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Muthusamy SK, Pushpitha P, Makeshkumar T, Sheela MN. Genome-wide identification and expression analysis of Hsp70 family genes in Cassava ( Manihot esculenta Crantz). 3 Biotech 2023; 13:341. [PMID: 37705861 PMCID: PMC10495308 DOI: 10.1007/s13205-023-03760-3] [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: 02/24/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023] Open
Abstract
Hsp70 proteins function as molecular chaperones, regulating various cellular processes in plants. In this study, a genome-wide analysis led to the identification of 22 Hsp70 (MeHsp70) genes in cassava. Phylogenetic relationship studies with other Malpighiales genomes (Populus trichocarpa, Ricinus communis and Salix purpurea) classified MeHsp70 proteins into eight groups (Ia, Ib, Ic, Id, Ie, If, IIa and IIb). Promoter analysis of MeHsp70 genes revealed the presence of tissue-specific, light, biotic and abiotic stress-responsive cis-regulatory elements showing their functional importance in cassava. Meta-analysis of publically available RNA-seq transcriptome datasets showed constitutive, tissue-specific, biotic and abiotic stress-specific expression patterns among MeHsp70s in cassava. Among 22 Hsp70, six MeHsp70s viz., MecHsp70-3, MecHsp70-6, MeBiP-1, MeBiP-2, MeBiP-3 and MecpHsp70-2 displayed constitutive expression, while three MecHsp70s were induced under both drought and cold stress conditions. Five MeHsp70s, MecHsp70-7, MecHsp70-11, MecHsp70-12, MecHsp70-13, and MecHsp70-14 were induced under drought stress conditions. We predicted that 19 MeHsp70 genes are under the regulation of 24 miRNAs. This comprehensive genome-wide analysis of the Hsp70 gene family in cassava provided valuable insights into their functional roles and identified various potential Hsp70 genes associated with stress tolerance and adaptation to environmental stimuli. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03760-3.
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Affiliation(s)
- Senthilkumar K. Muthusamy
- Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - P. Pushpitha
- Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - T. Makeshkumar
- Division of Crop Protection, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | - M. N. Sheela
- Division of Crop Improvement, ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
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Wang S, Li R, Zhou Y, Fernie AR, Ding Z, Zhou Q, Che Y, Yao Y, Liu J, Wang Y, Hu X, Guo J. Integrated Characterization of Cassava ( Manihot esculenta) Pectin Methylesterase ( MePME) Genes to Filter Candidate Gene Responses to Multiple Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:2529. [PMID: 37447090 DOI: 10.3390/plants12132529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023]
Abstract
Plant pectin methylesterases (PMEs) play crucial roles in regulating cell wall modification and response to various stresses. Members of the PME family have been found in several crops, but there is a lack of research into their presence in cassava (Manihot esculent), which is an important crop for world food security. In this research, 89 MePME genes were identified in cassava that were separated into two types (type-Ⅰ and type-Ⅱ) according to the existence or absence of a pro-region (PMEI domain). The MePME gene members were unevenly located on 17 chromosomes, with 19 gene pairs being identified that most likely arose via duplication events. The MePMEs could be divided into ten sub-groups in type-Ⅰ and five sub-groups in type-Ⅱ. The motif analysis revealed 11 conserved motifs in type-Ⅰ and 8 in type-Ⅱ MePMEs. The number of introns in the CDS region of type-Ⅰ MePMEs ranged between one and two, and the number of introns in type-Ⅱ MePMEs ranged between one and nine. There were 21 type-Ⅰ and 31 type-Ⅱ MePMEs that contained signal peptides. Most of the type-Ⅰ MePMEs had two conserved "RK/RLL" and one "FPSWVS" domain between the pro-region and the PME domain. Multiple stress-, hormone- and tissue-specific-related cis-acting regulatory elements were identified in the promoter regions of MePME genes. A total of five co-expressed genes (MePME1, MePME2, MePME27, MePME65 and MePME82) were filtered from different abiotic stresses via the use of UpSet Venn diagrams. The gene expression pattern analysis revealed that the expression of MePME1 was positively correlated with the degree of cassava postharvest physiological deterioration (PPD). The expression of this gene was also significantly upregulated by 7% PEG and 14 °C low-temperature stress, but slightly downregulated by ABA treatment. The tissue-specific expression analysis revealed that MePME1 and MePME65 generally displayed higher expression levels in most tissues than the other co-expressed genes. In this study, we obtain an in-depth understanding of the cassava PME gene family, suggesting that MePME1 could be a candidate gene associated with multiple abiotic tolerance.
