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Wang Y, Shi Y, Li H, Chang J. Understanding Citrus Viroid Interactions: Experience and Prospects. Viruses 2024; 16:577. [PMID: 38675919 PMCID: PMC11053686 DOI: 10.3390/v16040577] [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: 03/10/2024] [Revised: 03/28/2024] [Accepted: 04/05/2024] [Indexed: 04/28/2024] Open
Abstract
Citrus is the natural host of at least eight viroid species, providing a natural platform for studying interactions among viroids. The latter manifests as antagonistic or synergistic phenomena. The antagonistic effect among citrus viroids intuitively leads to reduced symptoms caused by citrus viroids, while the synergistic effect leads to an increase in symptom severity. The interaction phenomenon is complex and interesting, and a deep understanding of the underlying mechanisms induced during this viroid interaction is of great significance for the prevention and control of viroid diseases. This paper summarizes the research progress of citrus viroids in recent years, focusing on the interaction phenomenon and analyzing their interaction mechanisms. It points out the core role of the host RNA silencing mechanism and viroid-derived siRNA (vd-siRNA), and provides suggestions for future research directions.
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Affiliation(s)
- Yafei Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China; (Y.S.); (H.L.); (J.C.)
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Hayat F, Li J, Iqbal S, Peng Y, Hong L, Balal RM, Khan MN, Nawaz MA, Khan U, Farhan MA, Li C, Song W, Tu P, Chen J. A Mini Review of Citrus Rootstocks and Their Role in High-Density Orchards. PLANTS (BASEL, SWITZERLAND) 2022; 11:2876. [PMID: 36365327 PMCID: PMC9656899 DOI: 10.3390/plants11212876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/12/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Dwarfing is an important agricultural trait for intensive cultivation and effective orchard management in modern fruit orchards. Commercial citrus production relies on grafting with rootstocks that reduce tree vigor to control plant height. Citrus growers all over the world have been attracted to dwarfing trees because of their potential for higher planting density, increased productivity, easy harvest, pruning, and efficient spraying. Dwarfing rootstocks can be used to achieve high density. As a result, the use and development of dwarfing rootstocks are important. Breeding programs in several countries have led to the production of citrus dwarf rootstocks. For example, the dwarfing rootstocks 'Flying Dragon', 'FA 517', 'HTR-051', 'US-897', and 'Red tangerine' cultivated in various regions allow the design of dense orchards. Additionally, dwarf or short-stature trees were obtained using interstocks, citrus dwarfing viroid (CDVd) and various chemical applications. This review summarizes what is known about dwarf citrus rootstocks and the mechanisms underlying rootstock-scion interactions. Despite advances in recent decades, many questions regarding rootstock-induced scion development remain unanswered. Citrus rootstocks with dwarfing potential have been investigated regarding physiological aspects, hormonal communication, mineral uptake capacity, and horticultural performance. This study lays the foundation for future research into the genetic and molecular mechanisms underlying citrus dwarfing.
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Affiliation(s)
- Faisal Hayat
- College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
| | - Juan Li
- College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
| | - Shahid Iqbal
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Yang Peng
- College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
| | - Leming Hong
- College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
| | - Rashad Mukhtar Balal
- Department of Horticulture, College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan
| | | | - Muhammad Azher Nawaz
- Department of Horticulture, College of Agriculture, University of Sargodha, Sargodha 40100, Pakistan
| | - Ummara Khan
- Key Laboratory of Food Processing and Quality Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | | | - Caiqing Li
- College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
| | - Wenpei Song
- College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
| | - Panfeng Tu
- College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510408, China
| | - Jiezhong Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Joubert M, van den Berg N, Theron J, Swart V. Transcriptomics Advancement in the Complex Response of Plants to Viroid Infection. Int J Mol Sci 2022; 23:ijms23147677. [PMID: 35887025 PMCID: PMC9318114 DOI: 10.3390/ijms23147677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023] Open
Abstract
Viroids are the smallest plant pathogens, consisting of a single-stranded circular RNA of less than 500 ribonucleotides in length. Despite their noncoding nature, viroids elicit disease symptoms in many economically important plant hosts, and are, thus, a class of pathogens of great interest. How these viroids establish disease within host plants, however, is not yet fully understood. Recent transcriptomic studies have revealed that viroid infection influences the expression of genes in several pathways and processes in plants, including defence responses, phytohormone signalling, cell wall modification, photosynthesis, secondary metabolism, transport, gene expression and protein modification. There is much debate about whether affected pathways signify a plant response to viroid infection, or are associated with the appearance of disease symptoms in these interactions. In this review, we consolidate the findings of viroid–host transcriptome studies to provide an overview of trends observed in the data. When considered together, changes in the gene expression of different hosts upon viroid infection reveal commonalities and differences in diverse interactions. Here, we discuss whether trends in host gene expression can be correlated to plant defence or disease development during viroid infection, and highlight avenues for future research in this field.
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Affiliation(s)
- Melissa Joubert
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa; (M.J.); (N.v.d.B.)
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
| | - Noëlani van den Berg
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa; (M.J.); (N.v.d.B.)
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
| | - Jacques Theron
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
| | - Velushka Swart
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa; (M.J.); (N.v.d.B.)
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa;
- Correspondence:
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Lavagi-Craddock I, Dang T, Comstock S, Osman F, Bodaghi S, Vidalakis G. Transcriptome Analysis of Citrus Dwarfing Viroid Induced Dwarfing Phenotype of Sweet Orange on Trifoliate Orange Rootstock. Microorganisms 2022; 10:microorganisms10061144. [PMID: 35744662 PMCID: PMC9228058 DOI: 10.3390/microorganisms10061144] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
Dwarfed citrus trees for high-density plantings or mechanized production systems will be key for future sustainable citrus production. Citrus trees consist of two different species of scion and rootstock. Therefore, any observed phenotype results from gene expression in both species. Dwarfed sweet orange trees on trifoliate rootstock have been produced using citrus dwarfing viroid (CDVd). We performed RNA-seq transcriptome analysis of CDVd-infected stems and roots and compared them to non-infected controls. The identified differentially expressed genes validated with RT-qPCR corresponded to various physiological and developmental processes that could be associated with the dwarfing phenotype. For example, the transcription factors MYB13 and MADS-box, which regulate meristem functions and activate stress responses, were upregulated in the stems. Conversely, a calcium-dependent lipid-binding protein that regulates membrane transporters was downregulated in the roots. Most transcriptome reprogramming occurred in the scion rather than in the rootstock; this agrees with previous observations of CDVd affecting the growth of sweet orange stems while not affecting the trifoliate rootstock. Furthermore, the lack of alterations in the pathogen defense transcriptome supports the term “Transmissible small nuclear ribonucleic acid,” which describes CDVd as a modifying agent of tree performance with desirable agronomic traits rather than a disease-causing pathogen.
