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Abrahamian P, Tian T, Posis K, Guo YY, Yu D, Blomquist CL, Wei G, Adducci BA, Vidalakis G, Bodaghi S, Osman F, Roy A, Nunziata S, Nakhla MK, Mavrodieva V, Rivera Y. Genetic analysis of the emerging citrus yellow vein clearing virus reveals a divergent virus population in American isolates. Plant Dis 2023. [PMID: 38127632 DOI: 10.1094/pdis-09-23-1963-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Citrus yellow vein clearing virus (CYVCV) is a previously reported citrus virus from Asia with widespread distribution in China. In 2022 the California Department of Food and Agriculture (CDFA) conducted a multi-pest citrus survey targeting multiple citrus pathogens including CYVCV. In March 2022, a lemon tree with symptoms of vein clearing, chlorosis and mottling in a private garden in the city of Tulare, California tested positive for CYVCV, which triggered an intensive survey in the surrounding areas. A total of 3,019 plant samples, including citrus and non-citrus species, were collected, and tested for CYVCV using conventional RT-PCR, RT-qPCR, and Sanger sequencing. Five hundred eighty-six citrus trees tested positive for CYVCV, including eight citrus species not previously recorded infected under field conditions. Comparative genomic studies were conducted using seventeen complete viral genomes. Sequence analysis revealed two major phylogenetic groups. Known Asian isolates and five California isolates from this study comprised the first group, whereas all other CYVCV isolates from California formed a second group, distinct from all worldwide isolates. Overall, CYVCV population shows rapid expansion and high differentiation indicating a population bottleneck typical of a recent introduction into a new geographic area. .
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Affiliation(s)
- Peter Abrahamian
- USDA ARS National Germplasm Resources Laboratory, Beltsville, Maryland, United States;
| | - Tongyan Tian
- CDFA, Plant Pest Diagnostics Center, 3294 Meadowview Road, Sacramento, California, United States, 95832;
| | - Katie Posis
- California Department of Food and Agriculture, Plant Pest Diagnostics Center, 3294 Meadowview Rd., Sacramento, California, United States, 95832;
| | - Ying Yi Guo
- California Department of Food and Agriculture, Plant Pest Diagnostics, 3294 Meadowview Road, Sacramento, California, United States, 95832;
| | - Doris Yu
- California Department of Food and Agriculture, , Plant Pest Diagnostics Laboratory (CDFA-PPDC), Sacramento, California, United States;
| | - Cheryl L Blomquist
- California Department of Food and Agriculture, , Plant Pest Diagnostics Laboratory (CDFA-PPDC), 3294 Meadowview Road, Sacramento, California, United States, 95832;
| | - Gang Wei
- APHIS Plant Protection and Quarantine, 171300, S&T PPCDL, Laurel, Maryland, United States;
| | - Benjamin A Adducci
- APHIS Plant Protection and Quarantine, 171300, S&T PPCDL, Laurel, Maryland, United States;
| | - Georgios Vidalakis
- University of California, Plant Pathology, Department of Plant Pathology, University of California, Riverside, California, United States, 92521;
| | - Sohrab Bodaghi
- University of California Riverside, 8790, Microbiology and Plant Pathology, Riverside, California, United States;
| | - Fatima Osman
- University of California Davis, Foundation Plant Services, 455 Hopkins road, Davis, California, United States, 95616;
| | - Avijit Roy
- USDA Agricultural Research Service, 17123, Molecular Plant Pathology Laboratory, Building 004, Room 117, BARC-West, 10300 Baltimore Avenue, Washington, District of Columbia, United States, 20250;
| | - Schyler Nunziata
- PPQ, CPHST, National Plant Germplasm and Biotechnology Laboratory, Laurel, Maryland, United States;
| | - Mark K Nakhla
- USDA, Animal Plant Health Inspection Service; Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Laurel, Maryland, United States;
| | - Vessela Mavrodieva
- APHIS Plant Protection and Quarantine, 171300, S&T PPCDL, Laurel, Maryland, United States;
| | - Yazmin Rivera
- USDA, Animal Plant Health Inspection Service; Plant Protection and Quarantine, Science and Technology, Plant Pathogen Confirmatory Diagnostics Laboratory, Plant Pathogen Confirmatory Diagnostics Laboratory, 9901 Powder Mill Rd, Laurel, Maryland, United States, 20705;
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Ismail A, Pervaiz T, Comstock S, Bodaghi S, Rezk A, Vidalakis G, El-Sharkawy I, Obenland D, El-kereamy A. Unraveling the occasional occurrence of berry astringency in table grape cv. Scarlet Royal: a physiological and transcriptomic analysis. Front Plant Sci 2023; 14:1271251. [PMID: 37965000 PMCID: PMC10641383 DOI: 10.3389/fpls.2023.1271251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/27/2023] [Indexed: 11/16/2023]
Abstract
Scarlet Royal, a mid-season ripening table grape, is one of the popular red grape varieties in California. However, its berries develop an undesirable astringent taste under certain conditions. Among the various factors contributing to the degradation of berry attributes, the levels and compositions of polyphenols play a fundamental role in defining berry quality and sensory characteristics. To comprehend the underlying mechanism of astringency development, Scarlet Royal berries with non-astringent attributes at the V7 vineyard were compared to astringent ones at the V9 vineyard. Biochemical analysis revealed that the divergence in berry astringency stemmed from alterations in its polyphenol composition, particularly tannins, during the late ripening stage at the V9 vineyard. Furthermore, transcriptomic profiling of berries positively associated nineteen flavonoid/proanthocyanidins (PAs) structural genes with the accumulation of PAs in V9 berries. The identification of these genes holds significance for table grape genetic improvement programs. At a practical level, the correlation between the taste panel and tannin content revealed a threshold level of tannins causing an astringent taste at approximately 400 mg/L. Additionally, berry astringency at the V9 vineyard was linked to a lower number of clusters and yield during the two study seasons, 2016 and 2017. Furthermore, petiole nutrient analysis at bloom showed differences in nutrient levels between the two vineyards, including higher levels of nitrogen and potassium in V9 vines compared to V7. It's worth noting that V9 berries at harvest displayed a lower level of total soluble solids and higher titratable acidity compared to V7 berries. In conclusion, our results indicate that the accumulation of tannins in berries during the ripening process results in a reduction in their red color intensity but significantly increases the astringency taste, thereby degrading the berry quality attributes. This study also highlights the association of high nitrogen nutrient levels and a lower crop load with berry astringency in table grapes, paving the way for further research in this area.
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Affiliation(s)
- Ahmed Ismail
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, Riverside, CA, United States
- Department of Horticulture, Faculty of Agriculture, Damanhour University, Damanhour, Egypt
| | - Tariq Pervaiz
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, Riverside, CA, United States
| | - Stacey Comstock
- Department of Microbiology & Plant Pathology, University of California Riverside, Riverside, Riverside, CA, United States
| | - Sohrab Bodaghi
- Department of Microbiology & Plant Pathology, University of California Riverside, Riverside, Riverside, CA, United States
| | - Alaaeldin Rezk
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, Riverside, CA, United States
| | - Georgios Vidalakis
- Department of Microbiology & Plant Pathology, University of California Riverside, Riverside, Riverside, CA, United States
| | - Islam El-Sharkawy
- Center for Viticulture and Small Fruit Research, College of Agriculture and Food Sciences, Florida A&M University, Tallahassee, FL, United States
| | - David Obenland
- United States Department of Agriculture (USDA), Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, United States
| | - Ashraf El-kereamy
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, Riverside, CA, United States
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Pagliaccia D, Hill D, Dang E, Uribe G, De Francesco A, Milton R, De La Torre A, Mounkam A, Dang T, Botaghi S, Lavagi-Craddock I, Syed A, Grover W, Okamba A, Vidalakis G. Automating Citrus Budwood Processing for Downstream Pathogen Detection Through Instrument Engineering. J Vis Exp 2023. [PMID: 37154540 DOI: 10.3791/65159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Graft-transmissible, phloem-limited pathogens of citrus such as viruses, viroids, and bacteria are responsible for devastating epidemics and serious economic losses worldwide. For example, the citrus tristeza virus killed over 100 million citrus trees globally, while "Candidatus Liberibacter asiaticus" has cost Florida $9 billion. The use of pathogen-tested citrus budwood for tree propagation is key for the management of such pathogens. The Citrus Clonal Protection Program (CCPP) at the University of California, Riverside, uses polymerase chain reaction (PCR) assays to test thousands of samples from citrus budwood source trees every year to protect California's citrus and to provide clean propagation units to the National Clean Plant Network. A severe bottleneck in the high-throughput molecular detection of citrus viruses and viroids is the plant tissue processing step. Proper tissue preparation is critical for the extraction of quality nucleic acids and downstream use in PCR assays. Plant tissue chopping, weighing, freeze-drying, grinding, and centrifugation at low temperatures to avoid nucleic acid degradation is time-intensive and labor-intensive and requires expensive and specialized laboratory equipment. This paper presents the validation of a specialized instrument engineered to rapidly process phloem-rich bark tissues from citrus budwood, named the budwood tissue extractor (BTE). The BTE increases sample throughput by 100% compared to current methods. In addition, it decreases labor and the cost of equipment. In this work, the BTE samples had a DNA yield (80.25 ng/µL) that was comparable with the CCPP's hand-chopping protocol (77.84 ng/µL). This instrument and the rapid plant tissue processing protocol can benefit several citrus diagnostic laboratories and programs in California and become a model system for tissue processing for other woody perennial crops worldwide.