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Affiliation(s)
- Shijia Wang
- College of Life Sciences, Hainan University, Haikou 570228, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ruimei Li
- College of Life Sciences, Hainan University, Haikou 570228, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Yangjiao Zhou
- College of Life Sciences, Hainan University, Haikou 570228, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Zhongping Ding
- College of Life Sciences, Hainan University, Haikou 570228, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Qin Zhou
- College of Life Sciences, Hainan University, Haikou 570228, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yannian Che
- College of Life Sciences, Hainan University, Haikou 570228, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yuan Yao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jiao Liu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yajie Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xinwen Hu
- College of Life Sciences, Hainan University, Haikou 570228, China
- College of Chemical and Materials Engineering, Hainan Vocational University of Science and Technology, Haikou 571126, China
| | - Jianchun Guo
- College of Life Sciences, Hainan University, Haikou 570228, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
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Li L, Huang G, Xiang W, Zhu H, Zhang H, Zhang J, Ding Z, Liu J, Wu D. Integrated Transcriptomic and Proteomic Analyses Uncover the Regulatory Mechanisms of Myricaria laxiflora Under Flooding Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:924490. [PMID: 35755690 PMCID: PMC9226631 DOI: 10.3389/fpls.2022.924490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/23/2022] [Indexed: 06/01/2023]
Abstract
Flooding is one of the major environmental stresses that severely influence plant survival and development. However, the regulatory mechanisms underlying flooding stress remain largely unknown in Myricaria laxiflora, an endangered plant mainly distributed in the flood zone of the Yangtze River, China. In this work, transcriptome and proteome were performed in parallel in roots of M. laxiflora during nine time-points under the flooding and post-flooding recovery treatments. Overall, highly dynamic and stage-specific expression profiles of genes/proteins were observed during flooding and post-flooding recovery treatment. Genes related to auxin, cell wall, calcium signaling, and MAP kinase signaling were greatly down-regulated exclusively at the transcriptomic level during the early stages of flooding. Glycolysis and major CHO metabolism genes, which were regulated at the transcriptomic and/or proteomic levels with low expression correlations, mainly functioned during the late stages of flooding. Genes involved in reactive oxygen species (ROS) scavenging, mitochondrial metabolism, and development were also regulated exclusively at the transcriptomic level, but their expression levels were highly up-regulated upon post-flooding recovery. Moreover, the comprehensive expression profiles of genes/proteins related to redox, hormones, and transcriptional factors were also investigated. Finally, the regulatory networks of M. laxiflora in response to flooding and post-flooding recovery were discussed. The findings deepen our understanding of the molecular mechanisms of flooding stress and shed light on the genes and pathways for the preservation of M. laxiflora and other endangered plants in the flood zone.