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Affiliation(s)
- Irene Lavagi-Craddock
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (I.L.-C.); (T.D.); (S.C.); (S.B.)
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (I.L.-C.); (T.D.); (S.C.); (S.B.)
| | - Stacey Comstock
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (I.L.-C.); (T.D.); (S.C.); (S.B.)
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA 95616, USA;
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (I.L.-C.); (T.D.); (S.C.); (S.B.)
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA; (I.L.-C.); (T.D.); (S.C.); (S.B.)
- Correspondence:
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Aviña-Padilla K, Zambada-Moreno O, Herrera-Oropeza GE, Jimenez-Limas MA, Abrahamian P, Hammond RW, Hernández-Rosales M. Insights into the Transcriptional Reprogramming in Tomato Response to PSTVd Variants Using Network Approaches. Int J Mol Sci 2022; 23:ijms23115983. [PMID: 35682662 PMCID: PMC9181013 DOI: 10.3390/ijms23115983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 01/25/2023] Open
Abstract
Viroids are the smallest pathogens of angiosperms, consisting of non-coding RNAs that cause severe diseases in agronomic crops. Symptoms associated with viroid infection are linked to developmental alterations due to genetic regulation. To understand the global mechanisms of host viroid response, we implemented network approaches to identify master transcription regulators and their differentially expressed targets in tomato infected with mild and severe variants of PSTVd. Our approach integrates root and leaf transcriptomic data, gene regulatory network analysis, and identification of affected biological processes. Our results reveal that specific bHLH, MYB, and ERF transcription factors regulate genes involved in molecular mechanisms underlying critical signaling pathways. Functional enrichment of regulons shows that bHLH-MTRs are linked to metabolism and plant defense, while MYB-MTRs are involved in signaling and hormone-related processes. Strikingly, a member of the bHLH-TF family has a specific potential role as a microprotein involved in the post-translational regulation of hormone signaling events. We found that ERF-MTRs are characteristic of severe symptoms, while ZNF-TF, tf3a-TF, BZIP-TFs, and NAC-TF act as unique MTRs. Altogether, our results lay a foundation for further research on the PSTVd and host genome interaction, providing evidence for identifying potential key genes that influence symptom development in tomato plants.
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Affiliation(s)
- Katia Aviña-Padilla
- Centro de Investigación y de Estudios Avanzados del I.P.N Unidad Irapuato, Irapuato 36821, Mexico;
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: or (K.A.-P.); (R.W.H.); (M.H.-R.); Tel.: +1-301-504-5203 (R.W.H.)
| | - Octavio Zambada-Moreno
- Centro de Investigación y de Estudios Avanzados del I.P.N Unidad Irapuato, Irapuato 36821, Mexico;
| | - Gabriel Emilio Herrera-Oropeza
- Center for Developmental Neurobiology, Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London WC2R 2LS, UK;
| | - Marco A. Jimenez-Limas
- Centro de Investigación en Computación, Instituto Politécnico Nacional, Mexico City 07738, Mexico;
| | - Peter Abrahamian
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
| | - Rosemarie W. Hammond
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA;
- Correspondence: or (K.A.-P.); (R.W.H.); (M.H.-R.); Tel.: +1-301-504-5203 (R.W.H.)
| | - Maribel Hernández-Rosales
- Centro de Investigación y de Estudios Avanzados del I.P.N Unidad Irapuato, Irapuato 36821, Mexico;
- Correspondence: or (K.A.-P.); (R.W.H.); (M.H.-R.); Tel.: +1-301-504-5203 (R.W.H.)
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Li S, Wu ZG, Zhou Y, Dong ZF, Fei X, Zhou CY, Li SF. Changes in metabolism modulate induced by viroid infection in the orchid Dendrobium officinale. Virus Res 2021; 308:198626. [PMID: 34780884 DOI: 10.1016/j.virusres.2021.198626] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 12/15/2022]
Abstract
Dendrobium officinale is an important traditional Chinese medicinal herb, and the stem tissue is the main medicinal that is harvested from D. officinale. Recently, the first viroid was identified from D. officinale in China, and it has been named Dendrobium viroid (DVd). Whether DVd interferes with metabolic pathways in dendrobium plants and affects the medicinal value of the host is unknown. In this study, metabolomics data from stem tissues supported by transcriptome studies were used to investigate how metabolism modulate of D. officinale is altered by DVd infection. Our results show that metabolism of D. officinale is reprogrammed in many ways during DVd infection, and this is reflected by significant changes in the levels of flavonoids, alkaloids, and phenolic acids. Furthermore, we found that DVd infection significantly decreased the accumulation of flavonoids and alkaloid metabolites in infected stems, and the decreases in these metabolites appears to affect the medicinal components of the infected plants, weakening the host antiviral immune response as well. Conversely, phenolic acids occupy a larger proportion of the up-regulated metabolites from DVd infection in comparison with the mock-inoculated control, and the increase in the total phenolic acids may reflect the activation of the pathogen defense response in D. officinale. Taken together, our results provide an interesting overview and give a better understanding of the relationship between metabolism and DVd infection in the orchid D. officinale.
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Affiliation(s)
- Shuai Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing 400700, China
| | - Zhi-Gang Wu
- School of Pharmacy, Wenzhou Medical University, Wenzhou, 325035, China
| | - Ying Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Zhen-Fei Dong
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Xuan Fei
- School of Pharmacy, Wenzhou Medical University, Wenzhou, 325035, China
| | - Chang-Yong Zhou
- Citrus Research Institute, Chinese Academy of Agricultural Sciences/Southwest University, Chongqing 400700, China
| | - Shi-Fang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Góra-Sochacka A, Więsyk A, Fogtman A, Lirski M, Zagórski-Ostoja W. Root Transcriptomic Analysis Reveals Global Changes Induced by Systemic Infection of Solanum lycopersicum with Mild and Severe Variants of Potato Spindle Tuber Viroid. Viruses 2019; 11:v11110992. [PMID: 31671783 PMCID: PMC6893655 DOI: 10.3390/v11110992] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/24/2019] [Accepted: 10/26/2019] [Indexed: 12/11/2022] Open
Abstract
Potato spindle tuber viroid (PSTVd) causes systemic infection in plant hosts. There are many studies on viroid-host plant interactions, but they have predominantly focused on the aboveground part of the plant. Here, we investigated transcriptomic profile changes in tomato roots systemically infected with mild or severe PSTVd variants using a combined microarray/RNA-seq approach. Analysis indicated differential expression of genes related to various Gene Ontology categories depending on the stage of infection and PSTVd variant. A majority of cell-wall-related genes were down-regulated at early infection stages, but at the late stage, the number of up-regulated genes increased significantly. Along with observed alterations of many lignin-related genes, performed lignin quantification indicated their disrupted level in PSTVd-infected roots. Altered expression of genes related to biosynthesis and signaling of auxin and cytokinin, which are crucial for lateral root development, was also identified. Comparison of both PSTVd infections showed that transcriptional changes induced by the severe variant were stronger than those caused by the mild variant, especially at the late infection stage. Taken together, we showed that similarly to aboveground plant parts, PSTVd infection in the underground tissues activates the plant immune response.
