated in the ΔaurA mutant. This study enriches the endophytic fungal lncRNA database and provide a basis for further research.
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Affiliation(s)
- Chen-Fan Sun
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China
| | - Yuliang Guo
- Dublin High School, 8151 Village Parkway, Dublin, CA, 94568, USA
| | - Anish Kataria
- Dublin High School, 8151 Village Parkway, Dublin, CA, 94568, USA
| | - Shivam Annamalai
- Dublin High School, 8151 Village Parkway, Dublin, CA, 94568, USA
| | - Krish Malik
- Dublin High School, 8151 Village Parkway, Dublin, CA, 94568, USA
| | - Jin-Tao Cheng
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
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Li Y, Tan Z, Zeng C, Xiao M, Lin S, Yao W, Li Q, Guo L, Lu S. Regulation of seed oil accumulation by lncRNAs in Brassica napus. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:22. [PMID: 36765368 PMCID: PMC9921586 DOI: 10.1186/s13068-022-02256-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/28/2022] [Indexed: 02/12/2023]
Abstract
BACKGROUND Studies have indicated that long non-coding RNAs (lncRNAs) play important regulatory roles in many biological processes. However, the regulation of seed oil biosynthesis by lncRNAs remains largely unknown. RESULTS We comprehensively identified and characterized the lncRNAs from seeds in three developing stages in two accessions of Brassica napus (B. napus), ZS11 (high oil content) and WH5557 (low oil content). Finally, 8094 expressed lncRNAs were identified. LncRNAs MSTRG.22563 and MSTRG.86004 were predicted to be related to seed oil accumulation. Experimental results show that the seed oil content is decreased by 3.1-3.9% in MSTRG.22563 overexpression plants, while increased about 2% in MSTRG.86004, compared to WT. Further study showed that most genes related to lipid metabolism had much lower expression, and the content of some metabolites in the processes of respiration and TCA (tricarboxylic acid) cycle was reduced in MSTRG.22563 transgenic seeds. The expression of genes involved in fatty acid synthesis and seed embryonic development (e.g., LEC1) was increased, but genes related to TAG assembly was decreased in MSTRG.86004 transgenic seeds. CONCLUSION Our results suggest that MSTRG.22563 might impact seed oil content by affecting the respiration and TCA cycle, while MSTRG.86004 plays a role in prolonging the seed developmental time to increase seed oil accumulation.
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Affiliation(s)
- Yuqing Li
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Zengdong Tan
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Chenghao Zeng
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Mengying Xiao
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Shengli Lin
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Wei Yao
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Qing Li
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China
| | - Liang Guo
- grid.35155.370000 0004 1790 4137National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China ,Hubei Hongshan Laboratory, Wuhan, 430070 China ,grid.35155.370000 0004 1790 4137Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070 China ,grid.410727.70000 0001 0526 1937Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Genome Analysis Laboratory of the Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Shenzhen, 518120 China
| | - Shaoping Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China. .,Hubei Hongshan Laboratory, Wuhan, 430070, China.
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Fan K, Sze CC, Li MW, Lam HM. Roles of non-coding RNAs in the hormonal and nutritional regulation in nodulation and nitrogen fixation. FRONTIERS IN PLANT SCIENCE 2022; 13:997037. [PMID: 36330261 PMCID: PMC9623164 DOI: 10.3389/fpls.2022.997037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Symbiotic nitrogen fixation is an important component in the nitrogen cycle and is a potential solution for sustainable agriculture. It is the result of the interactions between the plant host, mostly restricted to legume species, and the rhizobial symbiont. From the first encounter between the host and the symbiont to eventual successful nitrogen fixation, there are delicate processes involved, such as nodule organogenesis, rhizobial infection thread progression, differentiation of the bacteroid, deregulation of the host defense systems, and reallocation of resources. All these processes are tightly regulated at different levels. Recent evidence revealed that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), participate in these processes by controlling the transcription and translation of effector genes. In general, ncRNAs are functional transcripts without translation potential and are important gene regulators. MiRNAs, negative gene regulators, bind to the target mRNAs and repress protein production by causing the cleavage of mRNA and translational silencing. LncRNAs affect the formation of chromosomal loops, DNA methylation, histone modification, and alternative splicing to modulate gene expression. Both lncRNAs and circRNAs could serve as target mimics of miRNA to inhibit miRNA functions. In this review, we summarized and discussed the current understanding of the roles of ncRNAs in legume nodulation and nitrogen fixation in the root nodule, mainly focusing on their regulation of hormone signal transduction, the autoregulation of nodulation (AON) pathway and nutrient homeostasis in nodules. Unraveling the mediation of legume nodulation by ncRNAs will give us new insights into designing higher-performance leguminous crops for sustainable agriculture.
