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Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics

Tomato (Lycopersicum esculentum L.) and pepper (Capsicum annuum L.) plants belonging to the family Solanaceae are cultivated worldwide. The rapid development of next-generation sequencing (NGS) technology facilitates the identification of viruses and viroids infecting plants. In this study, we carri...

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Autores principales: Choi, Hoseong, Jo, Yeonhwa, Cho, Won Kyong, Yu, Jisuk, Tran, Phu-Tri, Salaipeth, Lakha, Kwak, Hae-Ryun, Choi, Hong-Soo, Kim, Kook-Hyung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7593927/
https://www.ncbi.nlm.nih.gov/pubmed/33066322
http://dx.doi.org/10.3390/ijms21207565
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author Choi, Hoseong
Jo, Yeonhwa
Cho, Won Kyong
Yu, Jisuk
Tran, Phu-Tri
Salaipeth, Lakha
Kwak, Hae-Ryun
Choi, Hong-Soo
Kim, Kook-Hyung
author_facet Choi, Hoseong
Jo, Yeonhwa
Cho, Won Kyong
Yu, Jisuk
Tran, Phu-Tri
Salaipeth, Lakha
Kwak, Hae-Ryun
Choi, Hong-Soo
Kim, Kook-Hyung
author_sort Choi, Hoseong
collection PubMed
description Tomato (Lycopersicum esculentum L.) and pepper (Capsicum annuum L.) plants belonging to the family Solanaceae are cultivated worldwide. The rapid development of next-generation sequencing (NGS) technology facilitates the identification of viruses and viroids infecting plants. In this study, we carried out metatranscriptomics using RNA sequencing followed by bioinformatics analyses to identify viruses and viroids infecting tomato and pepper plants in Vietnam. We prepared a total of 16 libraries, including eight tomato and eight pepper libraries derived from different geographical regions in Vietnam. We identified a total of 602 virus-associated contigs, which were assigned to 18 different virus species belonging to nine different viral genera. We identified 13 different viruses and two viroids infecting tomato plants and 12 viruses and two viroids infecting pepper plants with viruses as dominantly observed pathogens. Our results showed that multiple infection of different viral pathogens was common in both plants. Moreover, geographical region and host plant were two major factors to determine viral populations. Taken together, our results provide the comprehensive overview of viral pathogens infecting two important plants in the family Solanaceae grown in Vietnam.
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spelling pubmed-75939272020-10-30 Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics Choi, Hoseong Jo, Yeonhwa Cho, Won Kyong Yu, Jisuk Tran, Phu-Tri Salaipeth, Lakha Kwak, Hae-Ryun Choi, Hong-Soo Kim, Kook-Hyung Int J Mol Sci Article Tomato (Lycopersicum esculentum L.) and pepper (Capsicum annuum L.) plants belonging to the family Solanaceae are cultivated worldwide. The rapid development of next-generation sequencing (NGS) technology facilitates the identification of viruses and viroids infecting plants. In this study, we carried out metatranscriptomics using RNA sequencing followed by bioinformatics analyses to identify viruses and viroids infecting tomato and pepper plants in Vietnam. We prepared a total of 16 libraries, including eight tomato and eight pepper libraries derived from different geographical regions in Vietnam. We identified a total of 602 virus-associated contigs, which were assigned to 18 different virus species belonging to nine different viral genera. We identified 13 different viruses and two viroids infecting tomato plants and 12 viruses and two viroids infecting pepper plants with viruses as dominantly observed pathogens. Our results showed that multiple infection of different viral pathogens was common in both plants. Moreover, geographical region and host plant were two major factors to determine viral populations. Taken together, our results provide the comprehensive overview of viral pathogens infecting two important plants in the family Solanaceae grown in Vietnam. MDPI 2020-10-13 /pmc/articles/PMC7593927/ /pubmed/33066322 http://dx.doi.org/10.3390/ijms21207565 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Choi, Hoseong
Jo, Yeonhwa
Cho, Won Kyong
Yu, Jisuk
Tran, Phu-Tri
Salaipeth, Lakha
Kwak, Hae-Ryun
Choi, Hong-Soo
Kim, Kook-Hyung
Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics
title Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics
title_full Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics
title_fullStr Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics
title_full_unstemmed Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics
title_short Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics
title_sort identification of viruses and viroids infecting tomato and pepper plants in vietnam by metatranscriptomics
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7593927/
https://www.ncbi.nlm.nih.gov/pubmed/33066322
http://dx.doi.org/10.3390/ijms21207565
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