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Zhao H, Qin L, Deng X, Wang Z, Jiang R, Reitz SR, Wu S, He Z. Nucleotide and dinucleotide preference of segmented viruses are shaped more by segment: In case study of tomato spotted wilt virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 122:105608. [PMID: 38796047 DOI: 10.1016/j.meegid.2024.105608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024]
Abstract
Several studies have showed that the nucleotide and dinucleotide composition of viruses possibly follows their host species or protein coding region. Nevertheless, the influence of viral segment on viral nucleotide and dinucleotide composition is still unknown. Here, we explored through tomato spotted wilt virus (TSWV), a segmented virus that seriously threatens the production of tomatoes all over the world. Through nucleotide composition analysis, we found the same over-representation of A across all viral segments at the first and second codon position, but it exhibited distinct in segments at the third codon position. Interestingly, the protein coding regions which encoded by the same or different segments exhibit obvious distinct nucleotide preference. Then, we found that the dinucleotides UpG and CpU were overrepresented and the dinucleotides UpA, CpG and GpU were underrepresented, not only in the complete genomic sequences, but also in different segments, protein coding regions and host species. Notably, 100% of the data investigated here were predicted to the correct viral segment and protein coding region, despite the fact that only 67% of the data analyzed here were predicted to the correct viral host species. In conclusion, in case study of TSWV, nucleotide composition and dinucleotide preference of segment viruses are more strongly dependent on segment and protein coding region than on host species. This research provides a novel perspective on the molecular evolutionary mechanisms of TSWV and provides reference for future research on genetic diversity of segmented viruses.
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Affiliation(s)
- Haiting Zhao
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Lang Qin
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Xiaolong Deng
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Zhilei Wang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Runzhou Jiang
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China
| | - Stuart R Reitz
- Malheur Experiment Station, Oregon State University, Ontario, OR, USA
| | - Shengyong Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Zhen He
- College of Plant Protection, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
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Peng C, Fan B, Zhu H, Liu L, Zhao Z, Huang L. Establishment of dual reverse transcriptase-polymerase chain reaction for detection system for Areca palm velarivirus 1. PLoS One 2024; 19:e0303941. [PMID: 38838001 DOI: 10.1371/journal.pone.0303941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/03/2024] [Indexed: 06/07/2024] Open
Abstract
Areca palm velarivirus 1 (APV1) is one of the main pathogen causing yellow leaf disease, and leading to considerable losses in the Areca palm industry. The detection methods for APV1 are primarily based on phenotype determination and molecular techniques, such as polymerase chain reaction (PCR). However, a single PCR has limitations in accuracy and sensitivity. Therefore, in the present study, we established a dual RT-PCR APV1-detection system with enhanced accuracy and sensitivity using two pairs of specific primers, YLDV2-F/YLDV2-R and YLDV4-F/YLDV4-R. Moreover, two cDNA fragments covering different regions of the viral genome were simultaneously amplified, with PCR amplicon of 311 and 499 bp, respectively. The dual RT-PCR detection system successfully amplified the two target regions of the APV1, demonstrating high specificity and sensitivity and compensating for the limitations of single-primer detection methods. We tested 60 Areca palm samples from different geographical regions, highlighting its advantages in that the dual RT-PCR system efficiently and accurately detected APV1 in samples across diverse areas. The dual RT-PCR APV1 detection system provides a rapid, accurate, and sensitive method for detecting the virus and offers valuable technical support for research in preventing and managing yellow leaf diseases caused by APV1 in Areca palms. Moreover, the findings of this study can serve as a reference for establishing similar plants viral detection systems in the future.