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Corona-Gomez JA, Coss-Navarrete EL, Garcia-Lopez IJ, Klapproth C, Pérez-Patiño JA, Fernandez-Valverde SL. Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana. Sci Rep 2022; 12:14063. [PMID: 35982083 PMCID: PMC9388643 DOI: 10.1038/s41598-022-18254-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a prominent class of eukaryotic regulatory genes. Despite the numerous available transcriptomic datasets, the annotation of plant lncRNAs remains based on dated annotations that have been historically carried over. We present a substantially improved annotation of Arabidopsis thaliana lncRNAs, generated by integrating 224 transcriptomes in multiple tissues, conditions, and developmental stages. We annotate 6764 lncRNA genes, including 3772 that are novel. We characterize their tissue expression patterns and find 1425 lncRNAs are co-expressed with coding genes, with enriched functional categories such as chloroplast organization, photosynthesis, RNA regulation, transcription, and root development. This improved transcription-guided annotation constitutes a valuable resource for studying lncRNAs and the biological processes they may regulate.
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Affiliation(s)
| | | | | | - Christopher Klapproth
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center of Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107, Leipzig, Germany.,ScaDS.AI Leipzig (Center for Scalable Data Analytics and Artificial Intelligence), Humboldstrasse 25, 04105, Leipzig, Germany
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9
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Lu J, Xiao Z, Xu M, Li L. New Insights into LINC00346 and its Role in Disease. Front Cell Dev Biol 2022; 9:819785. [PMID: 35096842 PMCID: PMC8794746 DOI: 10.3389/fcell.2021.819785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022] Open
Abstract
Accumulating evidence has shown that long intergenic non-protein-coding RNA 346 (LINC00346) functions as an oncogene in the tumorigenesis of several cancers. The expression level of LINC00346 has been shown to be obviously correlated with prognosis, lymphoma metastasis, histological grade, TNM stage, tumor size and pathologic stage. LINC00346 has been found to regulate specific cellular functions by interacting with several molecules and signaling pathways. In this review, we summarize recent evidence concerning the role of LINC00346 in the occurrence and development of diseases. We also discuss the potential clinical utility of LINC00346, thereby providing new insight into the diagnosis and treatment of diseases. In addition, we further discuss the potential clinical utility of LINC00346 in the diagnosis, prognostication, and treatment of diseases.