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Affiliation(s)
- Anna Góra-Sochacka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
| | - Aneta Więsyk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
| | - Maciej Lirski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw, Poland.
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Global Transcriptomic Analysis Reveals Insights into the Response of 'Etrog' Citron ( Citrus medica L.) to Citrus Exocortis Viroid Infection. Viruses 2019; 11:v11050453. [PMID: 31109003 PMCID: PMC6563217 DOI: 10.3390/v11050453] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/11/2019] [Accepted: 05/15/2019] [Indexed: 12/11/2022] Open
Abstract
Citrus exocortis viroid (CEVd) is the causal agent of citrus exocortis disease. We employed CEVd-infected ‘Etrog’ citron as a system to study the feedback regulation mechanism using transcriptome analysis in this study. Three months after CEVd infection, the transcriptome of fresh leaves was analyzed, and 1530 differentially expressed genes were detected. The replication of CEVd in citron induced upregulation of genes encoding key proteins that were involved in the RNA silencing pathway such as Dicer-like 2, RNA-dependent RNA polymerase 1, argonaute 2, argonaute 7, and silencing defective 3, as well as those genes encoding proteins that are related to basic defense responses. Many genes involved in secondary metabolite biosynthesis and chitinase activity were upregulated, whereas other genes related to cell wall and phytohormone signal transduction were downregulated. Moreover, genes encoding disease resistance proteins, pathogenicity-related proteins, and heat shock cognate 70 kDa proteins were also upregulated in response to CEVd infection. These results suggest that basic defense and RNA silencing mechanisms are activated by CEVd infection, and this information improves our understanding of the pathogenesis of viroids in woody plants.
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Genome-Wide Transcriptomic Analysis Reveals Insights into the Response to Citrus bark cracking viroid (CBCVd) in Hop ( Humulus lupulus L.). Viruses 2018; 10:v10100570. [PMID: 30340328 PMCID: PMC6212812 DOI: 10.3390/v10100570] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/12/2018] [Accepted: 10/16/2018] [Indexed: 12/17/2022] Open
Abstract
Viroids are smallest known pathogen that consist of non-capsidated, single-stranded non-coding RNA replicons and they exploits host factors for their replication and propagation. The severe stunting disease caused by Citrus bark cracking viroid (CBCVd) is a serious threat, which spreads rapidly within hop gardens. In this study, we employed comprehensive transcriptome analyses to dissect host-viroid interactions and identify gene expression changes that are associated with disease development in hop. Our analysis revealed that CBCVd-infection resulted in the massive modulation of activity of over 2000 genes. Expression of genes associated with plant immune responses (protein kinase and mitogen-activated protein kinase), hypersensitive responses, phytohormone signaling pathways, photosynthesis, pigment metabolism, protein metabolism, sugar metabolism, and modification, and others were altered, which could be attributed to systemic symptom development upon CBCVd-infection in hop. In addition, genes encoding RNA-dependent RNA polymerase, pathogenesis-related protein, chitinase, as well as those related to basal defense responses were up-regulated. The expression levels of several genes identified from RNA sequencing analysis were confirmed by qRT-PCR. Our systematic comprehensive CBCVd-responsive transcriptome analysis provides a better understanding and insights into complex viroid-hop plant interaction. This information will assist further in the development of future measures for the prevention of CBCVd spread in hop fields.
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Więsyk A, Iwanicka-Nowicka R, Fogtman A, Zagórski-Ostoja W, Góra-Sochacka A. Time-Course Microarray Analysis Reveals Differences between Transcriptional Changes in Tomato Leaves Triggered by Mild and Severe Variants of Potato Spindle Tuber Viroid. Viruses 2018; 10:v10050257. [PMID: 29762480 PMCID: PMC5977250 DOI: 10.3390/v10050257] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/09/2018] [Accepted: 05/12/2018] [Indexed: 01/06/2023] Open
Abstract
Viroids are small non-capsidated non-coding RNA replicons that utilize host factors for efficient propagation and spread through the entire plant. They can incite specific disease symptoms in susceptible plants. To better understand viroid-plant interactions, we employed microarray analysis to observe the changes of gene expression in “Rutgers” tomato leaves in response to the mild (M) and severe (S23) variants of potato spindle tuber viroid (PSTVd). The changes were analyzed over a time course of viroid infection development: (i) the pre-symptomatic stage; (ii) early symptoms; (iii) full spectrum of symptoms and (iv) the so-called ‘recovery’ stage, when stem regrowth was observed in severely affected plants. Gene expression profiles differed depending on stage of infection and variant. In S23-infected plants, the expression of over 3000 genes was affected, while M-infected plants showed 3-fold fewer differentially expressed genes, only 20% of which were specific to the M variant. The differentially expressed genes included many genes related to stress; defense; hormone metabolism and signaling; photosynthesis and chloroplasts; cell wall; RNA regulation, processing and binding; protein metabolism and modification and others. The expression levels of several genes were confirmed by nCounter analysis.
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Affiliation(s)
- Aneta Więsyk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (A.W.); (R.I.-N.); (A.F.)
| | - Roksana Iwanicka-Nowicka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (A.W.); (R.I.-N.); (A.F.)
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Anna Fogtman
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (A.W.); (R.I.-N.); (A.F.)
| | - Włodzimierz Zagórski-Ostoja
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (A.W.); (R.I.-N.); (A.F.)
| | - Anna Góra-Sochacka
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland; (A.W.); (R.I.-N.); (A.F.)
