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4. Identification of Viruses Infecting Phalaenopsis Orchids Using Nanopore Sequencing and Development of an RT-RPA-CRISPR/Cas12a for Rapid Visual Detection of Nerine Latent Virus.

Author

Lee, Hyo-Jeong, Kim, Hae-Jun, Cho, In-Sook, and Jeong, Rae-Dong

Subjects
PHALAENOPSIS, VIRUS identification, ORCHIDS, ORNAMENTAL plants, PLANT viruses, PHYTOPATHOGENIC microorganisms
Abstract

Phalaenopsis orchids are one of the most popular ornamental plants. More than thirty orchid viruses have been reported, and virus-infected Phalaenopsis orchids significantly lose their commercial value. Therefore, the development of improved viral disease detection methods could be useful for quality control in orchid cultivation. In this study, we first utilized the MinION, a portable sequencing device based on Oxford Nanopore Technologies (ONT) to rapidly detect plant viruses in Phalaenopsis orchids. Nanopore sequencing revealed the presence of three plant viruses in Phalaenopsis orchids: odontoglossum ringspot virus, cymbidium mosaic virus, and nerine latent virus (NeLV). Furthermore, for the first time, we detected NeLV infection in Phalaenopsis orchids using nanopore sequencing and developed the reverse transcription–recombinase polymerase amplification (RT-RPA)-CRISPR/Cas12a method for rapid, instrument-flexible, and accurate diagnosis. The developed RT-RPA-CRISPR/Cas12a technique can confirm NeLV infection in less than 20 min and exhibits no cross-reactivity with other viruses. To determine the sensitivity of RT-RPA-CRISPR/Cas12a for NeLV, we compared it with RT-PCR using serially diluted transcripts and found a detection limit of 10 zg/μL, which is approximately 1000-fold more sensitive. Taken together, the ONT platform offers an efficient strategy for monitoring plant viral pathogens, and the RT-RPA-CRISPR/Cas12a method has great potential as a useful tool for the rapid and sensitive diagnosis of NeLV. [ABSTRACT FROM AUTHOR]

Published
2024
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25. Inhibitory effect of gamma irradiation against Cucumber green mottle mosaic virus

Author

Jeong Mi-Ae, Hong Jin-Sung, and Jeong Rae-Dong

Subjects
0106 biological sciences, viruses, fungi, food and beverages, Soil Science, 02 engineering and technology, Biology, 021001 nanoscience & nanotechnology, biology.organism_classification, 01 natural sciences, Virology, Cucumber green mottle mosaic virus, 0210 nano-technology, Agronomy and Crop Science, Inhibitory effect, 010606 plant biology & botany, Gamma irradiation
Published
2017

48. Resistance protein-mediated defense signalling in response to Turnip Crinkle Virusin Arabidopsis: recent advances

Author

Jeong, Mi-Ae and Jeong, Rae-Dong

Abstract

The Turnip Crinkle Virus(TCV)–Arabidopsis interaction is one of the best-characterized pathosystems, and studies of this system have contributed significantly to the understanding of plant resistance to viral pathogens. Inoculation of TCV on the resistant Arabidopsis ecotype Di-17 elicits the hypersensitive response (HR), and is accompanied by increased expression of defense genes. The HR to TCV infection is conferred by HRT(HR to TCV) gene, which encodes a CC-NBS-LRR class resistance (R) protein. In contrast to the HR, resistance requires the HRTgene and a recessive locus designated rrt. Unlike most CC-NBS-LRR R proteins, HRT-mediated resistance is dependent on EDS1 (enhanced disease susceptibility 1) and is independent of NDR1 (non-race-specific disease resistance). Resistance is also independent of RAR1 (required for Mla12 resistance), SGT1 (suppressor of the G2 allele of SKP1), and TCV-interacting protein (TIP) but is compromised in the salicylic acid (SA) deficient mutants eds5 (enhanced disease susceptibility 5), pad4(phytoalexin deficient 4), sid2(salicylic acid induction deficient 2), and sag101(senescence associated gene 101). EDS1 and SA have redundant functions in the induction of the HR by HRT. SAG101 interacts with PAD4, via EDS1, and EDS1, PAD4, and SAG101 form a ternary complex and perform independent functions in HRT-mediated resistance. HRT interacts with CRT1(compromised recognition of TCV), an ATPase and resistance to TCV is partially compromised by a mutation in CRT1. HRT-mediated HR and TCV resistance are also dependent on light. A dark treatment, immediately following TCV inoculation, suppresses the HR, TCV resistance, and the activation of a majority of the TCV-in-duced genes. Interestingly, a mutation in blue-light photo-receptors compromised TCV resistance and led to degradation of HRT via a proteasome-dependent pathway, resulting in susceptibility to TCV, which correlates with its interaction with the E3 ubiquitin ligase, COP1 (constitutively photo-morphogenesis 1). This review aims to document the advances in the understanding of the TCV-Arabidopsis patho-system as a case study and provide a valuable model for dissecting plant resistance to viral pathogens.

Published
2013
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49. Comprehensive Metatranscriptomic Analysis of Plant Viruses in Imported Frozen Cherries and Blueberries.

Author

Lee GE, Lee HJ, and Jeong RD

Abstract

The possibility of new viruses emerging in various regions worldwide has increased due to a combination of factors, including climate change and the expansion of international trading. Plant viruses spread through various transmission routes, encompassing well-known avenues such as pollen, seeds, and insects. However, research on potential transmission routes beyond these known mechanisms has remained limited. To address this gap, this study employed metatranscriptomic analysis to ascertain the presence of plant viruses in imported frozen fruits, specifically cherries and blueberries. This analysis aimed to identify pathways through which plant viruses may be introduced into countries. Virome analysis revealed the presence of six species of plant viruses in frozen cherries and blueberries: cherry virus A (CVA), prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), prunus virus F (PrVF), blueberry shock virus (BlShV), and blueberry latent virus (BlLV). Identifying these potential transmission routes is crucial for effectively managing and preventing the spread of plant viruses and crop protection. This study highlights the importance of robust quality control measures and monitoring systems for frozen fruits, emphasizing the need for proactive measures to mitigate the risk associated with the potential spread of plant viruses.

Published
2024
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50. Development and Application of Reverse Transcription Nanoplate-Based Digital PCR Assay for Sensitive and Accurate Detection of Rice Black-Streaked Dwarf Virus in Cereal Crops.

Author

Lee HJ, Kim HJ, Kim SM, and Jeong RD

Abstract

The emergence of rice black-streaked dwarf virus (RBSDV) poses a significant threat to global cereal crop cultivation, necessitating the urgent development of reliable detection and quantification techniques. This study introduces a reliable approach for the precise and sensitive quantification of the RBSDV in cereal crop samples, employing a reverse transcription digital polymerase chain reaction (RT-dPCR) assay. We assessed the specificity and sensitivity of the RT-dPCR assay proposed for precise RBSDV detection and quantification. Our findings demonstrate that RT-dPCR was specific for detection of RBSDV, with no cross-reactivity observed with other viruses infecting cereal crops. The RT-dPCR sensitivity was over 10 times that of RT-quantitative PCR (RT-qPCR). The detection limit of RT-dPCR was 0.096 copies/μl. In addition, evaluation of RT-dPCR assay with field samples was conducted on 60 different cereal crop samples revealed that RT-dPCR (45/60) exhibited superior accuracy compared with RT-qPCR (23/60). In this study, we present a specific and accurate RT-dPCR assay for the detection and quantification of RBSDV.

Published
2024
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