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Luha R, Rana V, Vainstein A, Kumar V. Nonsense-mediated mRNA decay pathway in plants under stress: general gene regulatory mechanism and advances. PLANTA 2024; 259:51. [PMID: 38289504 DOI: 10.1007/s00425-023-04317-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/23/2023] [Indexed: 02/01/2024]
Abstract
MAIN CONCLUSION Nonsense-mediated mRNA decay in eukaryotes is vital to cellular homeostasis. Further knowledge of its putative role in plant RNA metabolism under stress is pivotal to developing fitness-optimizing strategies. Nonsense-mediated mRNA decay (NMD), part of the mRNA surveillance pathway, is an evolutionarily conserved form of gene regulation in all living organisms. Degradation of mRNA-bearing premature termination codons and regulation of physiological RNA levels highlight NMD's role in shaping the cellular transcriptome. Initially regarded as purely a tool for cellular RNA quality control, NMD is now considered to mediate various aspects of plant developmental processes and responses to environmental changes. Here we offer a basic understanding of NMD in eukaryotes by explaining the concept of premature termination codon recognition and NMD complex formation. We also provide a detailed overview of the NMD mechanism and its role in gene regulation. The potential role of effectors, including ABCE1, in ribosome recycling during the translation process is also explained. Recent reports of alternatively spliced variants of corresponding genes targeted by NMD in Arabidopsis thaliana are provided in tabular format. Detailed figures are also provided to clarify the NMD concept in plants. In particular, accumulating evidence shows that NMD can serve as a novel alternative strategy for genetic manipulation and can help design RNA-based therapies to combat stress in plants. A key point of emphasis is its function as a gene regulatory mechanism as well as its dynamic regulation by environmental and developmental factors. Overall, a detailed molecular understanding of the NMD mechanism can lead to further diverse applications, such as improving cellular homeostasis in living organisms.
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Affiliation(s)
- Rashmita Luha
- Department of Botany, School for Basic Sciences, Central University of Punjab, Bathinda, India
- Centre for Biosystems Science and Engineering, Indian Institute of Science Bangalore, Bangaluru, India
| | - Varnika Rana
- Department of Botany, School for Basic Sciences, Central University of Punjab, Bathinda, India
| | - Alexander Vainstein
- Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Vinay Kumar
- Department of Botany, School for Basic Sciences, Central University of Punjab, Bathinda, India.
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Nong ML, Luo XH, Zhu LX, Zhang YN, Dun XY, Huang L. Insights into the Adaptation to High Altitudes from Transcriptome Profiling: A Case Study of an Endangered Species, Kingdonia uniflora. Genes (Basel) 2023; 14:1291. [PMID: 37372473 DOI: 10.3390/genes14061291] [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: 03/14/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Kingdonia uniflora is an endangered alpine herb that is distributed along an altitudinal gradient. The unique traits and important phylogenetic position make K. uniflora an ideal model for exploring how endangered plants react to altitude variation. In this study, we sampled nine individuals from three representative locations and adopted RNA-seq technology to sequence 18 tissues, aiming to uncover how K. uniflora responded to different altitudes at the gene expression level. We revealed that genes that responded to light stimuli and circadian rhythm genes were significantly enriched in DEGs in the leaf tissue group, while genes that were related to root development and peroxidase activity or involved in the pathways of cutin, suberin, wax biosynthesis, and monoterpenoid biosynthesis were significantly enriched in DEGs in the flower bud tissue group. All of the above genes may play an important role in the response of K. uniflora to various stresses, such as low temperatures and hypoxia in high-altitude environments. Furthermore, we proved that the discrepancy in gene expression patterns between leaf and flower bud tissues varied along the altitudinal gradient. Overall, our findings provide new insights into the adaptation of endangered species to high-altitude environments and further encourage parallel research to focus on the molecular mechanisms of alpine plant evolution.
