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Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing

Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing

Silva, Gonçalo ORCID: 0000-0001-5544-2947, Bömer, Moritz ORCID: 0000-0003-1003-9622, Rathnayake, Ajith I., Sewe, Steven O., Visendi, Paul, Oyekanmi, Joshua O., Quain, Marian D., Akomeah, Belinda, Kumar, P. Lava and Seal, Susan E. ORCID: 0000-0002-3952-1562 (2019) Molecular characterization of a new virus species identified in yam (Dioscorea spp.) by high-throughput sequencing. Plants, 8 (6):167. ISSN 2223-7747 (Print), 2223-7747 (Online) (doi:https://doi.org/10.3390/plants8060167)

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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.

Item Type: Article
Additional Information: This article belongs to the Special Issue "Diagnosis and Control of Plant Viral Diseases". *** © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
Uncontrolled Keywords: RNA-Seq; virus detection; Betaflexiviridae; next-generation sequencing; HTS
Subjects: Q Science > QR Microbiology
Q Science > QR Microbiology > QR355 Virology
S Agriculture > SB Plant culture
Faculty / Department / Research Group: Faculty of Engineering & Science
Faculty of Engineering & Science > Natural Resources Institute
Faculty of Engineering & Science > Natural Resources Institute > Agriculture, Health & Environment Department
Faculty of Engineering & Science > Natural Resources Institute > Molecular Virology and Entomology Research Group
Last Modified: 22 Jun 2019 04:06
Selected for GREAT 2016: None
Selected for GREAT 2017: None
Selected for GREAT 2018: None
Selected for GREAT 2019: None
URI: http://gala.gre.ac.uk/id/eprint/24648

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