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Affiliation(s)
- Linbao Li
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Guiyun Huang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Weibo Xiang
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Haofei Zhu
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Haibo Zhang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Jun Zhang
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
| | - Zehong Ding
- Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Jihong Liu
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China
| | - Di Wu
- Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China
- National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China
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Chen Y, Weng X, Zhou X, Gu J, Hu Q, Luo Q, Wen M, Li C, Wang ZY. Overexpression of cassava RSZ21b enhances drought tolerance in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153574. [PMID: 34890846 DOI: 10.1016/j.jplph.2021.153574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Drought is one of the major environmental constraints affecting crop productivity. Plants have to adjust their developmental and physiological processes to cope with drought. We previously identified 18 cassava serine/arginine-rich (SR) proteins that had a pivotal role in alternative splicing in response to environmental stress. However, functional characterization of SR proteins is rarely explored. Here, we characterized the RSZ subfamily gene MeRSZ21b in cassava. The RSZ21b belongs to the RSZ subfamily, which was widely distributed in major crops and was highly conserved. Quantitative RT-PCR assay showed that the expression of MeRSZ21b was significantly induced by drought. Moreover, overexpression of MeRSZ21b in Arabidopsis was hypersensitive to abscisic acid (ABA) in the phases of seed germination and post-germination seedling growth. Meantime, MeRSZ21b overexpression lines were resistant to sorbitol treatment, and quickly closed the stomata when compared with Col-0 under drought condition. Importantly, overexpression of MeRSZ21b resulted in improved drought tolerance through modulating ABA-dependent signaling. Therefore, our findings refine our knowledge of the SR protein-coding genes and provide novel insights for enhancing plant resistance to environmental stress.
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Affiliation(s)
- Yanhang Chen
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Xun Weng
- College of Life Sciences, South China Agricultural University, Guangdong, 510642, China
| | - Xiaoxia Zhou
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Jinbao Gu
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Qing Hu
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Qingwen Luo
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China
| | - Mingfu Wen
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China
| | - Cong Li
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China.
| | - Zhen-Yu Wang
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China; Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China.
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5
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Maleki M, Khelghati N, Alemi F, Younesi S, Asemi Z, Abolhasan R, Bazdar M, Samadi-Kafil H, Yousefi B. Multiple interactions between melatonin and non-coding RNAs in cancer biology. Chem Biol Drug Des 2021; 98:323-340. [PMID: 33905613 DOI: 10.1111/cbdd.13849] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022]
Abstract
The melatonin hormone secreted by the pineal gland is involved in physiological functions such as growth and maturation, circadian cycles, and biological activities including antioxidants, anti-tumor, and anti-ischemia. Melatonin not only interacts with proteins but also has functional effects on regulatory RNAs such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). In this study, we overview various physiological and pathological conditions affecting melatonin through lncRNA and miRNA. The information compiled herein will serve as a solid foundation to formulate ideas for future mechanistic studies on melatonin. It will also provide a chance to more clarify the emerging functions of the non-coding transcriptome.
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Affiliation(s)
- Masomeh Maleki
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Nafiseh Khelghati
- Department of Clinical Biochemistry, Urmia University of Medical Sciences, Urmia, Iran
| | - Forough Alemi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Simin Younesi
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Vic., Australia
| | - Zatollah Asemi
- School of Health and Biomedical Sciences, RMIT University, Melbourne, Vic., Australia.,Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, Iran
| | - Rozita Abolhasan
- Stem Cell and Regenerative Medicine Institute (SCARM), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahtab Bazdar
- Department of Clinical Biochemistry, Urmia University of Medical Sciences, Urmia, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Ding Z, Wu C, Tie W, Yan Y, He G, Hu W. Strand-specific RNA-seq based identification and functional prediction of lncRNAs in response to melatonin and simulated drought stresses in cassava. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 140:96-104. [PMID: 31085451 DOI: 10.1016/j.plaphy.2019.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 05/20/2023]
Abstract
Melatonin (MT) plays important roles in mediating plant responses to abiotic stresses such as drought. lncRNAs also play crucial roles in regulating responses to drought stress, however, their roles in MT-mediated drought stress responses in plants remain largely unknown. In this study, a total of 1405 high-confidence lncRNAs were identified in leaves of cassava, an important food crop in tropical and sub-tropical regions, using strand-specific RNA-seq technology. Of which, 185 were differentially expressed between polyethylene glycol (PEG) or MT treatment and the control condition. Trans-regulatory co-expression network revealed that MT-uniquely-responsive lncRNAs were mainly involved in tetrapyrrole synthesis, cytochrome P450, and cell wall modification; PEG-uniquely-responsive lncRNAs mainly participated in RNA regulation of transcription, calcium signaling, mitochondrial electron transport/ATP synthesis, hormone metabolism, and transport; and MT and PEG both-responsive lncRNAs were mainly involved in light reaction, light signaling, FA synthesis and FA elongation, secondary metabolism, and tetrapyrrole synthesis. In addition, 28 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes mainly through calcium signaling, RNA regulation of transcription, ABA and ethylene metabolism, and redox homeostasis. Besides, 78 lncRNAs (especially TCONS_00003360, TCONS_00015102, and TCONS_00149293) responsive to MT and/or PEG treatment were identified as putative targets of cassava known miRNAs. These findings provide a comprehensive view of the lncRNAs and their roles in response to MT and drought stress in cassava, which will enable in-depth functional analyses in the near future.