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Affiliation(s)
- Juan Lu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Zhaoying Xiao
- Department of Infectious Diseases Shengzhou People' Hospital, Shengzhou Branch, The Fisrt Affiliated Hospital of Zhejiang University, Shengzhou, China
| | - Mengqiu Xu
- Department of Infectious Diseases Shengzhou People' Hospital, Shengzhou Branch, The Fisrt Affiliated Hospital of Zhejiang University, Shengzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
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Abdel-Salam EM, Qahtan AA, Gaafar ARZ, Zein El-Abedein AI, Alshameri AM, Alhamdan AM. Tissue-specific analysis of Coffea arabica L. transcriptome revealed potential regulatory roles of lncRNAs. Saudi J Biol Sci 2021; 28:6023-6029. [PMID: 34764734 PMCID: PMC8568828 DOI: 10.1016/j.sjbs.2021.07.006] [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: 05/29/2021] [Revised: 06/13/2021] [Accepted: 07/04/2021] [Indexed: 11/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play pivot roles in regulating mRNA expression in eukaryotic organisms without coding any proteins. In the current study, a comprehensive analysis of 260 published RNA-Seq datasets collected from different tissues (fruits, leaves, stems, and roots) of Coffea arabica L. was performed to discover potential lncRNAs. A total of 10,564 unique lncRNAs were identified. Our results showed that 77.14% of the lncRNAs were intergenic and 60.39% of them are located within 5 Kbp from the partner gene. In general, all the identified lncRNAs showed shorter lengths, fewer number of exons, and lower expression levels as compared to mRNAs in different studied tissues. Several lncRNAs were determined as differentially expressed (DE) in fruits as compared to leaves, stems, or roots. The functional characterization of the DE lncRNAs revealed their roles in regulating significant biological processes in different tissues of C. arabica. The current study provides a comprehensive analysis and dataset of lncRNAs in C. arabica that could be utilized in further studies concerning the roles of these molecules in plant cells.
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Affiliation(s)
- Eslam M Abdel-Salam
- Department of Botany & Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ahmed A Qahtan
- Department of Botany & Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdel-Rhman Z Gaafar
- Department of Botany & Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Assem I Zein El-Abedein
- Chair of Dates Industry and Technology, College of Food and Agricultural Sciences, King Saud University, PO Box 2460, Riyadh 11451, Saudi Arabia
| | - Aref M Alshameri
- Department of Botany & Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Abdullah M Alhamdan
- Chair of Dates Industry and Technology, College of Food and Agricultural Sciences, King Saud University, PO Box 2460, Riyadh 11451, Saudi Arabia
- Department of Agricultural Engineering, College of Food and Agricultural Sciences, King Saud University, PO Box 2460, Riyadh 11451, Saudi Arabia
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11
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Ghorbani F, Abolghasemi R, Haghighi M, Etemadi N, Wang S, Karimi M, Soorni A. Global identification of long non-coding RNAs involved in the induction of spinach flowering. BMC Genomics 2021; 22:704. [PMID: 34587906 PMCID: PMC8482690 DOI: 10.1186/s12864-021-07989-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 09/09/2021] [Indexed: 12/11/2022] Open
Abstract
Background Spinach is a beneficial annual vegetable species and sensitive to the bolting or early flowering, which causes a large reduction in quality and productivity. Indeed, bolting is an event induced by the coordinated effects of various environmental factors and endogenous genetic components. Although some key flowering responsive genes have been identified in spinach, non-coding RNA molecules like long non-coding RNAs (lncRNAs) were not investigated yet. Herein, we used bioinformatic approaches to analyze the transcriptome datasets from two different accessions Viroflay and Kashan at two vegetative and reproductive stages to reveal novel lncRNAs and the construction of the lncRNA-mRNA co-expression network. Additionally, correlations among gene expression modules and phenotypic traits were investigated; day to flowering was chosen as our interesting trait. Results In the present study, we identified a total of 1141 lncRNAs, of which 111 were differentially expressed between vegetative and reproductive stages. The GO and KEGG analyses carried out on the cis target gene of lncRNAs showed that the lncRNAs play an important role in the regulation of flowering spinach. Network analysis pinpointed several well-known flowering-related genes such as ELF, COL1, FLT, and FPF1 and also some putative TFs like MYB, WRKY, GATA, and MADS-box that are important regulators of flowering in spinach and could be potential targets for lncRNAs. Conclusions This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07989-1.
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Affiliation(s)
- Fatemeh Ghorbani
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Reza Abolghasemi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Maryam Haghighi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Nematollah Etemadi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Shui Wang
- College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Marzieh Karimi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.,Department of Plant Breeding and Biotechnology, College of Agriculture, University of Shahrekord, Shahrekord, Iran
| | - Aboozar Soorni
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan, Iran.
