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

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 stud...

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Autores principales: Silva, Gonçalo, Bömer, Moritz, Rathnayake, Ajith I., Sewe, Steven O., Visendi, Paul, Oyekanmi, Joshua O., Quain, Marian D., Akomeah, Belinda, Kumar, P. Lava, Seal, Susan E.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630666/
https://www.ncbi.nlm.nih.gov/pubmed/31212654
http://dx.doi.org/10.3390/plants8060167
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author Silva, Gonçalo
Bömer, Moritz
Rathnayake, Ajith I.
Sewe, Steven O.
Visendi, Paul
Oyekanmi, Joshua O.
Quain, Marian D.
Akomeah, Belinda
Kumar, P. Lava
Seal, Susan E.
author_facet Silva, Gonçalo
Bömer, Moritz
Rathnayake, Ajith I.
Sewe, Steven O.
Visendi, Paul
Oyekanmi, Joshua O.
Quain, Marian D.
Akomeah, Belinda
Kumar, P. Lava
Seal, Susan E.
author_sort Silva, Gonçalo
collection PubMed
description 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.
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spelling pubmed-66306662019-08-19 Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing Silva, Gonçalo Bömer, Moritz Rathnayake, Ajith I. Sewe, Steven O. Visendi, Paul Oyekanmi, Joshua O. Quain, Marian D. Akomeah, Belinda Kumar, P. Lava Seal, Susan E. Plants (Basel) Article 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. MDPI 2019-06-11 /pmc/articles/PMC6630666/ /pubmed/31212654 http://dx.doi.org/10.3390/plants8060167 Text en © 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/).
spellingShingle Article
Silva, Gonçalo
Bömer, Moritz
Rathnayake, Ajith I.
Sewe, Steven O.
Visendi, Paul
Oyekanmi, Joshua O.
Quain, Marian D.
Akomeah, Belinda
Kumar, P. Lava
Seal, Susan E.
Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing
title Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing
title_full Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing
title_fullStr Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing
title_full_unstemmed Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing
title_short Molecular Characterization of a New Virus Species Identified in Yam (Dioscorea spp.) by High-Throughput Sequencing
title_sort molecular characterization of a new virus species identified in yam (dioscorea spp.) by high-throughput sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6630666/
https://www.ncbi.nlm.nih.gov/pubmed/31212654
http://dx.doi.org/10.3390/plants8060167
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