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Affiliation(s)
- Deborah Pagliaccia
- Department of Microbiology and Plant Pathology, University of California Riverside; California Agriculture and Food Enterprise (CAFÉ), University of California Riverside
| | | | - Emily Dang
- Department of Microbiology and Plant Pathology, University of California Riverside
| | - Gerardo Uribe
- Department of Microbiology and Plant Pathology, University of California Riverside
| | | | | | | | | | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California Riverside
| | - Sohrab Botaghi
- Department of Microbiology and Plant Pathology, University of California Riverside
| | | | - Alexandra Syed
- Department of Microbiology and Plant Pathology, University of California Riverside
| | - William Grover
- Department of Bioengineering, University of California Riverside
| | - Adriann Okamba
- Ecole Supérieure d'Ingénieurs Léonard de Vinci ESILV; University of California Riverside
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Abstract
Biological indexing is based upon the ability of certain plants, referred to as indicator plants or indicators, to produce specific symptoms when inoculated with a pathogen using mechanical means or grafting. In the case of citrus viroids, clonal indicators are grafted on to vigorous rootstocks such as rough lemon (Citrus × granulata Raf.). The 'Arizona-861-S-1' citron clonal indicator (C. medica L.) can detect and bioamplify all citrus viroids; however, for specific citrus variants of the hop stunt viroid (i.e., CVd-IIb and CVd-IIc), the clonal indicator 'Parson's special # 9' mandarin (C. reticulata Blanco) is preferred. Inoculation techniques and symptom expression are described in detail. Other supporting elements, such as greenhouse conditions and propagation techniques, are also presented.
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Affiliation(s)
- Robert R Krueger
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), National Clonal Germplasm Repository for Citrus and Dates, Riverside, CA, USA.
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
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6
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Vidalakis G, Wang J, Dang T, Rucker T, Bodaghi S, Tan SH, Lavagi-Craddock I, Syed A, Uribe G, Hsieh Y, Carbajal-Moreno J. SYBR ® Green RT-qPCR for the Universal Detection of Citrus Viroids. Methods Mol Biol 2022; 2316:211-217. [PMID: 34845697 DOI: 10.1007/978-1-0716-1464-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) and reverse transcription (RT)-qPCR have now become the gold standard for molecular diagnostics because of its sensitivity, specificity, and reproducibility. In addition, qPCR diagnostics are flexible because they can be scaled for high- or low-throughput applications. Here we describe an optimized assay and workflow for the universal detection of eight citrus viroid species and their variants by RT-qPCR. The assay allows for quick and efficient molecular detection of viroids without the need to run RT-qPCR for each individual viroid species.
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Affiliation(s)
- Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA.
| | - Jinbo Wang
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA.
- United States Department of Agriculture-APHIS-Biotechnology Regulatory Service-Biotechnology Risk Assessment Programs, Riverdale, MD, USA.
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Tavia Rucker
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Shi-Hua Tan
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Irene Lavagi-Craddock
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Alexandra Syed
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Gerardo Uribe
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Yi Hsieh
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Joana Carbajal-Moreno
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
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Hajeri S, Ng J, Grosser J, Vidalakis G. Isolation and Transfection of Citrus Protoplasts with Citrus Exocortis Viroid. Methods Mol Biol 2022; 2316:39-54. [PMID: 34845683 DOI: 10.1007/978-1-0716-1464-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Viroids are RNA-based infectious agents that are single-stranded, covalently closed circular, non-coding, and naked. Unlike RNA viruses, which at least encode proteins for replication, encapsidation, and movement, lack of protein-coding capacity of viroids makes them completely reliant on host for replication and movement. The high genetic diversity in viroids is believed to be due to the absence of proof-reading activity of the host RNA polymerases, the large population size, and the rapid rate of replication. Protoplasts are viable plant cells that are prepared by enzymatic removal of cell walls. Plant protoplasts provide a synchronous single-cell system for studying early events of viroid infection such as replication and genetic diversity at the cellular level. A simple and efficient method to isolate and transfect citrus protoplasts with transcript RNA of citrus exocortis viroid is described in this chapter.
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Affiliation(s)
- Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, CA, USA.
| | - James Ng
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Jude Grosser
- Horticultural Sciences Department, University of Florida-IFAS, Citrus Research and Education Center (CREC), Lake Alfred, FL, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
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8
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Dang T, Osman F, Wang J, Rucker T, Bodaghi S, Tan SH, Pagliaccia D, Lavagi-Craddock I, Vidalakis G. High-Throughput RNA Extraction from Citrus Tissues for the Detection of Viroids. Methods Mol Biol 2022; 2316:57-64. [PMID: 34845684 DOI: 10.1007/978-1-0716-1464-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High-throughput nucleic acid extraction is critical for the implementation of modern viroid detection assays. Successful large-scale nursery, field surveys, and other regulatory, quarantine, or research diagnostic programs are increasingly dependent on high-throughput tissue pulverization and nucleic acid extraction protocols. Magnetic bead-based approaches using semi-automated robotic equipment allow high-throughput extraction and purification of high-quality uniform total nucleic acids for each individual sample. Here, we describe a streamlined and optimized protocol for citrus tissue processing and RNA extraction that can be used for downstream applications such as viroid detection by reverse transcription-quantitative polymerase chain reaction.
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Affiliation(s)
- Tyler Dang
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Fatima Osman
- Department of Plant Pathology, University of California Davis, Davis, CA, USA
| | - Jinbo Wang
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
- United States Department of Agriculture-APHIS-Biotechnology Regulatory Service-Biotechnology Risk Assessment Program, Riverdale, MD, USA
| | - Tavia Rucker
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Shih-Hua Tan
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Deborah Pagliaccia
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Irene Lavagi-Craddock
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA.
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9
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Dang T, Espindola A, Vidalakis G, Cardwell K. An In Silico Detection of a Citrus Viroid from Raw High-Throughput Sequencing Data. Methods Mol Biol 2022; 2316:275-283. [PMID: 34845702 DOI: 10.1007/978-1-0716-1464-8_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
E-probe Diagnostic for Nucleic Acid Analysis (EDNA) is a user-friendly bioinformatic tool that has been adapted for the detection and identification of citrus exocortis viroid (CEVd). Here, we describe the procedures for RNA extraction from citrus tissues, library and sequencing preparation, and the utilization of EDNA Mi-Finder online platform on raw high-throughput sequencing (HTS) data.
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Affiliation(s)
- Tyler Dang
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Andres Espindola
- Institute of Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA.
| | - Kitty Cardwell
- Institute of Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, USA.
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10
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Hajeri S, Vidalakis G, Yokomi RK. Detection of Viroids Using RT-qPCR. Methods Mol Biol 2022; 2316:153-162. [PMID: 34845693 DOI: 10.1007/978-1-0716-1464-8_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Viroids are the smallest known infectious pathogens. They are nonprotein-encoding, single-stranded, circular, naked RNA molecules that can cause several diseases in economically important crops. With the advent of thermal cyclers incorporating fluorescent detection, reverse transcription coupled to the quantitative polymerase chain reaction (RT-qPCR) has transformed the way the viroids are detected. The method involves using sequence-specific primers that anneal to the viroid RNA of interest. The viroid RNA serves as a template during reverse transcription, in which the enzyme reverse transcriptase generates a cDNA copy of a portion of the target RNA molecule. After first-strand cDNA synthesis, RNA template from cDNA:RNA hybrid molecule is removed by digestion with RNase H to improve the sensitivity of PCR step. This cDNA is then be used as a template for amplification of viroid sequence in PCR.
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Affiliation(s)
- Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, CA, USA.
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA
| | - Raymond K Yokomi
- USDA-ARS San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA.
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11
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Dang T, Wang J, Rucker T, Bodaghi S, Lavagi-Craddock I, Vidalakis G. QuantiGene Plex Assay: A Method for High-Throughput Multiplex Citrus Viroid Detection and Identification. Methods Mol Biol 2022; 2316:243-250. [PMID: 34845700 DOI: 10.1007/978-1-0716-1464-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The QuantiGene Plex assay is a molecular non-polymerase chain reaction (PCR)-based multiplex method adapted for citrus viroid detection and identification. Here, we describe the procedures to utilize the QuantiGene Plex assay as a high-throughput screening tool for viroids in purified or crude RNA extracts from citrus tissues.
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Affiliation(s)
- Tyler Dang
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Jinbo Wang
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
- United States Department of Agriculture-APHIS-Biotechnology Regulatory Service-Biotechnology Risk Assessment Program, Riverdale, MD, USA
| | - Tavia Rucker
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Irene Lavagi-Craddock
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, CA, USA.
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12
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Osman F, Vidalakis G. Real-Time Detection of Viroids Using Singleplex and Multiplex Quantitative Polymerase Chain Reaction. Methods Mol Biol 2022; 2316:181-194. [PMID: 34845695 DOI: 10.1007/978-1-0716-1464-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Multiplex quantitative polymerase chain reaction (multiplex qPCR) enables the amplification of more than one target in a single reaction using different reporter dyes with distinct fluorescent spectra. The number of reporter fluorophores is typically restricted to three or four, depending upon the capability of the real-time PCR platform and software used. Each target is amplified by a different set of primers and a uniquely labeled probe that distinguishes each PCR amplicon. Thus, the levels of several targets of interest can be quantified in real time. By combining several reactions in a single tube, multiplex qPCR reduces the quantity, and cost of reagents needed to screen a sample for multiple targets. Specificity and efficiency are not affected by the inclusion of the three assays in a multiplex reaction.
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Affiliation(s)
- Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA, USA.
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, USA.
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13
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Chambers GA, Geering ADW, Holford P, Vidalakis G, Donovan NJ. Development of a one-step RT-qPCR detection assay for the newly described citrus viroid VII. J Virol Methods 2021; 299:114330. [PMID: 34648820 DOI: 10.1016/j.jviromet.2021.114330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 10/20/2022]
Abstract
An apscaviroid, tentatively named citrus viroid VII (CVd-VII), was recently discovered in citrus in Australia. A diagnostic assay using real-time reverse transcription polymerase chain reaction was developed and validated to detect the viroid in citrus plants. The assay showed a high level of sensitivity, reliably detecting 2000 plasmid copies per reaction, while down to 20 plasmid copies per reaction were occasionally detected. The assay showed high specificity, producing no false positives or cross-reactivity with a range of other citrus graft-transmissible pathogens, including viroids, viruses and bacteria. The real-time assay was also found to be more sensitive than the available end-point reverse transcription polymerase chain reaction assay by a factor of 100,000 and could be a useful tool for the rapid detection of CVd-VII in diagnostic and research environments.