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12
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Chand Jha U, Nayyar H, Mantri N, Siddique KHM. Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development. Cells 2021; 10:cells10071674. [PMID: 34359842 PMCID: PMC8306516 DOI: 10.3390/cells10071674] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022] Open
Abstract
Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.
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MESH Headings
- Fabaceae/genetics
- Fabaceae/growth & development
- Fabaceae/metabolism
- Food Security
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Humans
- MicroRNAs/classification
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Organ Specificity
- Protein Biosynthesis
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Plant/classification
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Species Specificity
- Stress, Physiological/genetics
- Transcription, Genetic
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Affiliation(s)
- Uday Chand Jha
- ICAR—Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
- Correspondence: (U.C.J.); (K.H.M.S.)
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India;
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne 3083, Australia;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth 6001, Australia
- Correspondence: (U.C.J.); (K.H.M.S.)
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13
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Hao Q, Yang L, Fan D, Zeng B, Jin J. The transcriptomic response to heat stress of a jujube (Ziziphus jujuba Mill.) cultivar is featured with changed expression of long noncoding RNAs. PLoS One 2021; 16:e0249663. [PMID: 34043642 PMCID: PMC8158912 DOI: 10.1371/journal.pone.0249663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNA (lncRNA) of plant species undergoes dynamic regulation and acts in developmental and stress regulation. Presently, there is little information regarding the identification of lncRNAs in jujube (Ziziphus jujuba Mill.), and it is uncertain whether the lncRNAs could respond to heat stress (HS) or not. In our previous study, a cultivar (Hqing1-HR) of Z. jujuba were treated by HS (45°C) for 0, 1, 3, 5 and 7 days, and it was found that HS globally changed the gene expression by RNA sequencing (RNA-seq) experiments and informatics analyses. In the current study, 8260 lncRNAs were identified successfully from the previous RNA-seq data, and it indicated that lncRNAs expression was also altered globally, suggesting that the lncRNAs might play vital roles in response to HS. Furthermore, bioinformatics analyses of potential target mRNAs of lncRNAs with cis-acting mechanism were performed, and it showed that multiple differentially expressed (DE) mRNAs co-located with DElncRNAs were highly enriched in pathways associated with response to stress and regulation of metabolic process. Taken together, these findings not only provide a comprehensive identification of lncRNAs but also useful clues for molecular mechanism response to HS in jujube.
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Affiliation(s)
- Qing Hao
- Institute of Horticulture crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
- * E-mail:
| | - Lei Yang
- Institute of Horticulture crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Dingyu Fan
- Institute of Horticulture crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Bin Zeng
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, China
- Department of Crop Genetics and Breeding, Sub-branch of National Melon and Fruit Improvement Centre, Urumqi, China
| | - Juan Jin
- Institute of Horticulture crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
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14
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Ma B, Zhang A, Zhao Q, Li Z, Lamboro A, He H, Li Y, Jiao S, Guan S, Liu S, Yao D, Zhang J. Genome-wide identification and analysis of long non-coding RNAs involved in fatty acid biosynthesis in young soybean pods. Sci Rep 2021; 11:7603. [PMID: 33828134 PMCID: PMC8027399 DOI: 10.1038/s41598-021-87048-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs of more than 200 nucleotides. To date, the roles of lncRNAs in soybean fatty acid synthesis have not been fully studied. Here, the low-linolenic acid mutant 'MT72' and the wild-type control 'JN18' were used as materials. The lncRNAs in young pods at 30 and 40 days (d) after flowering were systematically identified and analyzed using transcriptome sequencing technology combined with bioinformatics tools. A total of 39,324 lncRNAs and 561 differentially expressed lncRNAs were identified. A lncRNAs-miRNAs-protein-coding genes (mRNAs) network was constructed, and 46 lncRNAs, 46 miRNAs and 137 mRNAs were found to be correlated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of 12 targeted mRNAs in the competing endogenous RNA network showed that these lncRNAs may be involved in the biological processes of fatty acid transport, lipid synthesis and cell division. Finally, the expression levels of differentially expressed lncRNAs, miRNAs and mRNAs were verified using qRT-PCR. The expression patterns of most genes were consistent with the sequencing results. In conclusion, new information was provided for the study of fatty acid synthesis by lncRNAs in young soybean pods.
