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ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Pathogen Interactions
Volume 15 - 2024 |
doi: 10.3389/fpls.2024.1429402
This article is part of the Research Topic Pathogenesis, Detection, and Advanced Control Strategies in Plant Virus Diseases View all 10 articles
Meta-transcriptomic analysis reveals geographical expansion of known sugarbeet-infecting viruses and the occurrence of a novel virus in sugarbeet in the United States
Provisionally accepted- 1 North Dakota State University, Fargo, North Dakota, United States
- 2 Edward T. Schafer Agricultural Research Center, Agricultural Research Service (USDA), Fargo, North Dakota, United States
- 3 Amalgamated Sugar Company, Boise, Idaho, United States
- 4 American Crystal Sugar Company, Moorhead, MN, United States
- 5 Southern Minnesota Beet Sugar Cooperative, Renville, Minnesota, United States
- 6 Northwest Research and Outreach Center, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, Minneapolis, United States
In this study, meta-transcriptome sequencing was conducted on a total of 18 sugarbeet (Beta vulgaris L. subsp. vulgaris) sample libraries to profile the virome of field-grown sugarbeet to identify the occurrence and distribution of known and potentially new viruses from five different states in the United States. Sugarbeet roots with symptoms resembling of rhizomania caused by beet necrotic yellow vein virus (BNYVV), or leaves exhibiting leaf-curling, yellowing to browning, or green mosaic were collected from the sugarbeet growing area of California, Colorado, Idaho, Minnesota, and North Dakota. In silico analysis of de novo assembled contigs revealed the presence of nearly full-length genomes of BNYVV, beet soil-borne virus (BSBV), and beet soil-borne mosaic virus (BSBMV), which represent known sugarbeet-infecting viruses. Among those, BNYVV was widespread across the locations, whereas BSBV was prevalent in Minnesota and Idaho, and BSBMV only detected in Minnesota. In addition, two recently reported Beta vulgaris satellite virus isoforms (BvSatV-1A and BvSatV-1B) were detected in new locations, indicating the geographical expansion of this known virus. Besides these known sugarbeet-infecting viruses, bioinformatic analysis identified the widespread occurrence of a new uncharacterized Erysiphe necator-associated abispo virus (En_abispoV), a mycovirus-related virus that was identified in all 14 libraries. En_abispoV contains two RNA components, and the near complete sequence of both RNA1 and RNA2 were obtained from RNASeq and were further confirmed by primer-walking RT-PCR and Sanger sequencing. Phylogenetic comparison of En_abispoV isolates obtained in this study showed varying levels of genetic diversity within RNA1 and RNA2 to the previously reported isolates. The undertaken meta-transcriptomic approach revealed widespread nature of coexisting viruses associated with field-grown sugarbeet exhibiting virus disease-like symptoms in the United States.
Keywords: RNA sequencing, virome, rhizomania, Meta-transcriptomic, Sugarbeet, Beta vulgaris
Received: 08 May 2024; Accepted: 29 Jul 2024.
Copyright: © 2024 Chinnadurai, Wyatt, Weiland, Neher, Hastings, Bloomquist, Chu, Chanda, Khan, Bolton and Ramachandran. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Vanitharani Ramachandran, Edward T. Schafer Agricultural Research Center, Agricultural Research Service (USDA), Fargo, 58102-2765, North Dakota, United States
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