Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics
Tomato (<i>Lycopersicum esculentum</i> L.) and pepper (<i>Capsicum annuum</i> L.) plants belonging to the family <i>Solanaceae</i> are cultivated worldwide. The rapid development of next-generation sequencing (NGS) technology facilitates the identification of viru...
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| Format: | Article |
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MDPI AG
2020-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/20/7565 |
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| author | Hoseong Choi Yeonhwa Jo Won Kyong Cho Jisuk Yu Phu-Tri Tran Lakha Salaipeth Hae-Ryun Kwak Hong-Soo Choi Kook-Hyung Kim |
| author_facet | Hoseong Choi Yeonhwa Jo Won Kyong Cho Jisuk Yu Phu-Tri Tran Lakha Salaipeth Hae-Ryun Kwak Hong-Soo Choi Kook-Hyung Kim |
| author_sort | Hoseong Choi |
| collection | DOAJ |
| description | Tomato (<i>Lycopersicum esculentum</i> L.) and pepper (<i>Capsicum annuum</i> L.) plants belonging to the family <i>Solanaceae</i> 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 <i>Solanaceae</i> grown in Vietnam. |
| first_indexed | 2024-03-10T15:39:59Z |
| format | Article |
| id | doaj.art-f2dc822a7b014e12a8f7b37a5a32fc94 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T15:39:59Z |
| publishDate | 2020-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-f2dc822a7b014e12a8f7b37a5a32fc942023-11-20T16:57:59ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-10-012120756510.3390/ijms21207565Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by MetatranscriptomicsHoseong Choi0Yeonhwa Jo1Won Kyong Cho2Jisuk Yu3Phu-Tri Tran4Lakha Salaipeth5Hae-Ryun Kwak6Hong-Soo Choi7Kook-Hyung Kim8Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, KoreaResearch Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, KoreaResearch Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, KoreaPlant Genomics and Breeding Institute, Seoul National University, Seoul 08826, KoreaDepartment of Agricultural Biotechnology, Seoul National University, Seoul 08826, KoreaSchool of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkok 10150, ThailandCrop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, KoreaCrop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, KoreaResearch Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, KoreaTomato (<i>Lycopersicum esculentum</i> L.) and pepper (<i>Capsicum annuum</i> L.) plants belonging to the family <i>Solanaceae</i> 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 <i>Solanaceae</i> grown in Vietnam.https://www.mdpi.com/1422-0067/21/20/7565metatranscriptomicspeppertomatoVietnamvirus |
| spellingShingle | Hoseong Choi Yeonhwa Jo Won Kyong Cho Jisuk Yu Phu-Tri Tran Lakha Salaipeth Hae-Ryun Kwak Hong-Soo Choi Kook-Hyung Kim Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics International Journal of Molecular Sciences metatranscriptomics pepper tomato Vietnam virus |
| 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 | metatranscriptomics pepper tomato Vietnam virus |
| url | https://www.mdpi.com/1422-0067/21/20/7565 |
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