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Affiliation(s)
- Grant A Chambers
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Private Bag 4008, Narellan, NSW, 2567, Australia; Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland, 4001, Australia.
| | - Andrew D W Geering
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, GPO Box 267, Brisbane, Queensland, 4001, Australia
| | - Paul Holford
- Western Sydney University, School of Science, LB 1797, Penrith, NSW, 2752, Australia
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Nerida J Donovan
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Private Bag 4008, Narellan, NSW, 2567, Australia
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Di Serio F, Owens RA, Li SF, Matoušek J, Pallás V, Randles JW, Sano T, Verhoeven JTJ, Vidalakis G, Flores R, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Pospiviroidae. J Gen Virol 2021; 102. [PMID: 33331814 PMCID: PMC8116940 DOI: 10.1099/jgv.0.001543] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Members of the family Pospiviroidae have single-stranded circular RNA genomes that adopt a rod-like or a quasi-rod-like conformation. These genomes contain a central conserved region that is involved in replication in the nucleus through an asymmetric RNA-RNA rolling-circle mechanism. Members of the family Pospiviroidae lack the hammerhead ribozymes that are typical of viroids classified in the family Avsunviroidae. The family Pospiviroidae includes the genera Apscaviroid, Cocadviroid, Coleviroid, Hostuviroid and Pospiviroid, with >25 species. This is a summary of the ICTV Report on the family Pospiviroidae, which is available at ictv.global/report/pospiviroidae.
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Affiliation(s)
- Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, 70126, Italy
| | - Robert A Owens
- Molecular Plant Pathology Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Shi-Fang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China
| | - Jaroslav Matoušek
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, 37005 České Budějovice, Czech Republic
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, 46010, Spain
| | - John W Randles
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | | | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia, 46010, Spain
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15
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Kwon SJ, Bodaghi S, Dang T, Gadhave KR, Ho T, Osman F, Al Rwahnih M, Tzanetakis IE, Simon AE, Vidalakis G. Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV). Front Microbiol 2021; 12:683130. [PMID: 34168635 PMCID: PMC8218546 DOI: 10.3389/fmicb.2021.683130] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/05/2021] [Indexed: 12/22/2022] Open
Abstract
Citrus yellow-vein disease (CYVD) was first reported in California in 1957. We now report that CYVD is associated with a virus-like agent, provisionally named citrus yellow-vein associated virus (CYVaV). The CYVaV RNA genome has 2,692 nucleotides and codes for two discernable open reading frames (ORFs). ORF1 encodes a protein of 190 amino acid (aa) whereas ORF2 is presumably generated by a −1 ribosomal frameshifting event just upstream of the ORF1 termination signal. The frameshift product (717 aa) encodes the RNA-dependent RNA polymerase (RdRp). Phylogenetic analyses suggest that CYVaV is closely related to unclassified virus-like RNAs in the family Tombusviridae. Bio-indexing and RNA-seq experiments indicate that CYVaV can induce yellow vein symptoms independently of known citrus viruses or viroids.
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Affiliation(s)
- Sun-Jung Kwon
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States.,Institutes of Green Bio Science and Technology, Seoul National University, Pyeongchang, South Korea
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Kiran R Gadhave
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Thien Ho
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, United States
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Ioannis E Tzanetakis
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR, United States
| | - Anne E Simon
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
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16
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Rattner R, Thapa SP, Dang T, Osman F, Selvaraj V, Maheshwari Y, Pagliaccia D, Espindola AS, Hajeri S, Chen J, Coaker G, Vidalakis G, Yokomi R. Genome analysis of Spiroplasma citri strains from different host plants and its leafhopper vectors. BMC Genomics 2021; 22:373. [PMID: 34022804 PMCID: PMC8140453 DOI: 10.1186/s12864-021-07637-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 04/21/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Spiroplasma citri comprises a bacterial complex that cause diseases in citrus, horseradish, carrot, sesame, and also infects a wide array of ornamental and weed species. S. citri is transmitted in a persistent propagative manner by the beet leafhopper, Neoaliturus tenellus in North America and Circulifer haematoceps in the Mediterranean region. Leafhopper transmission and the pathogen's wide host range serve as drivers of genetic diversity. This diversity was examined in silico by comparing the genome sequences of seven S. citri strains from the United States (BR12, CC-2, C5, C189, LB 319, BLH-13, and BLH-MB) collected from different hosts and times with other publicly available spiroplasmas. RESULTS Phylogenetic analysis using 16S rRNA sequences from 39 spiroplasmas obtained from NCBI database showed that S. citri strains, along with S. kunkelii and S. phoeniceum, two other plant pathogenic spiroplasmas, formed a monophyletic group. To refine genetic relationships among S. citri strains, phylogenetic analyses with 863 core orthologous sequences were performed. Strains that clustered together were: CC-2 and C5; C189 and R8-A2; BR12, BLH-MB, BLH-13 and LB 319. Strain GII3-3X remained in a separate branch. Sequence rearrangements were observed among S. citri strains, predominantly in the center of the chromosome. One to nine plasmids were identified in the seven S. citri strains analyzed in this study. Plasmids were most abundant in strains isolated from the beet leafhopper, followed by strains from carrot, Chinese cabbage, horseradish, and citrus, respectively. All these S. citri strains contained one plasmid with high similarity to plasmid pSci6 from S. citri strain GII3-3X which is known to confer insect transmissibility. Additionally, 17 to 25 prophage-like elements were identified in these genomes, which may promote rearrangements and contribute to repetitive regions. CONCLUSIONS The genome of seven S. citri strains were found to contain a single circularized chromosome, ranging from 1.58 Mbp to 1.74 Mbp and 1597-2232 protein-coding genes. These strains possessed a plasmid similar to pSci6 from the GII3-3X strain associated with leafhopper transmission. Prophage sequences found in the S. citri genomes may contribute to the extension of its host range. These findings increase our understanding of S. citri genetic diversity.
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Affiliation(s)
- Rachel Rattner
- Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA
| | - Shree Prasad Thapa
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Vijayanandraj Selvaraj
- Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA
| | - Yogita Maheshwari
- Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA
| | - Deborah Pagliaccia
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Andres S Espindola
- Department of Entomology & Plant Pathology and Institute of Biosecurity and Microbial Forensics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, CA, 93274, USA
| | - Jianchi Chen
- Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Raymond Yokomi
- Crop Diseases, Pests, and Genetics Research Unit, San Joaquin Valley Agricultural Sciences Center, USDA Agricultural Research Service, Parlier, CA, 93648, USA.
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17
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Dang T, Lavagi-Craddock I, Bodaghi S, Vidalakis G. Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings. Front Microbiol 2021; 12:646273. [PMID: 33995303 PMCID: PMC8121382 DOI: 10.3389/fmicb.2021.646273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 04/06/2021] [Indexed: 11/19/2022] Open
Abstract
Citrus dwarfing viroid (CDVd) induces stunting on sweet orange trees [Citrus sinensis (L.) Osbeck], propagated on trifoliate orange rootstock [Citrus trifoliata (L.), syn. Poncirus trifoliata (L.) Raf.]. MicroRNAs (miRNAs) are a class of non-coding small RNAs (sRNAs) that play important roles in the regulation of tree gene expression. To identify miRNAs in dwarfed citrus trees, grown in high-density plantings, and their response to CDVd infection, sRNA next-generation sequencing was performed on CDVd-infected and non-infected controls. A total of 1,290 and 628 miRNAs were identified in stem and root tissues, respectively, and among those, 60 were conserved in each of these two tissue types. Three conserved miRNAs (csi-miR479, csi-miR171b, and csi-miR156) were significantly downregulated (adjusted p-value < 0.05) in the stems of CDVd-infected trees compared to the non-infected controls. The three stem downregulated miRNAs are known to be involved in various physiological and developmental processes some of which may be related to the characteristic dwarfed phenotype displayed by CDVd-infected C. sinensis on C. trifoliata rootstock field trees. Only one miRNA (csi-miR535) was significantly downregulated in CDVd-infected roots and it was predicted to target genes controlling a wide range of cellular functions. Reverse transcription quantitative polymerase chain reaction analysis performed on selected miRNA targets validated the negative correlation between the expression levels of these targets and their corresponding miRNAs in CDVd-infected trees. Our results indicate that CDVd-responsive plant miRNAs play a role in regulating important citrus growth and developmental processes that may participate in the cellular changes leading to the observed citrus dwarf phenotype.
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Affiliation(s)
- Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Irene Lavagi-Craddock
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
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18
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Fuchs M, Almeyda CV, Al Rwahnih M, Atallah SS, Cieniewicz EJ, Farrar K, Foote WR, Golino DA, Gómez MI, Harper SJ, Kelly MK, Martin RR, Martinson T, Osman FM, Park K, Scharlau V, Smith R, Tzanetakis IE, Vidalakis G, Welliver R. Economic Studies Reinforce Efforts to Safeguard Specialty Crops in the United States. Plant Dis 2021; 105:14-26. [PMID: 32840434 DOI: 10.1094/pdis-05-20-1061-fe] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Pathogen-tested foundation plant stocks are the cornerstone of sustainable specialty crop production. They provide the propagative units that are used to produce clean planting materials, which are essential as the first-line management option of diseases caused by graft-transmissible pathogens such as viruses, viroids, bacteria, and phytoplasmas. In the United States, efforts to produce, maintain, and distribute pathogen-tested propagative material of specialty crops are spearheaded by centers of the National Clean Plant Network (NCPN). Agricultural economists collaborated with plant pathologists, extension educators, specialty crop growers, and regulators to investigate the impacts of select diseases caused by graft-transmissible pathogens and to estimate the return on investments in NCPN centers. Economic studies have proven valuable to the NCPN in (i) incentivizing the use of clean planting material derived from pathogen-tested foundation plant stocks; (ii) documenting benefits of clean plant centers, which can outweigh operating costs by 10:1 to 150:1; (iii) aiding the development of disease management solutions that are not only ecologically driven but also profit maximizing; and (iv) disseminating integrated disease management recommendations that resonate with growers. Together, economic studies have reinforced efforts to safeguard specialty crops in the United States through the production and use of clean planting material.