- Correspondence: ; Tel.: +48-22-592-34-08; Fax: +48-22-592-21-90
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Xia C, Li S, Hou W, Fan Z, Xiao H, Lu M, Sano T, Zhang Z. Global Transcriptomic Changes Induced by Infection of Cucumber ( Cucumis sativus L.) with Mild and Severe Variants of Hop Stunt Viroid. Front Microbiol 2017; 8:2427. [PMID: 29312160 PMCID: PMC5733102 DOI: 10.3389/fmicb.2017.02427] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/23/2017] [Indexed: 11/13/2022] Open
Abstract
Fifteen years after transfer to hops, hop stunt viroid-grapevine (HSVd-g) was replaced by HSVd-hop (HSVd-h), a sequence variant that contains changes at five different positions. HSVd-g54 is a laboratory mutant derived from HSVd-g that differs from its progenitor by a single G to A substitution at position 54. While infection by HSVd-h induces only mild stunting in cucumber (Cucumis sativus L.), HSVd-g54 induces much more severe symptoms in this indicator host. Comparison of transcriptome profiles of cucumber infected with HSVd-h or HSVd-g54 with those of mock-inoculated controls obtained by whole transcriptome shotgun sequencing revealed that many genes related to photosynthesis were down-regulated following infection. In contrast, genes encoding RNA-dependent RNA polymerase 1 (CsRDR1), especially CsRDR1c1 and CsRDR1c2, as well as those related to basal defense responses were up-regulated. Expression of genes associated with phytohormone signaling pathways were also altered, indicating that viroid infection initiates a complex array of changes in the host transcriptome. HSVd-g54 induced an earlier and stronger response than HSVd-h, and further examination of these differences will contribute to a better understanding of the mechanisms that determine viroid pathogenicity.
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Affiliation(s)
- Changjian Xia
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory for Agro-Biotechnology, Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wanying Hou
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, State Tobacco Monopoly Bureau, Institue of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zaifeng Fan
- State Key Laboratory for Agro-Biotechnology, Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Hong Xiao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meiguang Lu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
| | - Zhixiang Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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12
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Visser M, Cook G, Burger JT, Maree HJ. In silico analysis of the grapefruit sRNAome, transcriptome and gene regulation in response to CTV-CDVd co-infection. Virol J 2017; 14:200. [PMID: 29058618 PMCID: PMC5651572 DOI: 10.1186/s12985-017-0871-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/16/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Small RNA (sRNA) associated gene regulation has been shown to play a significant role during plant-pathogen interaction. In commercial citrus orchards co-infection of Citrus tristeza virus (CTV) and viroids occur naturally. METHODS A next-generation sequencing-based approach was used to study the sRNA and transcriptional response in grapefruit to the co-infection of CTV and Citrus dwarfing viroid. RESULTS The co-infection resulted in a difference in the expression of a number of sRNA species when comparing healthy and infected plants; the majority of these were derived from transcripts processed in a phased manner. Several RNA transcripts were also differentially expressed, including transcripts derived from two genes, predicted to be under the regulation of sRNAs. These genes are involved in plant hormone systems; one in the abscisic acid, and the other in the cytokinin regulatory pathway. Additional analysis of virus- and viroid-derived small-interfering RNAs (siRNAs) showed areas on the pathogen genomes associated with increased siRNA synthesis. Most interestingly, the starting position of the p23 silencing suppressor's sub-genomic RNA generated a siRNA hotspot on the CTV genome. CONCLUSIONS This study showed the involvement of various genes, as well as endogenous and exogenous RNA-derived sRNA species in the plant-defence response. The results highlighted the role of sRNA-directed plant hormone regulation during biotic stress, as well as a counter-response of plants to virus suppressors of RNA-silencing.
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Affiliation(s)
- Marike Visser
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Glynnis Cook
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
- Citrus Research International, Nelspruit, South Africa
| | - Johan T. Burger
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Hans J. Maree
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
- Agricultural Research Council, Infruitec-Nietvoorbij: Institute for Deciduous Fruit, Vines and Wine, Stellenbosch, South Africa
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13
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Kappagantu M, Bullock JM, Nelson ME, Eastwell KC. Hop stunt viroid: Effect on Host (Humulus lupulus) Transcriptome and Its Interactions With Hop Powdery Mildew (Podospheara macularis). MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:842-851. [PMID: 28703029 DOI: 10.1094/mpmi-03-17-0071-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viroids are the smallest known plant pathogens that exploit host systems for their replication and cause diseases in many hosts. In this study, the host response of hop plants to Hop stunt viroid (HSVd) infection was studied through transcriptome analysis. RNA sequence analysis of hop leaves infected with HSVd revealed dynamic changes in hop gene expression. Defense-related genes and genes involved in lipid and terpenoid metabolism are the major categories that showed differential expression due to HSVd infection. Additionally, the effect of HSVd on development of hop powdery mildew (Podospheara macularis) (HPM) was studied. Transcriptome analysis followed by quantitative reverse transcription-polymerase chain reaction analysis showed that transcript levels of pathogenesis-related (PR) genes such as PR protein 1, chitinase, and thaumatin-like protein genes are induced in leaves infected with HPM alone. The response in these genes to HPM is significantly down-regulated in leaves with HSVd-HPM mixed infection. These results confirm that HSVd alters host metabolism, physiology, and plant defense responses. Nevertheless, in detached leaf assays, HPM consistently expanded faster on HSVd-negative leaves relative to HSVd-positive leaves. Although HSVd infection suppresses elements associated with the host immunity response, infection by HSVd is antagonistic to HPM infection of hops.
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Affiliation(s)
- Madhu Kappagantu
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
| | - Jeff M Bullock
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
| | - Mark E Nelson
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
| | - Kenneth C Eastwell
- Department of Plant Pathology, Washington State University-IAREC, 24106 N Bunn Road, Prosser 99350, WA, U.S.A
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14
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Bagherian SAA, Hamzehzarghani H, Izadpanah K, Djavaheri M. Effects of potato spindle tuber viroid infection on tomato metabolic profile. JOURNAL OF PLANT PHYSIOLOGY 2016; 201:42-53. [PMID: 27393919 DOI: 10.1016/j.jplph.2016.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 05/25/2016] [Accepted: 06/21/2016] [Indexed: 06/06/2023]
Abstract
Viroids are the smallest plant pathogens consisting of a single stranded circular RNA molecule with a strong secondary structure, lacking a coat protein or any other proteins. The mechanism of viroid pathogenicity has remained unclear. Recent advances in instrumentation and data mining have made it possible to study the effects of various stresses on primary and secondary metabolisms. Here, we have utilized metabolic profiling approach to show how PSTVd infection alters tomato metabolic profile and the related pathways. Three terminal leaflets of third true leaf of 20-day-old tolerant tomato cultivar 'Moneymaker' were mechanically inoculated by PSTVd intermediate variant cDNAs and samples were taken from eighth leaf, 19days post-inoculation. Metabolites were extracted and analyzed by gas chromatography/mass spectrometry (GC/MS) and subjected to statistical data analysis. Affected pathways were identified by Pathway Tools program and were compared with microarray data previously reported. The study showed that 79 metabolites changed significantly and 23 pathways were identified in relation to these metabolites. Fourteen of these pathways were similar to those reported in other works. The altered pathways in PSTVd infected tomato leaves included, eight cutin and wax biosynthesis, seven pathways that produce defense related compounds, two energy generator pathways, three hormone biosynthesis pathways, two signal transduction pathways, and one nucleotide biosynthesis pathway. Our data on up/down-regulation of pathways supported the data produced on their corresponding gene(s) up/down-regulation.
