High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management
Wheat viruses are major yield-reducing factors, with mixed infections causing substantial economic losses. Determining field virus populations is crucial for effective management and developing virus-resistant cultivars. This study utilized the high-throughput Oxford Nanopore sequencing technique (O...
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| author | Nar B. Ranabhat John P. Fellers Myron A. Bruce Jessica L. Shoup Rupp |
| author_facet | Nar B. Ranabhat John P. Fellers Myron A. Bruce Jessica L. Shoup Rupp |
| author_sort | Nar B. Ranabhat |
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| description | Wheat viruses are major yield-reducing factors, with mixed infections causing substantial economic losses. Determining field virus populations is crucial for effective management and developing virus-resistant cultivars. This study utilized the high-throughput Oxford Nanopore sequencing technique (ONT) to characterize wheat viral populations in major wheat-growing counties of Kansas from 2019 to 2021. Wheat leaves exhibiting virus-like symptoms were collected, total RNA was extracted, and cDNA libraries were prepared using a PCR-cDNA barcoding kit, then loaded onto ONT MinION flow cells. Sequencing reads aligned with cereal virus references identified eight wheat virus species. <i>Tritimovirus tritici</i> (wheat streak mosaic virus, WSMV), <i>Poacevirus tritici</i> (Triticum mosaic virus, <i>TriMV</i>), <i>Bromovirus BMV</i> (brome mosaic virus, <i>BMV</i>), as well as <i>Emaravirus tritici</i>, <i>Luteovirus pavhordei</i>, <i>L. sgvhordei</i>, <i>Bymovirus tritici</i>, and <i>Furovirus tritici.</i> Mixed infections involving two to five viruses in a single sample were common, with the most prevalent being WSMV + TriMV at 16.7% and WSMV + TriMV + BMV at 11.9%. Phylogenetic analysis revealed a wide distribution of WSMV isolates, including European and recombinant variants. A phylogenetic analysis of <i>Emaravirus tritici</i> based on RNA 3A and 3B segments and whole-genome characterization of <i>Furovirus tritici</i> were also conducted. These findings advance understanding of genetic variability, phylogenetics, and viral co-infections, supporting the development of sustainable management practices through host genetic resistance. |
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| spelling | doaj-art-51f0dd2a53574100afd1d3103c2a39db2025-01-24T13:52:40ZengMDPI AGViruses1999-49152025-01-0117112610.3390/v17010126High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus ManagementNar B. Ranabhat0John P. Fellers1Myron A. Bruce2Jessica L. Shoup Rupp3Department of Plant Pathology, Throckmorton Plant Science Center, Kansas State University, Manhattan, KS 66506, USAHard Winter Wheat Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Manhattan, KS 66506, USADepartment of Plant Pathology, Throckmorton Plant Science Center, Kansas State University, Manhattan, KS 66506, USADepartment of Plant Pathology, Throckmorton Plant Science Center, Kansas State University, Manhattan, KS 66506, USAWheat viruses are major yield-reducing factors, with mixed infections causing substantial economic losses. Determining field virus populations is crucial for effective management and developing virus-resistant cultivars. This study utilized the high-throughput Oxford Nanopore sequencing technique (ONT) to characterize wheat viral populations in major wheat-growing counties of Kansas from 2019 to 2021. Wheat leaves exhibiting virus-like symptoms were collected, total RNA was extracted, and cDNA libraries were prepared using a PCR-cDNA barcoding kit, then loaded onto ONT MinION flow cells. Sequencing reads aligned with cereal virus references identified eight wheat virus species. <i>Tritimovirus tritici</i> (wheat streak mosaic virus, WSMV), <i>Poacevirus tritici</i> (Triticum mosaic virus, <i>TriMV</i>), <i>Bromovirus BMV</i> (brome mosaic virus, <i>BMV</i>), as well as <i>Emaravirus tritici</i>, <i>Luteovirus pavhordei</i>, <i>L. sgvhordei</i>, <i>Bymovirus tritici</i>, and <i>Furovirus tritici.</i> Mixed infections involving two to five viruses in a single sample were common, with the most prevalent being WSMV + TriMV at 16.7% and WSMV + TriMV + BMV at 11.9%. Phylogenetic analysis revealed a wide distribution of WSMV isolates, including European and recombinant variants. A phylogenetic analysis of <i>Emaravirus tritici</i> based on RNA 3A and 3B segments and whole-genome characterization of <i>Furovirus tritici</i> were also conducted. These findings advance understanding of genetic variability, phylogenetics, and viral co-infections, supporting the development of sustainable management practices through host genetic resistance.https://www.mdpi.com/1999-4915/17/1/126wheat virusviromeRNA virusesphylogenymixed infectionhost plant resistance |
| spellingShingle | Nar B. Ranabhat John P. Fellers Myron A. Bruce Jessica L. Shoup Rupp High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management Viruses wheat virus virome RNA viruses phylogeny mixed infection host plant resistance |
| title | High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management |
| title_full | High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management |
| title_fullStr | High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management |
| title_full_unstemmed | High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management |
| title_short | High-Throughput Oxford Nanopore Sequencing Unveils Complex Viral Population in Kansas Wheat: Implications for Sustainable Virus Management |
| title_sort | high throughput oxford nanopore sequencing unveils complex viral population in kansas wheat implications for sustainable virus management |
| topic | wheat virus virome RNA viruses phylogeny mixed infection host plant resistance |
| url | https://www.mdpi.com/1999-4915/17/1/126 |
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