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Affiliation(s)
- M Fuchs
- School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - C V Almeyda
- Micropropagation and Repository Unit, North Carolina State University, Raleigh, NC 27695
| | - M Al Rwahnih
- Foundation Plant Services, Plant Pathology Department, University of California, Davis, CA 95616
| | - S S Atallah
- Department of Agricultural and Consumer Economics, University of Illinois, Urbana-Champaign, IL 61820
| | - E J Cieniewicz
- Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - K Farrar
- Foundation Plant Services, Plant Pathology Department, University of California, Davis, CA 95616
| | - W R Foote
- Crops and Soil Sciences, North Carolina State University, Raleigh, NC 27695
| | - D A Golino
- Foundation Plant Services, Plant Pathology Department, University of California, Davis, CA 95616
| | - M I Gómez
- Charles H. Dyson School of Applied Economics and Management, Cornell University, Ithaca, NY 14853
| | - S J Harper
- Department of Plant Pathology, Washington State University, Prosser, WA 99350
| | - M K Kelly
- Department of Agriculture and Markets, Division of Plant Industry, Albany, NY 12205
| | - R R Martin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - T Martinson
- School of Integrative Plant Science, Cornell University, Geneva, NY 14456
| | - F M Osman
- Foundation Plant Services, Plant Pathology Department, University of California, Davis, CA 95616
| | - K Park
- Charles H. Dyson School of Applied Economics and Management, Cornell University, Ithaca, NY 14853
| | - V Scharlau
- Washington Wine Industry Foundation, Cashmere, WA 98815
| | - R Smith
- University of California, Cooperative Extension, Sonoma County, Santa Rosa, CA 95403-2894
| | - I E Tzanetakis
- Department of Entomology and Plant Pathology, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701
| | - G Vidalakis
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA 92521
| | - R Welliver
- The Pennsylvania Department of Agriculture, Bureau of Plant Industry, Harrisburg, PA 17110
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19
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Pagliaccia D, Bodaghi S, Chen X, Stevenson D, Deyett E, De Francesco A, Borneman J, Ruegger P, Peacock B, Ellstrand N, Rolshausen PE, Popa R, Ying S, Vidalakis G. Two Food Waste By-Products Selectively Stimulate Beneficial Resident Citrus Host-Associated Microbes in a Zero-Runoff Indoor Plant Production System. Front Sustain Food Syst 2020. [DOI: 10.3389/fsufs.2020.593568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The global production of food waste is a far-reaching problem with sizable financial, ethical, social, and environmental costs. Over 66 million tons of food waste is produced annually in the United States alone. This waste can be converted into valuable digestate by-products that promote a circular economy within agri-food systems. The present work investigated the use of two liquid digestates of microaerobic fermentation from mixed food waste and beer mash, respectively, as biostimulants for non-bearing citrus plants (nursery stock) grown in a zero-runoff greenhouse system with recirculating irrigation. The digestates' impact on the structure and diversity of the microbiota was determined on the irrigation water, soil, leaves, roots, and rhizosphere of citrus plants. A combination of culture-dependent (selective media) and culture-independent approaches (Next-Generation Sequencing) was used to assess the composition of the microbial communities and to single out the presence of foodborne pathogens. Our results suggest that the use of digestates is safe (i.e., no human or plant pathogens were present in the digestates or enriched in the plant production system following amendments). Digestates application to the irrigation water reduced the bacterial diversity within 24–48 h and selectively and significantly stimulated beneficial resident host-associated microorganisms (Pseudomonas putida) by two to three orders of magnitude. Carbon dynamics were analyzed in the nutrient solutions by measuring dissolved organic carbon and characterizing carbon species through gas chromatography-electron ionization-mass spectrometry. Our results indicate that dissolved organic carbon in the recirculating irrigation water spikes after each digestate amendment and it is quickly metabolized by bacteria, plateauing 24 h after application. Soil carbon, nitrogen, and nutrient dynamics were also analyzed, and results suggest that digestates increased the concentration of some plant nutrients in soils without causing a surge of potentially toxic elements. This study represents a proof-of-concept for the safe re-use of organic wastes, from farming and consumers, in agriculture. Implementing this type of integrated plant production system could reduce the environmental impact of food waste and benefit the public by improving soil health, reducing agricultural footprint, and increasing crop fitness by deploying a method based on a circular economy and sustainable food production approaches.
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20
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Zuñiga C, Peacock B, Liang B, McCollum G, Irigoyen SC, Tec-Campos D, Marotz C, Weng NC, Zepeda A, Vidalakis G, Mandadi KK, Borneman J, Zengler K. Linking metabolic phenotypes to pathogenic traits among "Candidatus Liberibacter asiaticus" and its hosts. NPJ Syst Biol Appl 2020; 6:24. [PMID: 32753656 PMCID: PMC7403731 DOI: 10.1038/s41540-020-00142-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022] Open
Abstract
Candidatus Liberibacter asiaticus (CLas) has been associated with Huanglongbing, a lethal vector-borne disease affecting citrus crops worldwide. While comparative genomics has provided preliminary insights into the metabolic capabilities of this uncultured microorganism, a comprehensive functional characterization is currently lacking. Here, we reconstructed and manually curated genome-scale metabolic models for the six CLas strains A4, FL17, gxpsy, Ishi-1, psy62, and YCPsy, in addition to a model of the closest related culturable microorganism, L. crescens BT-1. Predictions about nutrient requirements and changes in growth phenotypes of CLas were confirmed using in vitro hairy root-based assays, while the L. crescens BT-1 model was validated using cultivation assays. Host-dependent metabolic phenotypes were revealed using expression data obtained from CLas-infected citrus trees and from the CLas-harboring psyllid Diaphorina citri Kuwayama. These results identified conserved and unique metabolic traits, as well as strain-specific interactions between CLas and its hosts, laying the foundation for the development of model-driven Huanglongbing management strategies.
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Affiliation(s)
- Cristal Zuñiga
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Beth Peacock
- Department of Microbiology and Plant Pathology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Bo Liang
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
- State Key Laboratory of Bioreactor Engineering and Institute of Applied Chemistry, East China University of Science and Technology, Shanghai, People's Republic of China
| | - Greg McCollum
- USDA, ARS, US Horticultural Research Laboratory, 2001 S. Rock Road, Fort Pierce, FL, 34945, USA
| | - Sonia C Irigoyen
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, Weslaco, TX, USA
| | - Diego Tec-Campos
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Campus de Ciencias Exactas e Ingenierías, Mérida, 97203, Yucatán, México
| | - Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Nien-Chen Weng
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA
| | - Alejandro Zepeda
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Campus de Ciencias Exactas e Ingenierías, Mérida, 97203, Yucatán, México
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Kranthi K Mandadi
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, Weslaco, TX, USA
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - James Borneman
- Department of Microbiology and Plant Pathology, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
| | - Karsten Zengler
- Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0760, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, 92093-0412, USA.
- Center for Microbiome Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0403, USA.
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21
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Yokomi R, Rattner R, Osman F, Maheshwari Y, Selvaraj V, Pagliaccia D, Chen J, Vidalakis G. Whole genome sequence of five strains of Spiroplasma citri isolated from different host plants and its leafhopper vector. BMC Res Notes 2020; 13:320. [PMID: 32620150 PMCID: PMC7333264 DOI: 10.1186/s13104-020-05160-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 06/27/2020] [Indexed: 11/12/2022] Open
Abstract
Objectives Spiroplasma citri is a bacterium with a wide host range and is the causal agent of citrus stubborn and brittle root diseases of citrus and horseradish, respectively. S. citri is transmitted in a circulative, persistent manner by the beet leafhopper, Neoaliturus (Circulifer) tenellus (Baker), in North America. Five strains of S. citri were cultured from citrus, horseradish, and N. tenellus from different habitats and times. DNA from cultures were sequenced and genome assembled to expand the database to improve detection assays and better understand its genetics and evolution. Data description The whole genome sequence of five strains of S. citri are described herein. The S. citri chromosome was circularized for all five strains and ranged from 1,576,550 to 1,742,208 bp with a G + C content of 25.4–25.6%. Characterization of extrachromosomal DNAs resulted in identification of one or two plasmids, with a G + C content of 23.3 to 27.6%, from plant hosts; and eight or nine plasmids, with a G + C content of 21.65 to 29.19%, from N. tenellus. Total genome size ranged from 1,611,714 to 1,832,173 bp from plants and 1,968,976 to 2,155,613 bp from the leafhopper. All sequence data has been deposited in DDBJ/ENA/GenBank under the accession numbers CP046368-CP046373 and CP047426-CP047446.
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Affiliation(s)
- Raymond Yokomi
- United States Department of Agriculture -Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA.
| | - Rachel Rattner
- United States Department of Agriculture -Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Yogita Maheshwari
- United States Department of Agriculture -Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Vijayanandraj Selvaraj
- United States Department of Agriculture -Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Deborah Pagliaccia
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Jianchi Chen
- United States Department of Agriculture -Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
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22
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Thapa SP, De Francesco A, Trinh J, Gurung FB, Pang Z, Vidalakis G, Wang N, Ancona V, Ma W, Coaker G. Genome-wide analyses of Liberibacter species provides insights into evolution, phylogenetic relationships, and virulence factors. Mol Plant Pathol 2020; 21:716-731. [PMID: 32108417 PMCID: PMC7170780 DOI: 10.1111/mpp.12925] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 05/04/2023]
Abstract
'Candidatus Liberibacter' species are insect-transmitted, phloem-limited α-Proteobacteria in the order of Rhizobiales. The citrus industry is facing significant challenges due to huanglongbing, associated with infection from 'Candidatus Liberibacter asiaticus' (Las). In order to gain greater insight into 'Ca. Liberibacter' biology and genetic diversity, we have performed genome sequencing and comparative analyses of diverse 'Ca. Liberibacter' species, including those that can infect citrus. Our phylogenetic analysis differentiates 'Ca. Liberibacter' species and Rhizobiales in separate clades and suggests stepwise evolution from a common ancestor splitting first into nonpathogenic Liberibacter crescens followed by diversification of pathogenic 'Ca. Liberibacter' species. Further analysis of Las genomes from different geographical locations revealed diversity among isolates from the United States. Our phylogenetic study also indicates multiple Las introduction events in California and spread of the pathogen from Florida to Texas. Texan Las isolates were closely related, while Florida and Asian isolates exhibited the most genetic variation. We have identified conserved Sec translocon (SEC)-dependent effectors likely involved in bacterial survival and virulence of Las and analysed their expression in their plant host (citrus) and insect vector (Diaphorina citri). Individual SEC-dependent effectors exhibited differential expression patterns between host and vector, indicating that Las uses its effector repertoire to differentially modulate diverse organisms. Collectively, this work provides insights into the evolution of 'Ca. Liberibacter' species, the introduction of Las in the United States and identifies promising Las targets for disease management.