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Affiliation(s)
| | | | | | - Mohammad Djavaheri
- Department of Plant Protection, College of Agriculture, Shiraz University, Shiraz, Iran
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15
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Martinez G, Castellano M, Tortosa M, Pallas V, Gomez G. A pathogenic non-coding RNA induces changes in dynamic DNA methylation of ribosomal RNA genes in host plants. Nucleic Acids Res 2013; 42:1553-62. [PMID: 24178032 PMCID: PMC3919566 DOI: 10.1093/nar/gkt968] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Viroids are plant-pathogenic non-coding RNAs able to interfere with as yet poorly known host-regulatory pathways and to cause alterations recognized as diseases. The way in which these RNAs coerce the host to express symptoms remains to be totally deciphered. In recent years, diverse studies have proposed a close interplay between viroid-induced pathogenesis and RNA silencing, supporting the belief that viroid-derived small RNAs mediate the post-transcriptional cleavage of endogenous mRNAs by acting as elicitors of symptoms expression. Although the evidence supporting the role of viroid-derived small RNAs in pathogenesis is robust, the possibility that this phenomenon can be a more complex process, also involving viroid-induced alterations in plant gene expression at transcriptional levels, has been considered. Here we show that plants infected with the ‘Hop stunt viroid’ accumulate high levels of sRNAs derived from ribosomal transcripts. This effect was correlated with an increase in the transcription of ribosomal RNA (rRNA) precursors during infection. We observed that the transcriptional reactivation of rRNA genes correlates with a modification of DNA methylation in their promoter region and revealed that some rRNA genes are demethylated and transcriptionally reactivated during infection. This study reports a previously unknown mechanism associated with viroid (or any other pathogenic RNA) infection in plants providing new insights into aspects of host alterations induced by the viroid infectious cycle.
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Affiliation(s)
- German Martinez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas (CSIC)-UPV, CPI, Edificio 8 E, Avenida de los Naranjos s/n, 46022 Valencia, Spain
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16
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A remarkable synergistic effect at the transcriptomic level in peach fruits doubly infected by prunus necrotic ringspot virus and peach latent mosaic viroid. Virol J 2013; 10:164. [PMID: 23710752 PMCID: PMC3672095 DOI: 10.1186/1743-422x-10-164] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 05/21/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Microarray profiling is a powerful technique to investigate expression changes of large amounts of genes in response to specific environmental conditions. The majority of the studies investigating gene expression changes in virus-infected plants are limited to interactions between a virus and a model host plant, which usually is Arabidopsis thaliana or Nicotiana benthamiana. In the present work, we performed microarray profiling to explore changes in the expression profile of field-grown Prunus persica (peach) originating from Chile upon single and double infection with Prunus necrotic ringspot virus (PNRSV) and Peach latent mosaic viroid (PLMVd), worldwide natural pathogens of peach trees. RESULTS Upon single PLMVd or PNRSV infection, the number of statistically significant gene expression changes was relatively low. By contrast, doubly-infected fruits presented a high number of differentially regulated genes. Among these, down-regulated genes were prevalent. Functional categorization of the gene expression changes upon double PLMVd and PNRSV infection revealed protein modification and degradation as the functional category with the highest percentage of repressed genes whereas induced genes encoded mainly proteins related to phosphate, C-compound and carbohydrate metabolism and also protein modification. Overrepresentation analysis upon double infection with PLMVd and PNRSV revealed specific functional categories over- and underrepresented among the repressed genes indicating active counter-defense mechanisms of the pathogens during infection. CONCLUSIONS Our results identify a novel synergistic effect of PLMVd and PNRSV on the transcriptome of peach fruits. We demonstrate that mixed infections, which occur frequently in field conditions, result in a more complex transcriptional response than that observed in single infections. Thus, our data demonstrate for the first time that the simultaneous infection of a viroid and a plant virus synergistically affect the host transcriptome in infected peach fruits. These field studies can help to fully understand plant-pathogen interactions and to develop appropriate crop protection strategies.
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17
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Gómez G, Pallás V. Viroids: a light in the darkness of the lncRNA-directed regulatory networks in plants. THE NEW PHYTOLOGIST 2013; 198:10-15. [PMID: 23397958 DOI: 10.1111/nph.12196] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Affiliation(s)
- Gustavo Gómez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, CPI - Av. Fausto Elio s/n, 46022, Valencia, Spain
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, CPI - Av. Fausto Elio s/n, 46022, Valencia, Spain
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18
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Tessitori M, Rizza S, Reina A, Causarano G, Di Serio F. The genetic diversity of Citrus dwarfing viroid populations is mainly dependent on the infected host species. J Gen Virol 2012; 94:687-693. [PMID: 23152366 DOI: 10.1099/vir.0.048025-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
As with viruses, viroids infect their hosts as polymorphic populations of variants. Identifying possible sources of genetic variability is significant in the case of the species Citrus dwarfing viroid (CDVd) which has been proposed as a dwarfing agent for high-density citrus plantings. Here, a natural CDVd isolate (CMC) was used as an inoculum source for long-term (25 years) and short-term (1 year) bioassays in different citrus host species. Characterization of progenies indicated that the genetic stability of CDVd populations was high in certain hosts (trifoliate orange, Troyer citrange, Etrog citron, Navelina sweet orange), which preserve viroid populations similar to the original CMC isolate even after 25 years. By contrast, CDVd variant populations in Interdonato lemon and Volkamer lemon were completely different to those in the inoculated sources, highlighting how influential the host is on the genetic variability of CDVd populations. Implications for risk assessment of CDVd as a dwarfing agent are discussed. The GenBank/EMBL/DDBJ accession numbers for the complete sequences of the Citrus dwarfing viroid variants are JF970266.1 forH2-2, JF970267.1 for H2-7, EU938647.1 for H6-2, EU938651.1 forH6-10, JF970268.1 for H10-7, EU938652.1 for H14-13, EU938653.1for H14-14, JF970269.1 for H14-16, EU938648.1 for H15-9,EU938649.1 for H16-2, JF970265.1 for H16-9, EU938654.1 forH16-13, EU938650.1 for H20-3, JF970270.1 for H20-7, EU938641.1for PR-1, EU938642.1 for PR-3, EU938643.1 for PR-7, EU938644.1for CR-1, EU938639.1 for VR-4, JF12070.1 for VR-15, JF812069.1LS-4, EU938640.1 for LS-10 and JF970264.1 for LS-11.