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Affiliation(s)
- Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
| | - Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China; Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China.
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
| | - Guangyuan He
- Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China.
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
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Cheng Z, Lei N, Li S, Liao W, Shen J, Peng M. The regulatory effects of MeTCP4 on cold stress tolerance in Arabidopsis thaliana: A transcriptome analysis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 138:9-16. [PMID: 30825725 DOI: 10.1016/j.plaphy.2019.02.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 05/01/2023]
Abstract
Cassava (Manihot esculenta), an important food crop in tropical areas, is well-adapted to drought conditions, but is sensitive to cold. The expression of MeTCP4, a transcription factor involved in the regulation of plant development and abiotic stresses responses, was altered under cold stress. However, its biological function under abiotic stress responses is still unclear. Here, we show that increased MeTCP4 expression enhances cold stress tolerance in Arabidopsis (Arabidopsis thaliana). To better understand the biological role of MeTCP4, the mRNA from overexpression and wild-type (WT) plants was isolated for whole genome sequencing to identify MeTCP4-mediated cold-responsive genes. Our results identify 1341 and 797 differentially expressed genes (DEGs) affected by MeTCP4 overexpression under normal and cold conditions, respectively. Gene ontology analysis revealed that a portion of the DEGs were involved in reactive oxygen species (ROS) metabolism process after cold treatment. qRT-PCR analysis revealed that the expression of cold-responsive genes and ROS-scavenging-related genes were increased in MeTCP4 overexpression plant, which could be responsible for the reduced ROS levels and enhanced cold resistance observed in transgenic plant. The findings provide insight into mechanisms of MeTCP4-mediated cold stress response, and provide clues for development of low temperature-tolerant cassava cultivars.
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Affiliation(s)
- Zhihao Cheng
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102, China
| | - Ning Lei
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Shuxia Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
| | - Wenbin Liao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Jie Shen
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.
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Ding Z, Fu L, Tie W, Yan Y, Wu C, Hu W, Zhang J. Extensive Post-Transcriptional Regulation Revealed by Transcriptomic and Proteomic Integrative Analysis in Cassava under Drought. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:3521-3534. [PMID: 30830777 DOI: 10.1021/acs.jafc.9b00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cassava is a major tropical/subtropical food crop and its yield is greatly restrained by drought; however, the mechanism underlying the drought stress remains largely unknown. In this study, totally 1242 and 715 differentially expressed genes (DEGs), together with 237 and 307 differentially expressed proteins (DEPs), were respectively identified in cassava leaves and roots through RNA-seq and iTRAQ techniques. The majority of DEGs and DEPs were exclusively regulated at the mRNA and protein level, respectively, whereas only a few were commonly regulated, indicating the major involvement of post-transcriptional regulation under drought. Subsequently, the functions of these specifically or commonly regulated DEGs and DEPs were analyzed, and the post-transcriptional regulation of genes involved in heat shock protein, secondary metabolism biosynthesis, and hormone biosynthesis was extensively discussed. This is the first report on an integration of transcriptomic and proteomic analysis in cassava, and it provides new insights into the post-transcriptional regulation of cassava drought stress.