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Affiliation(s)
- Shree P. Thapa
- Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
| | - Agustina De Francesco
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Jessica Trinh
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Fatta B. Gurung
- Citrus CenterDepartment of Agriculture, Agribusiness and Environmental SciencesTexas A&M University‐KingsvilleWeslacoTXUSA
| | - Zhiqian Pang
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceUniversity of FloridaLake AlfredFLUSA
| | - Georgios Vidalakis
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Nian Wang
- Citrus Research and Education CenterDepartment of Microbiology and Cell ScienceUniversity of FloridaLake AlfredFLUSA
| | - Veronica Ancona
- Citrus CenterDepartment of Agriculture, Agribusiness and Environmental SciencesTexas A&M University‐KingsvilleWeslacoTXUSA
| | - Wenbo Ma
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCAUSA
| | - Gitta Coaker
- Department of Plant PathologyUniversity of CaliforniaDavisCAUSA
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23
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Blacutt A, Ginnan N, Dang T, Bodaghi S, Vidalakis G, Ruegger P, Peacock B, Viravathana P, Vieira FC, Drozd C, Jablonska B, Borneman J, McCollum G, Cordoza J, Meloch J, Berry V, Salazar LL, Maloney KN, Rolshausen PE, Roper MC. An In Vitro Pipeline for Screening and Selection of Citrus-Associated Microbiota with Potential Anti-" Candidatus Liberibacter asiaticus" Properties. Appl Environ Microbiol 2020; 86:e02883-19. [PMID: 32086307 PMCID: PMC7117939 DOI: 10.1128/aem.02883-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
Huanglongbing (HLB) is a destructive citrus disease that is lethal to all commercial citrus plants, making it the most serious citrus disease and one of the most serious plant diseases. Because of the severity of HLB and the paucity of effective control measures, we structured this study to encompass the entirety of the citrus microbiome and the chemistries associated with that microbial community. We describe the spatial niche diversity of bacteria and fungi associated with citrus roots, stems, and leaves using traditional microbial culturing integrated with culture-independent methods. Using the culturable sector of the citrus microbiome, we created a microbial repository using a high-throughput bulk culturing and microbial identification pipeline. We integrated an in vitro agar diffusion inhibition bioassay into our culturing pipeline that queried the repository for antimicrobial activity against Liberibacter crescens, a culturable surrogate for the nonculturable "Candidatus Liberibacter asiaticus" bacterium associated with HLB. We identified microbes with robust inhibitory activity against L. crescens that include the fungi Cladosporium cladosporioides and Epicoccum nigrum and bacterial species of Pantoea, Bacillus, and Curtobacterium Purified bioactive natural products with anti-"Ca. Liberibacter asiaticus" activity were identified from the fungus C. cladosporioides Bioassay-guided fractionation of an organic extract of C. cladosporioides yielded the natural products cladosporols A, C, and D as the active agents against L. crescens This work serves as a foundation for unraveling the complex chemistries associated with the citrus microbiome to begin to understand the functional roles of members of the microbiome, with the long-term goal of developing anti-"Ca Liberibacter asiaticus" bioinoculants that thrive in the citrus holosystem.IMPORTANCE Globally, citrus is threatened by huanglongbing (HLB), and the lack of effective control measures is a major concern of farmers, markets, and consumers. There is compelling evidence that plant health is a function of the activities of the plant's associated microbiome. Using Liberibacter crescens, a culturable surrogate for the unculturable HLB-associated bacterium "Candidatus Liberibacter asiaticus," we tested the hypothesis that members of the citrus microbiome produce potential anti-"Ca Liberibacter asiaticus" natural products with potential anti-"Ca Liberibacter asiaticus" activity. A subset of isolates obtained from the microbiome inhibited L. crescens growth in an agar diffusion inhibition assay. Further fractionation experiments linked the inhibitory activity of the fungus Cladosporium cladosporioides to the fungus-produced natural products cladosporols A, C, and D, demonstrating dose-dependent antagonism to L. crescens.
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Affiliation(s)
- Alex Blacutt
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Nichole Ginnan
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Paul Ruegger
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Beth Peacock
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Polrit Viravathana
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Flavia Campos Vieira
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Christopher Drozd
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Barbara Jablonska
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - James Borneman
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
| | - Greg McCollum
- U.S. Department of Agriculture, Agricultural Research Service, Fort Pierce, Florida, USA
| | | | | | - Victoria Berry
- Point Loma Nazarene University, San Diego, California, USA
| | | | | | - Philippe E Rolshausen
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, California, USA
| | - M Caroline Roper
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, California, USA
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24
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Yokomi R, Chen J, Rattner R, Selvaraj V, Maheshwari Y, Osman F, Pagliaccia D, Vidalakis G. Genome Sequence Resource for Spiroplasma citri, Strain CC-2, Associated with Citrus Stubborn Disease in California. Phytopathology 2020; 110:254-256. [PMID: 31502518 DOI: 10.1094/phyto-08-19-0304-a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spiroplasma citri is a bacterium that causes stubborn disease of citrus and infects other crops, ornamentals, and weeds. It is transmitted by leafhoppers in a circulative manner. Due to limited sequence data on S. citri, the bacterium was isolated from naturally infected Chinese cabbage grown on a farm in Fresno County, CA. DNA from S. citri CC-2 was extracted from a pure culture in LD8 and subjected to PacBio sequencing. Four contigs were obtained with a single circular chromosome of 1,709,192 bp and three plasmids of 40,210, 39,313, and 2,921 bp in size. The genome developed herein extends the sequence database of S. citri and is the first whole-genome sequence record of S. citri from California.
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Affiliation(s)
- Raymond Yokomi
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Jianchi Chen
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Rachel Rattner
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Vijayanandraj Selvaraj
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Yogita Maheshwari
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Parlier, CA 93648
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Deborah Pagliaccia
- Department of Botany & Plant Sciences, University of California, Riverside, CA 92521
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside
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25
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Tan SH, Osman F, Bodaghi S, Dang T, Greer G, Huang A, Hammado S, Abu-Hajar S, Campos R, Vidalakis G. Full genome characterization of 12 citrus tatter leaf virus isolates for the development of a detection assay. PLoS One 2019; 14:e0223958. [PMID: 31622412 PMCID: PMC6797102 DOI: 10.1371/journal.pone.0223958] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/18/2019] [Indexed: 12/05/2022] Open
Abstract
Citrus tatter leaf virus (CTLV) threatens citrus production worldwide because it induces bud-union crease on the commercially important Citrange (Poncirus trifoliata × Citrus sinensis) rootstocks. However, little is known about its genomic diversity and how such diversity may influence virus detection. In this study, full-length genome sequences of 12 CTLV isolates from different geographical areas, intercepted and maintained for the past 60 years at the Citrus Clonal Protection Program (CCPP), University of California, Riverside, were characterized using next generation sequencing. Genome structure and sequence for all CTLV isolates were similar to Apple stem grooving virus (ASGV), the type species of Capillovirus genus of the Betaflexiviridae family. Phylogenetic analysis highlighted CTLV’s point of origin in Asia, the virus spillover to different plant species and the bottleneck event of its introduction in the United States of America (USA). A reverse transcription quantitative polymerase chain reaction assay was designed at the most conserved genome area between the coat protein and the 3’-untranslated region (UTR), as identified by the full genome analysis. The assay was validated with different parameters (e.g. specificity, sensitivity, transferability and robustness) using multiple CTLV isolates from various citrus growing regions and it was compared with other published assays. This study proposes that in the era of powerful affordable sequencing platforms the presented approach of systematic full-genome sequence analysis of multiple virus isolates, and not only a small genome area of a small number of isolates, becomes a guideline for the design and validation of molecular virus detection assays, especially for use in high value germplasm programs.
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Affiliation(s)
- Shih-hua Tan
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, California, United States of America
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Tyler Dang
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Greg Greer
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Amy Huang
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Sarah Hammado
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Shurooq Abu-Hajar
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Roya Campos
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
- * E-mail:
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26
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Varady ES, Bodaghi S, Vidalakis G, Douhan GW. Microsatellite characterization and marker development for the fungus Penicillium digitatum, causal agent of green mold of citrus. Microbiologyopen 2019; 8:e00788. [PMID: 30697963 PMCID: PMC6612547 DOI: 10.1002/mbo3.788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 01/24/2023] Open
Abstract
Penicillium digitatum is one of the most important postharvest pathogens of citrus on a global scale causing significant annual losses due to fruit rot. However, little is known about the diversity of P. digitatum populations. The genome of P. digitatum has been sequenced, providing an opportunity to determine the microsatellite distribution within P. digitatum to develop markers that could be valuable tools for studying the population biology of this pathogen. In the analyses, a total of 3,134 microsatellite loci were detected; 66.73%, 23.23%, 8.23%, 1.24%, 0.16%, and 0.77% were detected as mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats, respectively. As consistent with other ascomycete fungi, the genome size of P. digitatum does not seem to correlate with the density of microsatellite loci. However, significantly longer motifs of mono-, di-, and tetranucleotide repeats were identified in P. digitatum compared to 10 other published ascomycete species with repeats of over 800, 300, and 900 motifs found, respectively. One isolate from southern California and five additional isolates from other countries ("global isolates") were used to initially screen microsatellite markers developed in this study. Twelve additional isolates, referred to as the "local isolates," were also collected from citrus at the University of California Riverside agricultural experiment station and were subsequently used to screen the primers that sequenced well and were polymorphic based on the global isolates. Thirty-six primers were screened, and nine trinucleotide loci and one hexanucleotide locus were chosen as robust markers. These loci yielded two to seven alleles and will be useful to study population genetic structure of P. digitatum populations.