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Affiliation(s)
- Man-Li Nong
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Xiao-Hui Luo
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Li-Xin Zhu
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Ya-Nan Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Xue-Yi Dun
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Lei Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
- Key Laboratory of Medicinal Plant Resource and Natural Pharmaceutical Chemistry of Ministry of Education, College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
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3
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Jia ZC, Das D, Zhang Y, Fernie AR, Liu YG, Chen M, Zhang J. Plant serine/arginine-rich proteins: versatile players in RNA processing. PLANTA 2023; 257:109. [PMID: 37145304 DOI: 10.1007/s00425-023-04132-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/05/2023] [Indexed: 05/06/2023]
Abstract
MAIN CONCLUSION Serine/arginine-rich (SR) proteins participate in RNA processing by interacting with precursor mRNAs or other splicing factors to maintain plant growth and stress responses. Alternative splicing is an important mechanism involved in mRNA processing and regulation of gene expression at the posttranscriptional level, which is the main reason for the diversity of genes and proteins. The process of alternative splicing requires the participation of many specific splicing factors. The SR protein family is a splicing factor in eukaryotes. The vast majority of SR proteins' existence is an essential survival factor. Through its RS domain and other unique domains, SR proteins can interact with specific sequences of precursor mRNA or other splicing factors and cooperate to complete the correct selection of splicing sites or promote the formation of spliceosomes. They play essential roles in the composition and alternative splicing of precursor mRNAs, providing pivotal functions to maintain growth and stress responses in animals and plants. Although SR proteins have been identified in plants for three decades, their evolutionary trajectory, molecular function, and regulatory network remain largely unknown compared to their animal counterparts. This article reviews the current understanding of this gene family in eukaryotes and proposes potential key research priorities for future functional studies.
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Affiliation(s)
- Zi-Chang Jia
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Debatosh Das
- College of Agriculture, Food and Natural Resources (CAFNR), Division of Plant Sciences and Technology, 52 Agricultural Building, University of Missouri, Columbia, MO, 65201, USA
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Youjun Zhang
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
- Max-Planck-Institut Für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Ying-Gao Liu
- State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Taian, Shandong, China
| | - Moxian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong.
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Jin X. Regulatory Network of Serine/Arginine-Rich (SR) Proteins: The Molecular Mechanism and Physiological Function in Plants. Int J Mol Sci 2022; 23:ijms231710147. [PMID: 36077545 PMCID: PMC9456285 DOI: 10.3390/ijms231710147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/10/2022] [Accepted: 08/29/2022] [Indexed: 12/05/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are a type of splicing factor. They play significant roles in constitutive and alternative pre-mRNA splicing, and are involved in post-splicing activities, such as mRNA nuclear export, nonsense-mediated mRNA decay, mRNA translation, and miRNA biogenesis. In plants, SR proteins function under a complex regulatory network by protein–protein and RNA–protein interactions between SR proteins, other splicing factors, other proteins, or even RNAs. The regulatory networks of SR proteins are complex—they are regulated by the SR proteins themselves, they are phosphorylated and dephosphorylated through interactions with kinase, and they participate in signal transduction pathways, whereby signaling cascades can link the splicing machinery to the exterior environment. In a complex network, SR proteins are involved in plant growth and development, signal transduction, responses to abiotic and biotic stresses, and metabolism. Here, I review the current status of research on plant SR proteins, construct a model of SR proteins function, and ask many questions about SR proteins in plants.
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Affiliation(s)
- Xiaoli Jin
- Departmeng of Agronomy, College of Agriculture and Biotechnology, Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China
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Zhu H, Liu C, Qian H. Pharmaceutical Potential of High-Altitude Plants for Fatigue-Related Disorders: A Review. PLANTS 2022; 11:plants11152004. [PMID: 35956482 PMCID: PMC9370126 DOI: 10.3390/plants11152004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
Natural plants from plateaus have been the richest source of secondary metabolites extensively used in traditional and modern health care systems. They were submitted to years of natural selection, co-evolved within that habitat, and show significant anti-fatigue-related pharmacological effects. However, currently, no review on high-altitude plants with anti-fatigue related properties has been published yet. This study summarized several Chinese traditional high-altitude plants, including Rhodiola rosea L., Crocus sativus L., Lepidium meyenii W., Hippophaerhamnoides L., which are widely used in the Qinghai–Tibet Plateau and surrounding mountains, as well as herbal markets in the plains. Based on phytopharmacology studies, deeper questions can be further revealed regarding how these plants regulate fatigue and related mental or physical disease conditions. Many active derivatives in high-altitude medical plants show therapeutic potential for the management of fatigue and related disorders. Therefore, high-altitude plants significantly relieve central or peripheral fatigue by acting as neuroprotective agents, energy supplements, metabolism regulators, antioxidant, and inflammatory response inhibitors. Their applications on the highland or flatland and prospects in natural medicine are further forecast, which may open treatments to reduce or prevent fatigue-related disorders in populations with sub-optimal health.
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Affiliation(s)
- Hongkang Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (H.Z.); (C.L.)
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Chang Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (H.Z.); (C.L.)
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - He Qian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (H.Z.); (C.L.)