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Affiliation(s)
- Matilde Tessitori
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari - Sez. Fitopatologia e Genetica agraria, Università di Catania, 95123 Catania, Italy
| | - Serena Rizza
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari - Sez. Fitopatologia e Genetica agraria, Università di Catania, 95123 Catania, Italy
| | - Antonella Reina
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari - Sez. Fitopatologia e Genetica agraria, Università di Catania, 95123 Catania, Italy
| | - Giovanni Causarano
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari - Sez. Fitopatologia e Genetica agraria, Università di Catania, 95123 Catania, Italy
| | - Francesco Di Serio
- Istituto di Virologia Vegetale, UOS Bari, Consiglio Nazionale delle Ricerche, 70126 Bari, Italy
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19
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Rizza S, Conesa A, Juarez J, Catara A, Navarro L, Duran-Vila N, Ancillo G. Microarray analysis of Etrog citron (Citrus medica L.) reveals changes in chloroplast, cell wall, peroxidase and symporter activities in response to viroid infection. MOLECULAR PLANT PATHOLOGY 2012; 13:852-64. [PMID: 22420919 PMCID: PMC6638686 DOI: 10.1111/j.1364-3703.2012.00794.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Viroids are small (246-401 nucleotides), single-stranded, circular RNA molecules that infect several crop plants and can cause diseases of economic importance. Citrus are the hosts in which the largest number of viroids have been identified. Citrus exocortis viroid (CEVd), the causal agent of citrus exocortis disease, induces considerable losses in citrus crops. Changes in the gene expression profile during the early (pre-symptomatic) and late (post-symptomatic) stages of Etrog citron infected with CEVd were investigated using a citrus cDNA microarray. MaSigPro analysis was performed and, on the basis of gene expression profiles as a function of the time after infection, the differentially expressed genes were classified into five clusters. FatiScan analysis revealed significant enrichment of functional categories for each cluster, indicating that viroid infection triggers important changes in chloroplast, cell wall, peroxidase and symporter activities.
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Affiliation(s)
- Serena Rizza
- Department of Phytosanitary Sciences and Technologies-University of Catania, Via S. Sofia 102, 95123 Catania, Italy
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20
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Navarro B, Gisel A, Rodio ME, Delgado S, Flores R, Di Serio F. Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:991-1003. [PMID: 22332758 DOI: 10.1111/j.1365-313x.2012.04940.x] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
How viroids, tiny non-protein-coding RNAs (~250-400 nt), incite disease is unclear. One hypothesis is that viroid-derived small RNAs (vd-sRNAs; 21-24 nt) resulting from the host defensive response, via RNA silencing, may target for cleavage cell mRNAs and trigger a signal cascade, eventually leading to symptoms. Peach latent mosaic viroid (PLMVd), a chloroplast-replicating viroid, is particularly appropriate to tackle this question because it induces an albinism (peach calico, PC) strictly associated with variants containing a specific 12-14-nt hairpin insertion. By dissecting albino and green leaf sectors of Prunus persica (peach) seedlings inoculated with PLMVd natural and artificial variants, and cloning their progeny, we have established that the hairpin insertion sequence is involved in PC. Furthermore, using deep sequencing, semi-quantitative RT-PCR and RNA ligase-mediated rapid amplification of cDNA ends (RACE), we have determined that two PLMVd-sRNAs containing the PC-associated insertion (PC-sRNA8a and PC-sRNA8b) target for cleavage the mRNA encoding the chloroplastic heat-shock protein 90 (cHSP90), thus implicating RNA silencing in the modulation of host gene expression by a viroid. Chloroplast malformations previously reported in PC-expressing tissues are consistent with the downregulation of cHSP90, which participates in chloroplast biogenesis and plastid-to-nucleus signal transduction in Arabidopsis. Besides PC-sRNA8a and PC-sRNA8b, both deriving from the less-abundant PLMVd (-) strand, we have identified other PLMVd-sRNAs potentially targeting peach mRNAs. These results also suggest that sRNAs derived from other PLMVd regions may downregulate additional peach genes, ultimately resulting in other symptoms or in a more favorable host environment for viroid infection.
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Affiliation(s)
- Beatriz Navarro
- Istituto di Virologia Vegetale-CNR, Unità Organizzativa di Bari, Via Amendola 165/A, 70126 Bari, Italy
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21
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Owens RA, Tech KB, Shao JY, Sano T, Baker CJ. Global analysis of tomato gene expression during Potato spindle tuber viroid infection reveals a complex array of changes affecting hormone signaling. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:582-98. [PMID: 22217247 DOI: 10.1094/mpmi-09-11-0258] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Viroids like Potato spindle tuber viroid (PSTVd) are the smallest known agents of infectious disease-small, highly structured, circular RNA molecules that lack detectable messenger RNA activity, yet are able to replicate autonomously in susceptible plant species. To better understand the possible role of RNA silencing in disease induction, a combination of microarray analysis and large-scale RNA sequence analysis was used to compare changes in tomato gene expression and microRNA levels associated with PSTVd infection in two tomato cultivars plus a third transformed line expressing small PSTVd small interfering RNAs in the absence of viroid replication. Changes in messenger (m)RNA levels for the sensitive cultivar 'Rutgers' were extensive, involving more than half of the approximately 10,000 genes present on the array. Chloroplast biogenesis was down-regulated in both sensitive and tolerant cultivars, and effects on mRNAs encoding enzymes involved in the biosynthesis of gibberellin and other hormones were accompanied by numerous changes affecting their respective signaling pathways. In the dwarf cultivar 'MicroTom', a marked upregulation of genes involved in response to stress and other stimuli was observed only when exogenous brassinosteroid was applied to infected plants, thereby providing the first evidence for the involvement of brassinosteroid-mediated signaling in viroid disease induction.
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Affiliation(s)
- Robert A Owens
- Molecular Plant Pathology Laboratory (USDA/ARS), 10300 Baltimore Avenue, Beltsville, MD 20705, USA.