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Affiliation(s)
- Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
| | - Lili Fu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
| | - Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
- Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology , Huazhong University of Science and Technology (HUST) , Wuhan 430074 , China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
| | - Jiaming Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology , Chinese Academy of Tropical Agricultural Sciences , Xueyuan Road 4 , Haikou , Hainan 571101 , China
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9
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Ding Z, Tie W, Fu L, Yan Y, Liu G, Yan W, Li Y, Wu C, Zhang J, Hu W. Strand-specific RNA-seq based identification and functional prediction of drought-responsive lncRNAs in cassava. BMC Genomics 2019; 20:214. [PMID: 30866814 PMCID: PMC6417064 DOI: 10.1186/s12864-019-5585-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/05/2019] [Indexed: 12/21/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) have emerged as playing crucial roles in abiotic stress responsive regulation, however, the mechanism of lncRNAs underlying drought-tolerance remains largely unknown in cassava, an important tropical and sub-tropical root crop of remarkable drought tolerance. Results In this study, a total of 833 high-confidence lncRNAs, including 652 intergenic and 181 anti-sense lncRNAs, were identified in cassava leaves and root using strand-specific RNA-seq technology, of which 124 were drought-responsive. Trans-regulatory co-expression network revealed that lncRNAs exhibited tissue-specific expression patterns and they preferred to function differently in distinct tissues: e.g., cell-related metabolism, cell wall, and RNA regulation of transcription in folded leaf (FL); degradation of major carbohydrate (CHO) metabolism, calvin cycle and light reaction, light signaling, and tetrapyrrole synthesis in full expanded leaf (FEL); synthesis of major CHO metabolism, nitrogen-metabolism, photosynthesis, and redox in bottom leaf (BL); and hormone metabolism, secondary metabolism, calcium signaling, and abiotic stress in root (RT). In addition, 27 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes mainly through hormone metabolism, RNA regulation of transcription, and signaling of receptor kinase. Besides, 11 lncRNAs were identified acting as putative target mimics of known miRNAs in cassava. Finally, five drought-responsive lncRNAs and 13 co-expressed genes involved in trans-acting, cis-acting, or target mimic regulation were selected and confirmed by qRT-PCR. Conclusions These findings provide a comprehensive view of cassava lncRNAs in response to drought stress, which will enable in-depth functional analysis in the future. Electronic supplementary material The online version of this article (10.1186/s12864-019-5585-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China
| | - Lili Fu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China
| | - Guanghua Liu
- Institute of Tropical and Sub-tropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Wei Yan
- Institute of Tropical and Sub-tropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Yanan Li
- Institute of Tropical and Sub-tropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.,Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Jiaming Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
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The Late Embryogenesis Abundant Protein Family in Cassava ( Manihot esculenta Crantz): Genome-Wide Characterization and Expression during Abiotic Stress. Molecules 2018; 23:molecules23051196. [PMID: 29772750 PMCID: PMC6099554 DOI: 10.3390/molecules23051196] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 11/16/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins, as a highly diverse group of polypeptides, play an important role in plant adaptation to abiotic stress; however, LEAs from cassava have not been studied in cassava. In this study, 26 LEA members were genome-wide identified from cassava, which were clustered into seven subfamily according to evolutionary relationship, protein motif, and gene structure analyses. Chromosomal location and duplication event analyses suggested that 26 MeLEAs distributed in 10 chromosomes and 11 MeLEA paralogues were subjected to purifying selection. Transcriptomic analysis showed the expression profiles of MeLEAs in different tissues of stem, leaves, and storage roots of three accessions. Comparative transcriptomic analysis revealed that the function of MeLEAs in response to drought may be differentiated in different accessions. Compared with the wild subspecies W14, more MeLEA genes were activated in cultivated varieties Arg7 and SC124 after drought treatment. Several MeLEA genes showed induction under various stresses and related signaling treatments. Taken together, this study demonstrates the transcriptional control of MeLEAs in tissue development and the responses to abiotic stress in cassava and identifies candidate genes for improving crop resistance to abiotic stress.
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