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Affiliation(s)
- Bohan Ma
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Aijing Zhang
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Qiuzhu Zhao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Zeyuan Li
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Abraham Lamboro
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Haobo He
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Yue Li
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Suqi Jiao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Shuyan Guan
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Siyan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun, 130118, China.
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun, 130118, Jilin, China.
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15
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Cao W, Gan L, Wang C, Zhao X, Zhang M, Du J, Zhou S, Zhu C. Genome-Wide Identification and Characterization of Potato Long Non-coding RNAs Associated With Phytophthora infestans Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:619062. [PMID: 33643350 PMCID: PMC7902931 DOI: 10.3389/fpls.2021.619062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/06/2021] [Indexed: 05/26/2023]
Abstract
Long non-coding RNA (lncRNA) is a crucial regulatory mechanism in the plant response to biotic and abiotic stress. However, their roles in potato (Solanum tuberosum L.) resistance to Phytophthora infestans (P. infestans) largely remain unknown. In this study, we identify 2857 lncRNAs and 33,150 mRNAs of the potato from large-scale published RNA sequencing data. Characteristic analysis indicates a similar distribution pattern of lncRNAs and mRNAs on the potato chromosomes, and the mRNAs were longer and had more exons than lncRNAs. Identification of alternative splicing (AS) shows that there were a total of 2491 lncRNAs generated from AS and the highest frequency (46.49%) of alternative acceptors (AA). We performed R package TCseq to cluster 133 specific differentially expressed lncRNAs from resistance lines and found that the lncRNAs of cluster 2 were upregulated. The lncRNA targets were subject to KEGG pathway enrichment analysis, and the interactive network between lncRNAs and mRNAs was constructed by using GENIE3, a random forest machine learning algorithm. Transient overexpression of StLNC0004 in Nicotiana benthamiana significantly suppresses P. infestans growth compared with a control, and the expression of extensin (NbEXT), the ortholog of the StLNC0004 target gene, was significantly upregulated in the overexpression line. Together, these results suggest that lncRNAs play potential functional roles in the potato response to P. infestans infection.
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Feng S, Fang H, Liu X, Dong Y, Wang Q, Yang KQ. Genome-wide identification and characterization of long non-coding RNAs conferring resistance to Colletotrichum gloeosporioides in walnut (Juglans regia). BMC Genomics 2021; 22:15. [PMID: 33407106 PMCID: PMC7789297 DOI: 10.1186/s12864-020-07310-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/07/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease resistance, the molecular mechanisms underlying resistance to C. gloeosporioides in walnut remain poorly understood. RESULTS The anthracnose-resistant F26 fruits from the B26 clone and the anthracnose-susceptible F423 fruits from the 4-23 clone of walnut were used as the test materials. Specifically, we performed a comparative transcriptome analysis of F26 and F423 fruit bracts to identify differentially expressed LncRNAs (DELs) at five time-points (tissues at 0 hpi, pathological tissues at 24 hpi, 48 hpi, 72 hpi, and distal uninoculated tissues at 120 hpi). Compared with F423, a total of 14,525 DELs were identified, including 10,645 upregulated lncRNAs and 3846 downregulated lncRNAs in F26. The number of upregulated lncRNAs in F26 compared to in F423 was significantly higher at the early stages of C. gloeosporioides infection. A total of 5 modules related to disease resistance were screened by WGCNA and the target genes of lncRNAs were obtained. Bioinformatic analysis showed that the target genes of upregulated lncRNAs were enriched in immune-related processes during the infection of C. gloeosporioides, such as activation of innate immune response, defense response to bacterium, incompatible interaction and immune system process, and enriched in plant hormone signal transduction, phenylpropanoid biosynthesis and other pathways. And 124 known target genes for 96 hub lncRNAs were predicted, including 10 known resistance genes. The expression of 5 lncRNAs and 5 target genes was confirmed by qPCR, which was consistent with the RNA-seq data. CONCLUSIONS The results of this study provide the basis for future functional characterizations of lncRNAs regarding the C. gloeosporioides resistance of walnut fruit bracts.
