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

Gonçalo Silva,Paul Visendi,Ajith I Rathnayake,Steven O Sewe,Marian D Quain,Moritz Bömer,Belinda Akomeah,Susan E Seal,Joshua O Oyekanmi,P Lava Kumar

doi:10.3390/plants8060167

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.

Highlights

Yam (Dioscorea spp.) is a preferred staple food for over 90 million people in West Africa, with this region contributing over 95% of the world’s total yam production [1]
Our study shows that yam virus Y” (YVY) could be detected in several West African yam plants infected with Yam mosaic virus (YMV) and displaying symptoms associated with mosaic disease
Near-complete and complete genomes of known Yam mosaic virus (YMV), Dioscorea mosaic-associated virus (DMaV) RNA1 and RNA2, and yam badnavirus were obtained by directly mapping assembled contigs to a custom-made database containing viral reference sequence genomes publicly available from the NCBI GenBank

Summary

Introduction

Yam (Dioscorea spp.) is a preferred staple food for over 90 million people in West Africa, with this region contributing over 95% of the world’s total yam production [1]. Nigeria and Ghana are the major producer and exporter of yams worldwide, respectively. Yams are mainly produced by small-holder farmers who rely on the crop for food and income security. Farmers rely on obtaining their planting material either from their own farms, or by buying the surplus from neighbouring farmers. This means that the planting material is often of low quality and infected with several pathogens, mainly viruses. Despite its importance and high value, yam productivity is compromised severely by the impact of yam viruses and the unavailability and associated high costs of high-quality clean seed yam [2]

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