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Affiliation(s)
- Erika S. Varady
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCalifornia
- Department of Molecular Biology and BiochemistryUniversity of California IrvineIrvineCalifornia
| | - Sohrab Bodaghi
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCalifornia
| | - Georgios Vidalakis
- Department of Microbiology and Plant PathologyUniversity of CaliforniaRiversideCalifornia
| | - Greg W. Douhan
- University of California Cooperative ExtensionTulareCalifornia
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27
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Dang T, Tan SH, Bodaghi S, Greer G, Lavagi I, Osman F, Ramirez B, Kress J, Goodson T, Weber K, Zhang YP, Vidalakis G. First Report of Citrus viroid V Naturally Infecting Grapefruit and Calamondin Trees in California. Plant Dis 2018; 102:PDIS01180100PDN. [PMID: 30095323 DOI: 10.1094/pdis-01-18-0100-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Affiliation(s)
- T Dang
- Department of Microbiology and Plant Pathology, University of California Riverside, 92521
| | - S H Tan
- Department of Microbiology and Plant Pathology, University of California Riverside, 92521
| | - S Bodaghi
- Department of Microbiology and Plant Pathology, University of California Riverside, 92521
| | - G Greer
- Department of Microbiology and Plant Pathology, University of California Riverside, 92521
| | - I Lavagi
- Department of Microbiology and Plant Pathology, University of California Riverside, 92521
| | - F Osman
- Department Plant Pathology, University of California Davis, 95616
| | - B Ramirez
- Department of Microbiology and Plant Pathology, University of California Riverside, 92521
| | - J Kress
- California Department of Food and Agriculture Nursery Service Program, Sacramento, 95814
| | - T Goodson
- California Department of Food and Agriculture Nursery Service Program, Sacramento, 95814
| | - K Weber
- California Department of Food and Agriculture Nursery Service Program, Sacramento, 95814
| | - Y P Zhang
- California Department of Food and Agriculture Nursery Service Program, Sacramento, 95814
| | - G Vidalakis
- Department of Microbiology and Plant Pathology, University of California Riverside, CA 92521
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28
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Di Serio F, Li SF, Matoušek J, Owens RA, Pallás V, Randles JW, Sano T, Verhoeven JTJ, Vidalakis G, Flores R, Ictv Report Consortium. ICTV Virus Taxonomy Profile: Avsunviroidae. J Gen Virol 2018; 99:611-612. [PMID: 29580320 DOI: 10.1099/jgv.0.001045] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Members of the family Avsunviroidae have a single-stranded circular RNA genome that adopts a rod-like or branched conformation and can form, in the strands of either polarity, hammerhead ribozymes involved in their replication in plastids through a symmetrical RNA-RNA rolling-circle mechanism. These viroids lack the central conserved region typical of members of the family Pospiviroidae. The family Avsunviroidae includes three genera, Avsunviroid, Pelamoviroid and Elaviroid, with a total of four species. This is a summary of the ICTV Report on the taxonomy of the family Avsunviroidae, which is available at http://www.ictv.global/report/avsunviroidae.
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Affiliation(s)
- Francesco Di Serio
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari 70126, Italy
| | - Shi-Fang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Jaroslav Matoušek
- Biology Centre of the Czech Academy of Sciences v.v.i, Institute of Plant Molecular Biology, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Robert A Owens
- Molecular Plant Pathology Laboratory, US Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA
| | - Vicente Pallás
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia 46010, Spain
| | - John W Randles
- School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Teruo Sano
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki 036-8561, Japan
| | | | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, Valencia 46010, Spain
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29
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Pagliaccia D, Urak RZ, Wong F, Douhan LI, Greer CA, Vidalakis G, Douhan GW. Genetic Structure of the Rice Blast Pathogen (Magnaporthe oryzae) over a Decade in North Central California Rice Fields. Microb Ecol 2018; 75:310-317. [PMID: 28755027 PMCID: PMC5742603 DOI: 10.1007/s00248-017-1029-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
Rice blast, caused by the ascomycete Magnaporthe oryzae, is one of the most destructive rice diseases worldwide. Even though the disease has been present in California since 1996, there is no data for the pathogen population biology in the state. Using amplified fragment length polymorphisms and mating-type markers, the M. oryzae population diversity was investigated using isolates collected when the disease was first established in California and isolates collected a decade later. While in the 1990 samples, a single multilocus genotype (MLG) was identified (MLG1), over a decade later, we found 14 additional MLGs in the 2000 isolates. Some of these MLGs were found to infect the only rice blast-resistant cultivar (M-208) available for commercial production in California. The same samples also had a significant decrease of MLG1. MLG1 was found infecting the resistant rice cultivar M-208 on one occasion whereas MLG7 was the most common genotype infecting the M-208. MLG7 was identified in the 2000 samples, and it was not present in the M. oryzae population a decade earlier. Our results demonstrate a significant increase in genotypic diversity over time with no evidence of sexual reproduction and suggest a recent introduction of new virulent race(s) of the pathogen. In addition, our data could provide information regarding the durability of the Pi-z resistance gene of the M-208. This information will be critical to plant breeders in developing strategies for deployment of other rice blast resistance genes/cultivars in the future.
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Affiliation(s)
- Deborah Pagliaccia
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA.
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
| | - Ryan Z Urak
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
| | - Frank Wong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- Bayer's Environmental Health Division, Bayer, Durham, NC, USA
| | - LeAnn I Douhan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- Val Verde Unified School District, Perris, CA, USA
| | - Christopher A Greer
- Cooperative Extension, University of California, Sutter-Yuba, Yuba City, CA, 95991, USA
| | - Georgios Vidalakis
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
| | - Greg W Douhan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- Cooperative Extension Tulare County, Tulare, CA, USA
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30
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Pagliaccia D, Shi J, Pang Z, Hawara E, Clark K, Thapa SP, De Francesco AD, Liu J, Tran TT, Bodaghi S, Folimonova SY, Ancona V, Mulchandani A, Coaker G, Wang N, Vidalakis G, Ma W. A Pathogen Secreted Protein as a Detection Marker for Citrus Huanglongbing. Front Microbiol 2017; 8:2041. [PMID: 29403441 PMCID: PMC5776943 DOI: 10.3389/fmicb.2017.02041] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/06/2017] [Indexed: 11/26/2022] Open
Abstract
The citrus industry is facing an unprecedented crisis due to Huanglongbing (HLB, aka citrus greening disease), a bacterial disease associated with the pathogen Candidatus Liberibacter asiaticus (CLas) that affects all commercial varieties. Transmitted by the Asian citrus psyllid (ACP), CLas colonizes citrus phloem, leading to reduced yield and fruit quality, and eventually tree decline and death. Since adequate curative measures are not available, a key step in HLB management is to restrict the spread of the disease by identifying infected trees and removing them in a timely manner. However, uneven distribution of CLas cells in infected trees and the long latency for disease symptom development makes sampling of trees for CLas detection challenging. Here, we report that a CLas secreted protein can be used as a biomarker for detecting HLB infected citrus. Proteins secreted from CLas cells can presumably move along the phloem, beyond the site of ACP inoculation and CLas colonized plant cells, thereby increasing the chance of detecting infected trees. We generated a polyclonal antibody that effectively binds to the secreted protein and developed serological assays that can successfully detect CLas infection. This work demonstrates that antibody-based diagnosis using a CLas secreted protein as the detection marker for infected trees offers a high-throughput and economic approach that complements the approved quantitative polymerase chain reaction-based methods to enhance HLB management programs.
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Affiliation(s)
- Deborah Pagliaccia
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jinxia Shi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
- Center for Plant Cell Biology, University of California, Riverside, Riverside, CA, United States
| | - Zhiqian Pang
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Eva Hawara
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Kelley Clark
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Shree P. Thapa
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Agustina D. De Francesco
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jianfeng Liu
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Thien-Toan Tran
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, United States
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | | | - Veronica Ancona
- Texas A&M University – Kingsville Citrus Center, Weslaco, TX, United States
| | - Ashok Mulchandani
- Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, United States
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, Davis, CA, United States
| | - Nian Wang
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Wenbo Ma
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
- Center for Plant Cell Biology, University of California, Riverside, Riverside, CA, United States
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Osman F, Dang T, Bodaghi S, Vidalakis G. One-step multiplex RT-qPCR detects three citrus viroids from different genera in a wide range of hosts. J Virol Methods 2017; 245:40-52. [PMID: 28300606 DOI: 10.1016/j.jviromet.2017.03.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 02/27/2017] [Accepted: 03/10/2017] [Indexed: 01/23/2023]
Abstract
A one-step multiplex reverse transcription real-time quantitative polymerase chain reaction (RT-qPCR) based on species-specific minor groove binding (MGB) probes, was developed for the simultaneous detection, identification, and quantification of three citrus viroids belonging to different genera. Citrus exocortis viroid (Pospiviroid), Hop stunt viroid (Hostuviroid), and Citrus bark cracking viroid (Cocadviroid) cause a variety of maladies in agriculturally significant crops. Therefore, reliable assays for their detection are essential tools for various government and industry organizations implementing disease management programs. Singleplex qPCR primers and MGB probes were designed individually for the detection of the three targeted viroids, and subsequently combined in a one-step multiplex RT-qPCR reaction. A wide host range of woody plants, including citrus, grapevines, apricots, plums and herbaceous plants such as tomato, cucumber, eggplant and chrysanthemum different world regions were used to validate the assay. Single, double and triple viroid infections were identified in the tested samples. The developed multiplex RT-qPCR assay was compared with a previously reported SYBR Green I RT-qPCR for the universal detection of citrus viroids. Both assays accurately identified all citrus viroid infected samples. The multiplex assay complemented the SYBR Green I universal detection assay by differentiating among citrus viroid species in the positive samples. The developed multiplex RT-qPCR assay has the potential to simultaneously detect each targeted viroid and could be used in high throughput screenings for citrus viroids in field surveys, germplasm banks, nurseries and other viroid disease management programs.