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Affiliation(s)
- Chunlin Peng
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Benyi Fan
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Hui Zhu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Liyun Liu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Zhengwu Zhao
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Liyun Huang
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
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Attaluri S, Dharavath R. Novel plant disease detection techniques-a brief review. Mol Biol Rep 2023; 50:9677-9690. [PMID: 37823933 DOI: 10.1007/s11033-023-08838-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
Plant pathogens cause severe losses to agricultural yield worldwide. Tracking plant health and early disease detection is important to reduce the disease spread and thus economic loss. Though visual scouting has been practiced from former times, detection of asymptomatic disease conditions is difficult. So, DNA-based and serological methods gained importance in plant disease detection. The progress in advanced technologies challenges the development of rapid, non-invasive, and on-field detection techniques such as spectroscopy. This review highlights various direct and indirect ways of detecting plant diseases like Enzyme-linked immunosorbent assay, Lateral flow assays, Polymerase chain reaction, spectroscopic techniques and biosensors. Although these techniques are sensitive and pathogen-specific, they are more laborious and time-intensive. As a consequence, a lot of interest is gained in in-field adaptable point-of-care devices with artificial intelligence-assisted pathogen detection at an early stage. More recently computer-aided techniques like neural networks are gaining significance in plant disease detection by image processing. In addition, a concise report on the latest progress achieved in plant disease detection techniques is provided.
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Wu X, Chen S, Zhang Z, Zhang Y, Li P, Chen X, Liu M, Lu Q, Li Z, Wei Z, Xu P. Development of Recombinase Polymerase Amplification Combined with Lateral Flow Strips for Rapid Detection of Cowpea Mild Mottle Virus. THE PLANT PATHOLOGY JOURNAL 2023; 39:486-493. [PMID: 37817494 PMCID: PMC10580057 DOI: 10.5423/ppj.oa.02.2023.0033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 08/31/2023] [Accepted: 09/10/2023] [Indexed: 10/12/2023]
Abstract
Cowpea mild mottle virus (CPMMV) is a global plant virus that poses a threat to the production and quality of legume crops. Early and accurate diagnosis is essential for effective managing CPMMV outbreaks. With the advancement in isothermal recombinase polymerase amplification and lateral flow strips technologies, more rapid and sensitive methods have become available for detecting this pathogen. In this study, we have developed a reverse transcription recombinase polymerase amplification combined with lateral flow strips (RT-RPA-LFS) method for the detection of CPMMV, specifically targeting the CPMMV coat protein (CP) gene. The RT-RPA-LFS assay only requires 20 min at 40°C and demonstrates high specificity. Its detection limit was 10 copies/μl, which is approximately up to 100 times more sensitive than RT-PCR on agarose gel electrophoresis. The developed RT-RPA-LFS method offers a rapid, convenient, and sensitive approach for field detection of CPMMV, which contribute to controlling the spread of the virus.
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Affiliation(s)
- Xinyang Wu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou 310018, China
| | - Shuting Chen
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zixin Zhang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yihan Zhang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Pingmei Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xinyi Chen
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Miaomiao Liu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Qian Lu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhongyi Li
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhongyan Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, Hangzhou 310018, China
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Yamamoto D, Neriya Y, Suzuki T, Nishigawa H, Natsuaki T. Construction of an infectious dahlia common mosaic virus clone. Arch Virol 2021; 166:3179-3182. [PMID: 34498122 DOI: 10.1007/s00705-021-05225-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 07/15/2021] [Indexed: 11/29/2022]
Abstract
Dahlia is a major ornamental plant that is cultivated worldwide. However, dahlia plants, which are mainly propagated through vegetative reproduction, are susceptible to widespread damage by viruses, and viral control requires that the nature of the infecting virus(es) be known. In this study, dahlia common mosaic virus (DCMV) was detected for the first time in Japan and sequenced. This is the first report of an infectious DCMV clone being constructed, and it will aid in the characterization of DCMV.
