Identification of an emerging cucumber virus in Taiwan using Oxford nanopore sequencing technology
Abstract Background In June 2020, severe symptoms of leaf mosaic and fruit malformation were observed on greenhouse-grown cucumber plants in Xizhou Township of Changhua County, Taiwan. An unknown virus, designated CX-2, was isolated from a diseased cucumber sample by single lesion isolation on Cheno...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2022-12-01
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| Series: | Plant Methods |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13007-022-00976-x |
| _version_ | 1797977381446615040 |
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| author | Zi-Xuan Dong Chian-Chi Lin Yuh-Kun Chen Chia-Cheng Chou Tsung-Chi Chen |
| author_facet | Zi-Xuan Dong Chian-Chi Lin Yuh-Kun Chen Chia-Cheng Chou Tsung-Chi Chen |
| author_sort | Zi-Xuan Dong |
| collection | DOAJ |
| description | Abstract Background In June 2020, severe symptoms of leaf mosaic and fruit malformation were observed on greenhouse-grown cucumber plants in Xizhou Township of Changhua County, Taiwan. An unknown virus, designated CX-2, was isolated from a diseased cucumber sample by single lesion isolation on Chenopodium quinoa leaves. Identification of CX-2 was performed. Moreover, the incidence of cucumber viruses in Taiwan was also investigated. Methods Transmission electron microscopy was performed to examine virion morphology. The portable MinION sequencer released by Oxford Nanopore Technologies was used to detect viral sequences in dsRNA of CX-2-infected leaf tissue. The whole genome sequence of CX-2 was completed by Sanger sequencing and analyzed. Reverse transcription-polymerase chain reaction (RT-PCR) with species-specific primers and indirect enzyme-linked immunosorbent assay (ELISA) with anti-coat protein antisera were developed for virus detection in the field [see Additional file 1]. Results Icosahedral particles about 30 nm in diameter were observed in the crud leaf sap of CX-2-infected C. quinoa plant. The complete genome sequence of CX-2 was determined as 4577 nt long and shared 97.0–97.2% of nucleotide identity with that of two cucumber Bulgarian latent virus (CBLV) isolates in Iran and Bulgaria. Therefore, CX-2 was renamed CBLV-TW. In 2020–2022 field surveys, melon yellow spot virus (MYSV) had the highest detection rate of 74.7%, followed by cucurbit chlorotic yellows virus (CCYV) (32.0%), papaya ringspot virus virus watermelon type (PRSV-W) (10.7%), squash leaf curl Philippines virus (SLCuPV) (9.3%), CBLV (8.0%) and watermelon silver mottle virus (WSMoV) (4.0%). Co-infection of CBLV and MYSV could be detected in field cucumbers. Conclusion The emerging CBLV-TW was identified by nanopore sequencing. Whole genome sequence analysis revealed that CBLV-TW is closely related, but phylogenetically distinct, to two known CBLV isolates in Bulgaria and Iran. Detection methods including RT-PCR and indirect ELISA have been developed to detect CBLV and to investigate cucumber viruses in central Taiwan. The 2020–2022 field survey results showed that MYSV and CCYV were the main threats to cucumbers, with CBLV, SLCuPV and WSMoV were occasionally occurring. |
| first_indexed | 2024-04-11T05:05:58Z |
| format | Article |
| id | doaj.art-0c0fc5ee9f0b49368577aeed00bb61f1 |
| institution | Directory Open Access Journal |
| issn | 1746-4811 |
| language | English |
| last_indexed | 2024-04-11T05:05:58Z |
| publishDate | 2022-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Plant Methods |