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22
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Ding B. Viroids: self-replicating, mobile, and fast-evolving noncoding regulatory RNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 1:362-75. [PMID: 21956936 DOI: 10.1002/wrna.22] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Viroids are small, circular, and noncoding RNAs that infect plants. They replicate in the nucleus or chloroplast and then traffic from cell to cell and from organ to organ to establish systemic infection. Viroids achieve nearly all of the biological functions by directly interacting with host cellular factors. Viroid replication, together with replication of human hepatitis delta virus, demonstrates the biological novelty and significance of RNA-dependent RNA polymerase activities of DNA-dependent RNA polymerases. Viroid systemic infection uncovers a new biological principle--the role of three-dimensional RNA structural motifs mediating RNA trafficking between specific cells. Viroid diseases are virtually the consequences of host gene regulation by noncoding RNAs. A viroid RNA has the highest in vivo mutation rate among all known nucleic acid replicons. The host range of many viroids is expanding, essentially as a result of continuing and fast evolution of noncoding sequences/structures to gain new biological functions. Here, I discuss recent progress in these areas, emphasizing the broad significance of viroid research to the discovery of fundamental biological principles.
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Affiliation(s)
- Biao Ding
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Center for RNA Biology, and Molecular, Cellular and Developmental Biology Program, The Ohio State University, 207 Rightmire Hall, 1060 Carmack Road, Columbus, OH 43210, USA.
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23
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Di Serio F, De Stradis A, Delgado S, Flores R, Navarro B. Cytopathic Effects Incited by Viroid RNAs and Putative Underlying Mechanisms. FRONTIERS IN PLANT SCIENCE 2012; 3:288. [PMID: 23308076 PMCID: PMC3538276 DOI: 10.3389/fpls.2012.00288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 12/03/2012] [Indexed: 05/10/2023]
Abstract
Viroids are infectious agents identified only in plants so far. In contrast to viruses, the genome of viroids is composed of a tiny circular RNA (250-400 nt) not coding for proteins, but containing in its compact structure all the information needed for parasitizing the transcriptional and RNA trafficking machineries of their hosts. Viroid infections are frequently accompanied by cellular and developmental disorders that ultimately result in macroscopic symptoms. The molecular events linking the structural domains of viroid RNAs with cellular and macroscopic alterations remain largely unexplored, although significant progress has been lately achieved in one specific viroid-host combination, highlighting the ability of viroids to strongly interfere with their host RNA regulatory networks. Cytopathic effects induced by nuclear-replicating viroids, which were investigated since early studies on viroids, consist in irregular proliferations of cell membranes (paramural bodies or plasmalemmasomes), cell wall distortions, and chloroplast malformations. Different alternatives have been proposed regarding how these cytological alterations may influence the onset of macroscopic symptoms. Recently, the cytopathology and histopathology incited by a chloroplast-replicating viroid have been investigated in depth, with defects in chloroplast development having been related to specific molecular events that involve RNA silencing and impairment of chloroplast ribosomal RNA maturation. On this basis, a tentative model connecting specific cytopathologic alterations with symptoms has been put forward. Here, early and more recent studies addressing this issue will be reviewed and reassessed in the light of recent advances in the regulatory roles of small RNAs.
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Affiliation(s)
- Francesco Di Serio
- Istituto di Virologia Vegetale, UOS Bari, Consiglio Nazionale delle RicercheBari, Italy
- *Correspondence: Francesco Di Serio, Istituto di Virologia Vegetale, UOS Bari, Consiglio Nazionale delle Ricerche, Via Amendola 165/A, 70126 Bari, Italy. e-mail:
| | - Angelo De Stradis
- Istituto di Virologia Vegetale, UOS Bari, Consiglio Nazionale delle RicercheBari, Italy
| | - Sonia Delgado
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones CientíficasValencia, Spain
| | - Beatriz Navarro
- Istituto di Virologia Vegetale, UOS Bari, Consiglio Nazionale delle RicercheBari, Italy
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Murcia N, Bernad L, Duran-Vila N, Serra P. Two nucleotide positions in the Citrus exocortis viroid RNA associated with symptom expression in Etrog citron but not in experimental herbaceous hosts. MOLECULAR PLANT PATHOLOGY 2011; 12:203-8. [PMID: 21199569 PMCID: PMC6640353 DOI: 10.1111/j.1364-3703.2010.00662.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Citrus exocortis viroid (CEVd) is the causal agent of exocortis disease of citrus. CEVd has a wide host range that includes woody and herbaceous species. A new CEVd strain (CEVd(COL)), phylogenetically clustering with CEVd variants of Class A inducing severe symptoms in tomato, was identified in Colombia and shown to induce only extremely mild symptoms in Etrog citron indicator plants. Using site-directed mutagenesis, two nucleotide substitutions (314A → G and 315U → A) in the lower strand of the P domain of the predicted CEVd(COL) secondary structure resulted in a severe artificial CEVd(MCOL) variant. Conversely, two nucleotide exchanges (314G → A and 315A → U) in the same region of the severe variant CEVd(E-117) resulted in a symptomless artificial CEVd(ME-117) variant. Infectivity assays conducted with the natural and mutated variants showed that all induced severe symptoms in Gynura aurantiaca, tomato and chrysanthemum. This is the first report of the identification of pathogenic determinants of CEVd in citrus, and shows that these pathogenicity determinants are host dependent.
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Affiliation(s)
- Nubia Murcia
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Apartado Oficial, 46113-Moncada, Valencia, Spain
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25
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Bhardwaj PK, Ahuja PS, Kumar S. Characterization of gene expression of QM from Caragana jubata, a plant species that grows under extreme cold. Mol Biol Rep 2010; 37:1003-10. [PMID: 19757181 DOI: 10.1007/s11033-009-9791-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Accepted: 09/02/2009] [Indexed: 10/20/2022]
Abstract
Caragana [Caragana jubata (Pall.) Poir] is a temperate plant that thrives well under extremes of cold in high altitude of Himalaya and hence the plant is expected to be a source of genes that might play an important role in tolerance to low temperature (LT). In order to identify LT inducible gene(s), differential display of mRNA (DD) was performed using the apical buds growing under snow as well as growing in the near vicinity without snow, and a LT inducible QM gene (CjQM) homologue was identified. Realizing the importance of QM gene (which encodes human Wilms' tumor suppressor QM protein) in aggregation of 40 and 60S ribosomal subunit and that not much has been reported on this gene in plant systems in relation to its relationship with LT, full length cDNA of CjQM was cloned through rapid amplification of cDNA ends. The gene (977 bp), encoded by small gene family, had an open reading frame of 651 bp and was found to be intronless. The gene exhibited up-regulation within 20 min of exposure to LT and abscisic acid (ABA), but no significant change in gene expression was observed in response to drought stress (DS), salicylic acid (SA) and methyl jasmonate (MJ) application. Up-regulation of CjQM was obtained in the tissues growing in situ under snow. Non-responsiveness of CjQM towards DS, SA and MJ, but up-regulation in response to LT and ABA suggested a specific regulation of the gene in Caragana under varied cues.
