Molecular Evidence of Recombination on Korean Isolates of Tomato yellow leaf curl virus by Nucleotide Transversions and Transitions

Lee, Hye Jung; Park, Jung An; Auh, Chung Kyoon; Lee, Kyeong Yeoll; Kim, Chang Seok; Lee, Gwan Seok; Soh, Hyun Cheol; Choi, Hong Soo; Lee, Suk Chan

doi:10.5423/ppj.2011.27.4.378

The Plant Pathology Journal

2011

DOI: 10.5423/ppj.2011.27.4.378

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Molecular Evidence of Recombination on Korean Isolates of Tomato yellow leaf curl virus by Nucleotide Transversions and Transitions

Hye Jung Lee¹,

Jung An Park²,

Chung Kyoon Auh³

et al.

Abstract: Tomato yellow leaf curl virus (TYLCV), a member of genus Begomovirus, was isolated in Korea in 2008. We sequenced and analyzed the DNA-A of 51 TYLCV isolates from Korea, and 13 of the TYLCV isolates were selected as type representatives of TYLCV from six Korean provinces. The 13 TYLCV isolates were classified into Korea Group 1 (KG1, nine isolates) and Korea Group 2 (KG2, four isolates) based on the results of phylogenetic analysis and genome size (2774 and 2781 nucleotides, respectively). A recombination dete… Show more

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Cited by 4 publications

References 31 publications

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Sweet pepper confirmed as a reservoir host for tomato yellow leaf curl virus by both agro-inoculation and whitefly-mediated inoculation

et al. 2014

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Tomato yellow leaf curl virus (TYLCV), a member of the genus Begomovirus, has a single-stranded DNA genome. TYLCV can induce severe disease symptoms on tomato plants, but other hosts plants such as cucurbits and peppers are asymptomatic. A full-length DNA clone of a Korean TYLCV isolate was constructed by rolling-circle amplification from TYLCV-infected tomatoes in Korea. To assess relative susceptibility of sweet pepper varieties to TYLCV, 19 cultivars were inoculated with cloned TYLCV by agro-inoculation. All TYLCV-infected sweet peppers were asymptomatic, even though Southern hybridization and polymerase chain reaction analysis showed TYLCV genomic DNA accumulation in roots, stems, and newly produced shoots. Southern hybridization indicated that TYLCV replicated and moved systemically from agro-inoculated apical shoot tips to roots or newly produced shoots of sweet peppers. Whitefly-mediated inoculation experiments showed that TYLCV can be transmitted to tomatoes from TYLCV-infected sweet peppers. Taken together, these results indicate that sweet pepper can be a reservoir for TYLCV in nature.

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Sweet pepper confirmed as a reservoir host for tomato yellow leaf curl virus by both agro-inoculation and whitefly-mediated inoculation

et al. 2014

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Emergence and diversity of begomoviruses infecting solanaceous crops in East and Southeast Asia

et al. 2014

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An Effective Integrated Machine Learning Framework for Identifying Severity of Tomato Yellow Leaf Curl Virus and Their Experimental Validation

et al. 2023

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Tomato yellow leaf curl virus (TYLCV) dispersed across different countries, specifically to subtropical regions, associated with more severe symptoms. Since TYLCV was first isolated in 1931, it has been a menace to tomato industrial production worldwide over the past century. Three groups were newly isolated from TYLCV-resistant tomatoes in 2022; however, their functions are unknown. The development of machine learning (ML)-based models using characterized sequences and evaluating blind predictions is one of the major challenges in interdisciplinary research. The purpose of this study was to develop an integrated computational framework for the accurate identification of symptoms (mild or severe) based on TYLCV sequences (isolated in Korea). For the development of the framework, we first extracted 11 different feature encodings and hybrid features from the training data and then explored 8 different classifiers and developed their respective prediction models by using randomized 10-fold cross-validation. Subsequently, we carried out a systematic evaluation of these 96 developed models and selected the top 90 models, whose predicted class labels were combined and considered as reduced features. On the basis of these features, a multilayer perceptron was applied and developed the final prediction model (IML-TYLCVs). We conducted blind prediction on 3 groups using IML-TYLCVs, and the results indicated that 2 groups were severe and 1 group was mild. Furthermore, we confirmed the prediction with virus-challenging experiments of tomato plant phenotypes using infectious clones from 3 groups. Plant virologists and plant breeding professionals can access the user-friendly online IML-TYLCVs web server at https://balalab-skku.org/IML-TYLCVs , which can guide them in developing new protection strategies for newly emerging viruses.

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Molecular Evidence of Recombination on Korean Isolates of Tomato yellow leaf curl virus by Nucleotide Transversions and Transitions

Cited by 4 publications

References 31 publications

Sweet pepper confirmed as a reservoir host for tomato yellow leaf curl virus by both agro-inoculation and whitefly-mediated inoculation

Sweet pepper confirmed as a reservoir host for tomato yellow leaf curl virus by both agro-inoculation and whitefly-mediated inoculation

Emergence and diversity of begomoviruses infecting solanaceous crops in East and Southeast Asia

An Effective Integrated Machine Learning Framework for Identifying Severity of Tomato Yellow Leaf Curl Virus and Their Experimental Validation

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