| spelling | doaj.art-0c0fc5ee9f0b49368577aeed00bb61f12022-12-25T12:17:48ZengBMCPlant Methods1746-48112022-12-0118111210.1186/s13007-022-00976-xIdentification of an emerging cucumber virus in Taiwan using Oxford nanopore sequencing technologyZi-Xuan Dong0Chian-Chi Lin1Yuh-Kun Chen2Chia-Cheng Chou3Tsung-Chi Chen4Department of Medical Laboratory Science and Biotechnology, Asia UniversityDepartment of Medical Laboratory Science and Biotechnology, Asia UniversityDepartment of Plant Pathology, National Chung Hsing UniversityNational Laboratory Animal Center, National Applied Research LaboratoriesDepartment of Medical Laboratory Science and Biotechnology, Asia UniversityAbstract Background In June 2020, severe symptoms of leaf mosaic and fruit malformation were observed on greenhouse-grown cucumber plants in Xizhou Township of Changhua County, Taiwan. An unknown virus, designated CX-2, was isolated from a diseased cucumber sample by single lesion isolation on Chenopodium quinoa leaves. Identification of CX-2 was performed. Moreover, the incidence of cucumber viruses in Taiwan was also investigated. Methods Transmission electron microscopy was performed to examine virion morphology. The portable MinION sequencer released by Oxford Nanopore Technologies was used to detect viral sequences in dsRNA of CX-2-infected leaf tissue. The whole genome sequence of CX-2 was completed by Sanger sequencing and analyzed. Reverse transcription-polymerase chain reaction (RT-PCR) with species-specific primers and indirect enzyme-linked immunosorbent assay (ELISA) with anti-coat protein antisera were developed for virus detection in the field [see Additional file 1]. Results Icosahedral particles about 30 nm in diameter were observed in the crud leaf sap of CX-2-infected C. quinoa plant. The complete genome sequence of CX-2 was determined as 4577 nt long and shared 97.0–97.2% of nucleotide identity with that of two cucumber Bulgarian latent virus (CBLV) isolates in Iran and Bulgaria. Therefore, CX-2 was renamed CBLV-TW. In 2020–2022 field surveys, melon yellow spot virus (MYSV) had the highest detection rate of 74.7%, followed by cucurbit chlorotic yellows virus (CCYV) (32.0%), papaya ringspot virus virus watermelon type (PRSV-W) (10.7%), squash leaf curl Philippines virus (SLCuPV) (9.3%), CBLV (8.0%) and watermelon silver mottle virus (WSMoV) (4.0%). Co-infection of CBLV and MYSV could be detected in field cucumbers. Conclusion The emerging CBLV-TW was identified by nanopore sequencing. Whole genome sequence analysis revealed that CBLV-TW is closely related, but phylogenetically distinct, to two known CBLV isolates in Bulgaria and Iran. Detection methods including RT-PCR and indirect ELISA have been developed to detect CBLV and to investigate cucumber viruses in central Taiwan. The 2020–2022 field survey results showed that MYSV and CCYV were the main threats to cucumbers, with CBLV, SLCuPV and WSMoV were occasionally occurring.https://doi.org/10.1186/s13007-022-00976-xCucumber Bulgarian latent virus (CBLV)TombusvirusNanopore sequencingCucumis sativusVirus detection |
| spellingShingle | Zi-Xuan Dong Chian-Chi Lin Yuh-Kun Chen Chia-Cheng Chou Tsung-Chi Chen Identification of an emerging cucumber virus in Taiwan using Oxford nanopore sequencing technology Plant Methods Cucumber Bulgarian latent virus (CBLV) Tombusvirus Nanopore sequencing Cucumis sativus Virus detection |
| title | Identification of an emerging cucumber virus in Taiwan using Oxford nanopore sequencing technology |
| title_full | Identification of an emerging cucumber virus in Taiwan using Oxford nanopore sequencing technology |
| title_fullStr | Identification of an emerging cucumber virus in Taiwan using Oxford nanopore sequencing technology |
| title_full_unstemmed | Identification of an emerging cucumber virus in Taiwan using Oxford nanopore sequencing technology |
| title_short | Identification of an emerging cucumber virus in Taiwan using Oxford nanopore sequencing technology |
| title_sort | identification of an emerging cucumber virus in taiwan using oxford nanopore sequencing technology |
| topic | Cucumber Bulgarian latent virus (CBLV) Tombusvirus Nanopore sequencing Cucumis sativus Virus detection |
| url | https://doi.org/10.1186/s13007-022-00976-x |
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