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Correspondence:
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Yang H, Li P, Jin G, Gui D, Liu L, Zhang C. Temporal regulation of alternative splicing events in rice memory under drought stress. PLANT DIVERSITY 2022; 44:116-125. [PMID: 35281128 PMCID: PMC8897166 DOI: 10.1016/j.pld.2020.11.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 10/29/2020] [Accepted: 11/02/2020] [Indexed: 05/03/2023]
Abstract
Plant adaptation to drought stress is essential for plant survival and crop yield. Recently, harnessing drought memory, which is induced by repeated stress and recovery cycles, was suggested as a means to improve drought resistance at the transcriptional level. However, the genetic mechanism underlying drought memory is unclear. Here, we carried out a quantitative analysis of alternative splicing (AS) events in rice memory under drought stress, generating 12 transcriptome datasets. Notably, we identified exon skipping (ES) as the predominant AS type (>80%) in differential alternative splicing (DAS) in response to drought stress. Applying our analysis pipeline to investigate DAS events following drought stress in six other plant species revealed variable ES frequencies ranging from 9.94% to 60.70% depending on the species, suggesting that the relative frequency of DAS types in plants is likely to be species-specific. The dinucleotide sequence at AS splice sites in rice following drought stress was preferentially GC-AG and AT-AC. Since U12-type splicing uses the AT-AC site, this suggests that drought stress may increase U12-type splicing, and thus increase ES frequency. We hypothesize that multiple isoforms derived from exon skipping may be induced by drought stress in rice. We also identified 20 transcription factors and three highly connected hub genes with potential roles in drought memory that may be good targets for plant breeding.
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Affiliation(s)
- Hong Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Guihua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Daping Gui
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Li Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
- Corresponding author. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Haiyan Engineering & Technology Center, Kunming Institute of Botany, Chinese Academy of Science, Kunming, Yunnan, 650201, China
- Corresponding author. Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
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7
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Peng X, Zhang R, Liu J, Li Z, Zhou L, Qiu M. Lepithiohydimerins A—D: Four Pairs of Neuroprotective Thiohydantoin Dimers Bearing a Disulfide Bond from Maca (
Lepidium meyenii
Walp.). CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xing‐Rong Peng
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan 650201 China
| | - Ran‐Ran Zhang
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan 650201 China
- University of the Chinese Academy of Sciences Beijing 100049 China
| | - Jun‐Hong Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan 650201 China
- University of the Chinese Academy of Sciences Beijing 100049 China
| | - Zhong‐Rong Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan 650201 China
| | - Lin Zhou
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan 650201 China
| | - Ming‐Hua Qiu
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany Chinese Academy of Sciences Kunming Yunnan 650201 China
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Wang ZQ, Zhao QM, Zhong X, Xiao L, Ma LX, Wu CF, Zhang Z, Zhang LQ, Tian Y, Fan W. Comparative analysis of maca (Lepidium meyenii) proteome profiles reveals insights into response mechanisms of herbal plants to high-temperature stress. BMC PLANT BIOLOGY 2020; 20:431. [PMID: 32938390 PMCID: PMC7493174 DOI: 10.1186/s12870-020-02645-4] [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: 03/31/2020] [Accepted: 09/10/2020] [Indexed: 05/14/2023]
Abstract
BACKGROUND High-temperature stress (HTS) is one of the main environmental stresses that limit plant growth and crop production in agricultural systems. Maca (Lepidium meyenii) is an important high-altitude herbaceous plant adapted to a wide range of environmental stimuli such as cold, strong wind and UV-B exposure. However, it is an extremely HTS-sensitive plant species. Thus far, there is limited information about gene/protein regulation and signaling pathways related to the heat stress responses in maca. In this study, proteome profiles of maca seedlings exposed to HTS for 12 h were investigated using a tandem mass tag (TMT)-based proteomic approach. RESULTS In total, 6966 proteins were identified, of which 300 showed significant alterations in expression following HTS. Bioinformatics analyses indicated that protein processing in endoplasmic reticulum was the most significantly up-regulated metabolic pathway following HTS. Quantitative RT-PCR (qRT-PCR) analysis showed that the expression levels of 19 genes encoding proteins mapped to this pathway were significantly up-regulated under HTS. These results show that protein processing in the endoplasmic reticulum may play a crucial role in the responses of maca to HTS. CONCLUSIONS Our proteomic data can be a good resource for functional proteomics of maca and our results may provide useful insights into the molecular response mechanisms underlying herbal plants to HTS.
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Affiliation(s)
- Zhan Qi Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Qi Ming Zhao
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
| | - Xueting Zhong
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Li Xiao
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Li Xuan Ma
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Chou Fei Wu
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Zhongshan Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
| | - Li Qin Zhang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Sciences, Huzhou University, Huzhou, 313000 China
- Huzhou central hospital, Huzhou University, Huzhou, 313000 China
| | - Yang Tian
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Wei Fan
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan, The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, 650201 China
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