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Affiliation(s)
- Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA 95616, USA
| | - Tyler Dang
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Sohrab Bodaghi
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Georgios Vidalakis
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.
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da Graça JV, Douhan GW, Halbert SE, Keremane ML, Lee RF, Vidalakis G, Zhao H. Huanglongbing: An overview of a complex pathosystem ravaging the world's citrus. J Integr Plant Biol 2016; 58:373-87. [PMID: 26466921 DOI: 10.1111/jipb.12437] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/12/2015] [Indexed: 05/24/2023]
Abstract
Citrus huanglongbing (HLB) has become a major disease and limiting factor of production in citrus areas that have become infected. The destruction to the affected citrus industries has resulted in a tremendous increase to support research that in return has resulted in significant information on both applied and basic knowledge concerning this important disease to the global citrus industry. Recent research indicates the relationship between citrus and the causal agent of HLB is shaped by multiple elements, in which host defense responses may also play an important role. This review is intended to provide an overview of the importance of HLB to a wider audience of plant biologists. Recent advances on host-pathogen interactions, population genetics and vectoring of the causal agent are discussed.
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Affiliation(s)
- John V da Graça
- Texas A&M University-Kingsville Citrus Center, Weslaco, Texas 78599, USA
| | - Greg W Douhan
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521, USA
| | - Susan E Halbert
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, P.O. Box 147100, Gainesville, Florida 32614, USA
| | - Manjunath L Keremane
- USDA ARS National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507, USA
| | - Richard F Lee
- USDA ARS National Clonal Germplasm Repository for Citrus and Dates, Riverside, California 92507, USA
| | - Georgios Vidalakis
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521, USA
| | - Hongwei Zhao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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Gergerich RC, Welliver RA, Osterbauer NK, Kamenidou S, Martin RR, Golino DA, Eastwell K, Fuchs M, Vidalakis G, Tzanetakis IE. Safeguarding Fruit Crops in the Age of Agricultural Globalization. Plant Dis 2015; 99:176-187. [PMID: 30699566 DOI: 10.1094/pdis-07-14-0762-fe] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The expansion of fruit production and markets into new geographic areas provides novel opportunities and challenges for the agricultural and marketing industries. Evidence that fruit consumption helps prevent nutrient deficiencies and reduces the risk of cardiovascular disease and cancer has assisted in the expansion of all aspects of the fruit industry. In today's competitive global market environment, producers need access to the best plant material available in terms of genetics and health if they are to maintain a competitive advantage in the market. An ever-increasing amount of plant material in the form of produce, nursery plants, and breeding stock moves vast distances, and this has resulted in an increased risk of pest and disease introductions into new areas. One of the primary concerns of the global fruit industry is a group of systemic pathogens for which there are no effective remedies once plants are infected. These pathogens and diseases require expensive management and control procedures at nurseries and by producers locally and nationally. Here, we review (i) the characteristics of some of these pathogens, (ii) the history and economic consequences of some notable disease epidemics caused by these pathogens, (iii) the changes in agricultural trade that have exacerbated the risk of pathogen introduction, (iv) the path to production of healthy plants through the U.S. National Clean Plant Network and state certification programs, (v) the economic value of clean stock to nurseries and fruit growers in the United States, and (vi) current efforts to develop and harmonize effective nursery certification programs within the United States as well as with global trading partners.
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Affiliation(s)
- Rose C Gergerich
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System
| | - Ruth A Welliver
- Bureau of Plant Industry, Pennsylvania Department of Agriculture
| | | | - Sophia Kamenidou
- Department of Plant Pathology and Microbiology, University of California-Riverside
| | - Robert R Martin
- Horticultural Crops Research Laboratory, USDA-ARS, Corvallis
| | | | | | - Marc Fuchs
- Department of Plant Pathology and Plant Microbe Biology, Cornell University
| | - Georgios Vidalakis
- Department of Plant Pathology and Microbiology, University of California-Riverside
| | - Ioannis E Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System
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Shi J, Pagliaccia D, Morgan R, Qiao Y, Pan S, Vidalakis G, Ma W. Novel diagnosis for citrus stubborn disease by detection of a spiroplasma citri-secreted protein. Phytopathology 2014; 104:188-195. [PMID: 23931112 DOI: 10.1094/phyto-06-13-0176-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Citrus stubborn disease (CSD), first identified in California, is a widespread bacterial disease found in most arid citrus-producing regions in the United States and the Mediterranean Region. The disease is caused by Spiroplasma citri, an insect-transmitted and phloem-colonizing bacterium. CSD causes significant tree damage resulting in loss of fruit production and quality. Detection of CSD is challenging due to low and fluctuating titer and sporadic distribution of the pathogen in infected trees. In this study, we report the development of a novel diagnostic method for CSD using an S. citri-secreted protein as the detection marker. Microbial pathogens secrete a variety of proteins during infection that can potentially disperse systemically in infected plants with the vascular flow. Therefore, their distribution may not be restricted to the pathogen infection sites and could be used as a biological marker for infection. Using mass spectrometry analysis, we identified a unique secreted protein from S. citri that is highly expressed in the presence of citrus phloem extract. ScCCPP1, an antibody generated against this protein, was able to distinguish S. citri-infected citrus and periwinkle from healthy plants. In addition, the antiserum could be used to detect CSD using a simple direct tissue print assay without the need for sample processing or specialized lab equipment and may be suitable for field surveys. This study provides proof of a novel concept of using pathogen-secreted protein as a marker for diagnosis of a citrus bacterial disease and can probably be applied to other plant diseases.
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Wang J, Bozan O, Kwon SJ, Dang T, Rucker T, Yokomi RK, Lee RF, Folimonova SY, Krueger RR, Bash J, Greer G, Diaz J, Serna R, Vidalakis G. Past and future of a century old Citrus tristeza virus collection: a California citrus germplasm tale. Front Microbiol 2013; 4:366. [PMID: 24339822 PMCID: PMC3857578 DOI: 10.3389/fmicb.2013.00366] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 11/18/2013] [Indexed: 01/30/2023] Open
Abstract
Citrus tristeza virus (CTV) isolates collected from citrus germplasm, dooryard and field trees in California from 1914 have been maintained in planta under quarantine in the Citrus Clonal Protection Program (CCPP), Riverside, California. This collection, therefore, represents populations of CTV isolates obtained over time and space in California. To determine CTV genetic diversity in this context, genotypes of CTV isolates from the CCPP collection were characterized using multiple molecular markers (MMM). Genotypes T30, VT, and T36 were found at high frequencies with T30 and T30+VT genotypes being the most abundant. The MMM analysis did not identify T3 and B165/T68 genotypes; however, biological and phylogenetic analysis suggested some relationships of CCPP CTV isolates with these two genotypes. Phylogenetic analysis of the CTV coat protein (CP) gene sequences classified the tested isolates into seven distinct clades. Five clades were in association with the standard CTV genotypes T30, T36, T3, VT, and B165/T68. The remaining two identified clades were not related to any standard CTV genotypes. Spatiotemporal analysis indicated a trend of reduced genotype and phylogenetic diversity as well as virulence from southern California (SC) at early (1907-1957) in comparison to that of central California (CC) isolates collected from later (1957-2009) time periods. CTV biological characterization also indicated a reduced number and less virulent stem pitting (SP) CTV isolates compared to seedling yellows isolates introduced to California. This data provides a historical insight of the introduction, movement, and genetic diversity of CTV in California and provides genetic and biological information useful for CTV quarantine, eradication, and disease management strategies such as CTV-SP cross protection.
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Affiliation(s)
- Jinbo Wang
- Department of Plant Pathology and Microbiology, University of CaliforniaRiverside, USA
| | - Orhan Bozan
- Department of Plant Protection, University of ÇukurovaAdana, Turkey
| | - Sun-Jung Kwon
- Department of Plant Pathology and Microbiology, University of CaliforniaRiverside, USA
| | - Tyler Dang
- Department of Plant Pathology and Microbiology, University of CaliforniaRiverside, USA
| | - Tavia Rucker
- Department of Plant Pathology and Microbiology, University of CaliforniaRiverside, USA
| | - Raymond K. Yokomi
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences CenterParlier, CA, USA
| | - Richard F. Lee
- United States Department of Agriculture-Agricultural Research Service, National Clonal Germplasm Repository for Citrus and DatesRiverside, CA, USA
| | | | - Robert R. Krueger
- United States Department of Agriculture-Agricultural Research Service, National Clonal Germplasm Repository for Citrus and DatesRiverside, CA, USA
| | - John Bash
- Department of Plant Pathology and Microbiology, University of CaliforniaRiverside, USA
| | - Greg Greer
- Department of Plant Pathology and Microbiology, University of CaliforniaRiverside, USA
| | - James Diaz
- Department of Plant Pathology and Microbiology, University of CaliforniaRiverside, USA
| | - Ramon Serna
- Department of Plant Pathology and Microbiology, University of CaliforniaRiverside, USA
| | - Georgios Vidalakis
- Department of Plant Pathology and Microbiology, University of CaliforniaRiverside, USA
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Zhao H, Sun R, Albrecht U, Padmanabhan C, Wang A, Coffey MD, Girke T, Wang Z, Close TJ, Roose M, Yokomi RK, Folimonova S, Vidalakis G, Rouse R, Bowman KD, Jin H. Small RNA profiling reveals phosphorus deficiency as a contributing factor in symptom expression for citrus huanglongbing disease. Mol Plant 2013; 6:301-10. [PMID: 23292880 PMCID: PMC3716302 DOI: 10.1093/mp/sst002] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 12/21/2012] [Indexed: 05/19/2023]
Abstract
Huanglongbing (HLB) is a devastating citrus disease that is associated with bacteria of the genus 'Candidatus Liberibacter' (Ca. L.). Powerful diagnostic tools and management strategies are desired to control HLB. Host small RNAs (sRNA) play a vital role in regulating host responses to pathogen infection and are used as early diagnostic markers for many human diseases, including cancers. To determine whether citrus sRNAs regulate host responses to HLB, sRNAs were profiled from Citrus sinensis 10 and 14 weeks post grafting with Ca. L. asiaticus (Las)-positive or healthy tissue. Ten new microRNAs (miRNAs), 76 conserved miRNAs, and many small interfering RNAs (siRNAs) were discovered. Several miRNAs and siRNAs were highly induced by Las infection, and can be potentially developed into early diagnosis markers of HLB. miR399, which is induced by phosphorus starvation in other plant species, was induced specifically by infection of Las but not Spiroplasma citri that causes citrus stubborn-a disease with symptoms similar to HLB. We found a 35% reduction of phosphorus in Las-positive citrus trees compared to healthy trees. Applying phosphorus oxyanion solutions to HLB-positive sweet orange trees reduced HLB symptom severity and significantly improved fruit production during a 3-year field trial in south-west Florida. Our molecular, physiological, and field data suggest that phosphorus deficiency is linked to HLB disease symptomology.