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Affiliation(s)
- Shan Feng
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Tai'an, 271018, Shandong Province, China
- Shandong Taishan Forest Ecosystem Research Station, Tai'an, 271018, Shandong Province, China
| | - Xia Liu
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
- Department of Science and Technology, Qingdao Agricultural University, Qingdao, 266109, Shandong Province, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Qingpeng Wang
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Tai'an, 271018, Shandong Province, China.
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Tai'an, 271018, Shandong Province, China.
- Shandong Taishan Forest Ecosystem Research Station, Tai'an, 271018, Shandong Province, China.
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Zhao X, Li C, Zhang H, Yan C, Sun Q, Wang J, Yuan C, Shan S. Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development. BMC PLANT BIOLOGY 2020; 20:488. [PMID: 33096983 PMCID: PMC7585205 DOI: 10.1186/s12870-020-02702-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 10/14/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, and the generation of pegs and formation of subterranean pods are essential processes in peanut reproductive development. However, little information has been reported about alternative splicing (AS) in peanut peg formation and development. RESULTS Herein, we presented a comprehensive full-length (FL) transcriptome profiling of AS isoforms during peanut peg and early pod development. We identified 1448, 1102, 832, and 902 specific spliced transcripts in aerial pegs, subterranean pegs, subterranean unswollen pegs, and early swelling pods, respectively. A total of 184 spliced transcripts related to gravity stimulation, light and mechanical response, hormone mediated signaling pathways, and calcium-dependent proteins were identified as possibly involved in peanut peg development. For aerial pegs, spliced transcripts we got were mainly involved in gravity stimulation and cell wall morphogenetic processes. The genes undergoing AS in subterranean peg were possibly involved in gravity stimulation, cell wall morphogenetic processes, and abiotic response. For subterranean unswollen pegs, spliced transcripts were predominantly related to the embryo development and root formation. The genes undergoing splice in early swelling pods were mainly related to ovule development, root hair cells enlargement, root apex division, and seed germination. CONCLUSION This study provides evidence that multiple genes are related to gravity stimulation, light and mechanical response, hormone mediated signaling pathways, and calcium-dependent proteins undergoing AS express development-specific spliced isoforms or exhibit an obvious isoform switch during the peanut peg development. AS isoforms in subterranean pegs and pods provides valuable sources to further understand post-transcriptional regulatory mechanisms of AS in the generation of pegs and formation of subterranean pods.
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Affiliation(s)
- Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao, China
| | - Hao Zhang
- Shandong Peanut Research Institute, Qingdao, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao, China
| | - Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao, China
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao, China
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Tian H, Guo F, Zhang Z, Ding H, Meng J, Li X, Peng Z, Wan S. Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L. BMC PLANT BIOLOGY 2020; 20:308. [PMID: 32615935 PMCID: PMC7330965 DOI: 10.1186/s12870-020-02510-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/22/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs), which are typically > 200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. RESULTS A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. Approximately 44.17% of the lncRNAs with an exon/intron structure were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. CONCLUSIONS This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.
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Affiliation(s)
- Haiying Tian
- College of Life Science, Shandong University, Jinan, 250014 China
| | - Feng Guo
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Zhimeng Zhang
- Peanut Research Institute of Shandong, Qingdao, 266100 China
| | - Hong Ding
- Peanut Research Institute of Shandong, Qingdao, 266100 China
| | - Jingjing Meng
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Xinguo Li
- College of Life Science, Shandong University, Jinan, 250014 China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Zhenying Peng
- College of Life Science, Shandong University, Jinan, 250014 China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Shubo Wan
- College of Life Science, Shandong University, Jinan, 250014 China
- Shandong Academy of Agricultural Science, Jinan, 250014 China
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