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Affiliation(s)
- Daiki Yamamoto
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi, 321-8505, Japan
| | - Yutaro Neriya
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi, 321-8505, Japan.
| | - Tomohiro Suzuki
- Center for Bioscience Research and Education, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi, 321-8505, Japan
| | - Hisashi Nishigawa
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi, 321-8505, Japan
| | - Tomohide Natsuaki
- School of Agriculture, Utsunomiya University, Mine-machi 350, Utsunomiya, Tochigi, 321-8505, Japan
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Alvarez-Díaz JC, Ortiz-Echeverry BA, Velásquez N. Duplex RT-PCR assay for simultaneous detection of TSWV and CSVd in chrysanthemum. J Virol Methods 2018; 266:41-48. [PMID: 30578896 DOI: 10.1016/j.jviromet.2018.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023]
Abstract
A novel duplex RT-PCR assay for simultaneous detection of TSWV and CSVd in chrysanthemums was developed. Previous reported primers for amplification of TSWV and CSVd were used and a novel pair of primers for CSVd was designed to improve duplex amplification compatibility. Sensitivity and efficiency of the previous reported and novel primers for CSVd were assessed. Then, the sensitivity of the combined primers to amplify both TSWV and CSVd cDNA were also evaluated. Both TSWV and CSVd were detected in preparations diluted up to 10-4 and 10-5 respectively, from total RNA extracts. This duplex RT-PCR method showed an estimated diagnostic sensitivity (DSe) of 97% and diagnostic specificity (DSp) of 99%. For combination of the primers TSWV L1/ L2 and CSVd UCO-1 F/ UCO-1R, the protocol could detect pathogen RNA from naturally infected plants until 0.1 ng and 1 ng respectively. This novel protocol for detection of TSWV/CSVd represents a useful diagnostic tool without the need of expensive probes and less extensive laboratory work. This method could be helpful to assist the selection and further propagation of healthy chrysanthemums on the field as well as to understand the dynamics and the interaction of this virus and viroid within farms.
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Affiliation(s)
- Juan C Alvarez-Díaz
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia.
| | - Bianor A Ortiz-Echeverry
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia
| | - Nubia Velásquez
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia
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Asano S, Hirayama Y, Matsushita Y. Distribution of Tomato spotted wilt virus in dahlia plants. Lett Appl Microbiol 2017; 64:297-303. [PMID: 28129432 DOI: 10.1111/lam.12720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/05/2017] [Accepted: 01/10/2017] [Indexed: 11/29/2022]
Abstract
Tomato spotted wilt virus (TSWV) causes significant losses in the production of the ornamental plant Dahlia variabilis in Japan. The purpose of this study was to examine the distribution of TSWV in dahlia plants and identify plant parts that can be used in the selection of TSWV-free plants. The distribution of TSWV was investigated using reverse transcriptional polymerase chain reaction (RT-PCR) and tissue blot immunoassay. The detection rate of TSWV in latent infected compound leaves was the highest in the petiole, and it decreased from the veins and rachis to the lamina. The tissue blot immunoassays of the leaflets showed an uneven distribution of TSWV, especially along the edge of the leaf blade. In stems, the detection rate of TSWV was high partway up the stem compared to that in the upper and the lower parts of the stem during the vegetative growth stage. A highly uneven distribution was observed in the bulb. Our results indicated that middle parts of the stem as well as the petioles, rachis, and veins of compound leaves are suitable for detection of TSWV in dahlias. This study is the first to report uneven distribution of TSWV in dahlia plants. SIGNIFICANCE AND IMPACT OF THE STUDY In this study, the distribution of Tomato spotted wilt virus (TSWV) in various parts of dahlia plants was investigated for the first time. The distribution of TSWV was uneven in compound leaves, leaflets, stems, and bulbs. The middle parts of the stem or the petiole and leaf veins should be sampled to detect TSWV when selecting healthy plants.
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Affiliation(s)
- S Asano
- Nara Prefecture Agricultural Research and Development Center, Sakurai, Japan
| | - Y Hirayama
- Nara Prefecture Agricultural Research and Development Center, Sakurai, Japan
| | - Y Matsushita
- Institute of Vegetable and Floriculture Science, NARO, Tsukuba, Japan
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