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Affiliation(s)
- Hongwei Zhao
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Present address: Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ruobai Sun
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Ute Albrecht
- US Horticultural Research Laboratory, US Department of Agriculture, Agricultural Research Service, 2001 South Rock Road, Fort Pierce, FL 34945, USA
| | - Chellappan Padmanabhan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Airong Wang
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Michael D. Coffey
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Thomas Girke
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Zonghua Wang
- Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Timothy J. Close
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Mikeal Roose
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Raymond K. Yokomi
- San Joaquin Valley Agricultural Research Center, US Department of Agriculture, Agricultural Research Service, 9611 S. Riverbend Ave, Parlier, CA 93648, USA
| | - Svetlana Folimonova
- Citrus Research and Education Center, University of Florida, 700 Experiment Station Road, Lake Alfred, FL 33850, USA
| | - Georgios Vidalakis
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Robert Rouse
- University of Florida, 2685 State Road 29 North, Immokalee, FL 34142, USA
| | - Kim D. Bowman
- US Horticultural Research Laboratory, US Department of Agriculture, Agricultural Research Service, 2001 South Rock Road, Fort Pierce, FL 34945, USA
| | - Hailing Jin
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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Hajeri S, Ramadugu C, Manjunath K, Ng J, Lee R, Vidalakis G. In vivo generated Citrus exocortis viroid progeny variants display a range of phenotypes with altered levels of replication, systemic accumulation and pathogenicity. Virology 2011; 417:400-9. [DOI: 10.1016/j.virol.2011.06.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 06/11/2011] [Accepted: 06/13/2011] [Indexed: 02/06/2023]
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Hajeri S, Ramadugu C, Keremane M, Vidalakis G, Lee R. Nucleotide sequence and genome organization of Dweet mottle virus and its relationship to members of the family Betaflexiviridae. Arch Virol 2010; 155:1523-7. [PMID: 20644968 PMCID: PMC2943576 DOI: 10.1007/s00705-010-0758-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 07/12/2010] [Indexed: 11/28/2022]
Abstract
The nucleotide sequence of Dweet mottle virus (DMV) was determined and compared to sequences of members of the families Alphaflexiviridae and Betaflexiviridae. The DMV genome has 8,747 nucleotides (nt) excluding the 3′ poly-(A) tail. DMV genomic RNA contains three putative open reading frames (ORFs) and untranslated regions of 73 nt at the 5′ and 541 nt at 3′ termini. ORF1 potentially encoding a 227.48-kDa polyprotein, which has methyltransferase, oxygenase, endopeptidase, helicase, and RNA-dependent RNA polymerase (RdRP) domains. ORF2 encodes a movement protein of 40.25 kDa, while ORF3 encodes a coat protein of 40.69 kDa. Protein database searches showed 98–99% matches of DMV ORFs with citrus leaf blotch virus (CLBV) sequences. Phylogenetic analysis based on the RdRP core domain revealed that DMV is closely related to CLBV as a member of the genus Citrivirus. DMV did not satisfy the molecular criteria for demarcation of an independent species within the genus Citrivirus, family Betaflexiviridae, and hence, DMV can be considered a CLBV isolate.
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Affiliation(s)
- Subhas Hajeri
- Department of Plant Pathology and Microbiology, University of California, 900 Unv. Ave., Riverside, CA 92521, USA
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Abstract
It has been suggested that Citrus viroid IV (CVd-IV) be classified as a species within the genus Cocadviroid. This relationship was based on the presence of a terminal conserved hairpin (TCH) and absence of a terminal conserved region (TCR) as specific structural motifs in common with isolates of Coconut cadang-cadang viroid (CCCVd) as well as phylogenetic relationships with members of the genus Cocadviroid. Evidence is presented for a "vestigial" TCR in CVd-IV as well as the introduction of the terminal repeat region (TRR) motif and an alternative sequence analysis that suggests a closer phylogenetic relationship of CVd-IV to isolates of Citrus exocortis viroid (CEVd), a species within the genus Pospiviroid than to CCCVd. This position is further supported by the striking similarity of biological properties between CVd-IV and CEVd with the suggestion offered that biological evidence be considered for specific adjustments to any overall classification scheme for viroids.
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Affiliation(s)
- J S Semancik
- Department of Plant Pathology, University of California, Riverside, California 92521-0122, USA.
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Abstract
Prolonged infection of tomato hybrid (Lycopersicon esculentum x Lycopersicon peruvianum) by Citrus exocortis viroid (CEVd) resulted in viroid-like enlarged structures, detected by gel electrophoresis. This population included two new enlarged variants or D-variants, D-87 and D-76, and three transient species or D-forms, D-38, D-40 and D-43. Sequence analyses exposed a locus near the terminal repeat region where major changes appeared consistently. In transmission tests to CEVd hosts, a variety of progeny populations were recovered, including progeny enlargements of and reversions to CEVd, as well as sequence fidelity to the inoculum. Transmission tests to citrus hosts of the genera Citrus, Poncirus or Fortunella were unsuccessful. The importance of host specificity to the recovery and processing of the various CEVd-related structures, as well as the temporal variability of progeny populations, was demonstrated.
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Affiliation(s)
- J A Szychowski
- Department of Plant Pathology, University of California, Riverside, CA 92521, USA
| | - G Vidalakis
- Department of Plant Pathology, University of California, Riverside, CA 92521, USA
| | - J S Semancik
- Department of Plant Pathology, University of California, Riverside, CA 92521, USA
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Vidalakis G, Garnsey SM, Bash JA, Greer GD, Gumpf DJ. Efficacy of Bioindexing for Graft-Transmissible Citrus Pathogens in Mixed Infections. Plant Dis 2004; 88:1328-1334. [PMID: 30795193 DOI: 10.1094/pdis.2004.88.12.1328] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biological indexing for graft-transmissible pathogens of citrus in the presence of additional pathogens was investigated. The probability for symptom expression, the efficacy of the bio-indexing tests, and the number of citrus indicators required for pathogen detection were statistically evaluated. Multiple infections did not preclude symptom expression or reduce the diagnostic efficacy of the primary indexing hosts for Citrus tristeza virus (CTV), Citrus psorosis virus (CPsV), and Citrus tatter leaf virus (Apple stem grooving virus). Symptoms of Citrus vein enation virus (CVEV) and the diagnostic efficacy of Mexican lime were suppressed by the T30 group CTV isolates, but not by other CTV isolates tested. CPsV suppressed symptom expression and diagnostic efficiency of Dweet tangor and sweet orange for concave gum. The application of alternate bioassay hosts for indexing was also investigated. Dweet tangor, sweet orange, and Citrus excelsa are not typically used for bioindexing of CVEV, however, Dweet tangor and C. excelsa detected CVEV in single infections, whereas in sweet orange, CVEV was detected only when CPsV, concave gum, or citrus viroids were present. CTV was readily detected using the alternative indicator C. excelsa, whereas only shock reacting CPsV isolates were effectively indexed by Mexican lime.
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Affiliation(s)
- G Vidalakis
- Department of Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - S M Garnsey
- Department of Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - J A Bash
- Department of Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - G D Greer
- Department of Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - D J Gumpf
- Department of Plant Pathology, University of California, Riverside, CA 92521, U.S.A
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42
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Vidalakis G, Gumpf DJ, Bash JA, Semancik JS. Finger Imprint of Poncirus trifoliata: A Specific Interaction of a Viroid, a Host, and Irrigation. Plant Dis 2004; 88:709-713. [PMID: 30812480 DOI: 10.1094/pdis.2004.88.7.709] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The unusual symptom, "finger imprint", described exclusively on Poncirus trifoliata, has been reported in only a single field trial investigating the effects of citrus viroids on crop performance. With this, the question has persisted whether the observed growth abnormality was a disease symptom induced by Citrus viroid IIIb (CVd-IIIb) or a consequence of mechanical damage caused by the handling of young trees during propagation or cultural practices in the field. The recurrence of finger imprint symptoms on trees after 5 years in the field in which no abnormal growth features were previously noted now supports the proposition of a viroid-induced disease. The symptom expression results from an unusual etiology of a complex relationship of the specific viroid CVd-IIIb on the specific rootstock P. trifoliata only when supplemental water is applied by sprinkler irrigation.
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Affiliation(s)
- G Vidalakis
- Department of Plant Pathology, University of California, Riverside 92521
| | - D J Gumpf
- Department of Plant Pathology, University of California, Riverside 92521
| | - J A Bash
- Department of Plant Pathology, University of California, Riverside 92521
| | - J S Semancik
- Department of Plant Pathology, University of California, Riverside 92521
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