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Open AccessArticle

Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing

1
Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
2
International Institute of Tropical Agriculture (IITA), Oyo Road, PMB 5320, Ibadan, Nigeria
3
Council for Scientific and Industrial Research-Crops Research Institute (CSIR-CRI), Fumesua, P. O. BOX 3785, Kumasi, Ghana
*
Author to whom correspondence should be addressed.
Present address: Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, Queensland, 4001, Australia.
Plants 2019, 8(6), 167; https://doi.org/10.3390/plants8060167
Received: 13 May 2019 / Revised: 6 June 2019 / Accepted: 9 June 2019 / Published: 11 June 2019
(This article belongs to the Special Issue Diagnosis and Control of Plant Viral Diseases)
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Abstract

To date, several viruses of different genera have been reported to infect yam (Dioscorea spp.). The full diversity of viruses infecting yam, however, remains to be explored. High-throughput sequencing (HTS) methods are increasingly being used in the discovery of new plant viral genomes. In this study, we employed HTS on yam to determine whether any undiscovered viruses were present that would restrict the international distribution of yam germplasm. We discovered a new virus sequence present in 31 yam samples tested and have tentatively named this virus “yam virus Y” (YVY). Twenty-three of the samples in which YVY was detected showed mosaic and chlorotic leaf symptoms, but Yam mosaic virus was also detected in these samples. Complete genome sequences of two YVY viral isolates were assembled and found to contain five open reading frames (ORFs). ORF1 encodes a large replication-associated protein, ORF2, ORF3 and ORF4 constitute the putative triple gene block proteins, and ORF5 encodes a putative coat protein. Considering the species demarcation criteria of the family Betaflexiviridae, YVY should be considered as a novel virus species in the family Betaflexiviridae. Further work is needed to understand the association of this new virus with any symptoms and yield loss and its implication on virus-free seed yam production. View Full-Text
Keywords: RNA-Seq; virus detection; Betaflexiviridae; next-generation sequencing; HTS RNA-Seq; virus detection; Betaflexiviridae; next-generation sequencing; HTS
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

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Silva, G.; Bömer, M.; Rathnayake, A.I.; Sewe, S.O.; Visendi, P.; Oyekanmi, J.O.; Quain, M.D.; Akomeah, B.; Kumar, P.L.; Seal, S.E. Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing. Plants 2019, 8, 167.

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