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Affiliation(s)
- Pardeep Kumar Bhardwaj
- Biotechnology Division, Institute of Himalayan Bioresource, Technology, Council of Scientific and Industrial Research, P.O. Box 6, Palampur, Himachal Pradesh 176061, India
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Gene expression profiling of phytoplasma-infected Madagascar periwinkle leaves using differential display. Mol Biol Rep 2010; 38:2993-3000. [PMID: 20127177 DOI: 10.1007/s11033-010-9964-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2010] [Accepted: 01/15/2010] [Indexed: 10/19/2022]
Abstract
Phytoplasmas are small (0.2-0.8 μm), wall-less, pleiomorphic prokaryotes responsible of numerous economically important plant diseases. They are characterized by a very small genome and are obligate parasites of phloem tissues and some insects that act as vectors of infection. To investigate molecular mechanisms involved in pathogenesis, the differential display technique was here applied to identify plant genes whose transcription was significantly altered in leaves of Madagascar periwinkle (Catharanthus roseus (L.) G.Don) infected by 'Candidatus Phytoplasma pyri'. We detected, reamplified, cloned, and sequenced 16 putative differentially expressed cDNA fragments. Northern blot analysis revealed that seven of the 16 genes identified were up-regulated following phytoplasma infection, while three genes were down-regulated. The remaining six genes did not show significant changes in the level of expression. Identified genes are mainly involved in plant defence/stress responses, protein metabolism and transport, transcriptional regulation, vesicle trafficking, and carbohydrate metabolism. The possible role played by these genes in the phytoplasma infection is discussed.
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Owens RA, Hammond RW. Viroid pathogenicity: one process, many faces. Viruses 2009; 1:298-316. [PMID: 21994551 PMCID: PMC3185495 DOI: 10.3390/v1020298] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 08/31/2009] [Accepted: 09/01/2009] [Indexed: 12/28/2022] Open
Abstract
Despite the non-coding nature of their small RNA genomes, the visible symptoms of viroid infection resemble those associated with many plant virus diseases. Recent evidence indicates that viroid-derived small RNAs acting through host RNA silencing pathways play a key role in viroid pathogenicity. Host responses to viroid infection are complex, involving signaling cascades containing host-encoded protein kinases and crosstalk between hormonal and defense-signaling pathways. Studies of viroid-host interaction in the context of entire biochemical or developmental pathways are just beginning, and many working hypotheses have yet to be critically tested.
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Affiliation(s)
- Robert A. Owens
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD 20705, USA; E-mail:
| | - Rosemarie W. Hammond
- Molecular Plant Pathology Laboratory, USDA/ARS, Beltsville, MD 20705, USA; E-mail:
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Serra P, Bani Hashemian SM, Pensabene-Bellavia G, Gago S, Duran-Vila N. An artificial chimeric derivative of Citrus viroid V involves the terminal left domain in pathogenicity. MOLECULAR PLANT PATHOLOGY 2009; 10:515-22. [PMID: 19523104 PMCID: PMC6640387 DOI: 10.1111/j.1364-3703.2009.00553.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The recently described Citrus viroid V (CVd-V) induces, in Etrog citron, mild stunting and very small necrotic lesions and cracks, sometimes filled with gum. As Etrog citron plants co-infected with Citrus dwarfing viroid (CDVd) and CVd-V show synergistic interactions, these host-viroid combinations provide a convenient model to identify the pathogenicity determinant(s). The biological effects of replacing limited portions of the rod-like structure of CVd-V with the corresponding portions of CDVd are reported. Chimeric constructs were synthesized using a novel polymerase chain reaction-based approach, much more flexible than those based on restriction enzymes used in previous studies. Of the seven chimeras (Ch) tested, only one (Ch5) proved to be infectious. Plants infected with Ch5 showed no symptoms and, although this novel chimera was able to replicate to relatively high titres in singly infected plants, it was rapidly displaced by either CVd-V or CDVd in doubly infected plants. The results demonstrate that direct interaction(s) between structural elements in the viroid RNA (in this case, the terminal left domain) and as yet unidentified host factors play an important role in modulating viroid pathogenicity. This is the first pathogenic determinant mapped in species of the genus Apscaviroid.
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Affiliation(s)
- Pedro Serra
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain
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Abstract
Viroids are single-stranded, circular, and noncoding RNAs that infect plants. They replicate in the nucleus or chloroplast and then traffic cell-to-cell through plasmodesmata and long distance through the phloem to establish systemic infection. They also cause diseases in certain hosts. All functions are mediated directly by the viroid RNA genome or genome-derived RNAs. I summarize recent advances in the understanding of viroid structures and cellular factors enabling these functions, emphasizing conceptual developments, major knowledge gaps, and future directions. Newly emerging experimental systems and research tools are discussed that are expected to enable significant progress in a number of key areas. I highlight examples of groundbreaking contributions of viroid research to the development of new biological principles and offer perspectives on using viroid models to continue advancing some frontiers of life science.
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Affiliation(s)
- Biao Ding
- Department of Plant Cellular and Molecular Biology and Plant Biotechnology Center, The Ohio State University, Columbus, Ohio 43210, USA.
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30
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Abstract
Viroids are small, circular RNA pathogens, which infect several crop plants and can cause diseases of economic importance. They do not code for proteins but they contain a number of RNA structural elements, which interact with factors of the host. The resulting set of sophisticated and specific interactions enables them to use the host machinery for their replication and transport, circumvent its defence reactions and alter its gene expression. Although found in plants, viroids have a distant relative in the animal world: hepatitis delta virus (HDV), a satellite virus of hepatitis B virus, which has a similar rod-like structure and replicates in the nucleus of infected cells. Viroids have also a cellular relative: the retroviroids, found in some plants as independent (non-infectious) RNA replicons with a DNA copy. In this review, we summarize recent progress in understanding viroid biology. We discuss the possible role of recently identified viroid-binding host proteins as well as the recent data on the interaction of viroids with one part of the host's defence machinery, the RNA-mediated gene silencing and how this might be connected to viroid replication and pathogenicity.
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Affiliation(s)
- Efthimia Mina Tsagris
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, PO Box 1385, 71110 Heraklion, Greece.
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