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

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.

Molecular Viral Diagnosis and Sanitation of Yam Genetic Resources: Implications for Safe Yam Germplasm Exchange

“…When applied to axillary buds of white yam ( Dioscorea rotundata Poir. ), this approach led to the regeneration of 70% virus-free plants from YMV-infected plants [ 14 ]. This sanitation success rate is very similar to that obtained by the method described in this paper (62.7%) therefore cryotherapy should be evaluated on other yam species and yam-infecting viruses.…”

“…These efforts led to the characterization of several novel viruses and/or the sequencing of the complete genomes belonging to genera Ampelovirus , Aureusvirus , Badnavirus , Carlavirus , Comovirus , Cucumovirus , Fabavirus , Macluravirus , Potexvirus and Potyvirus . Thus, within the last five years alone, the complete genomes of 13 novel yam viral species were sequenced: one potyvirus, Dioscorea mosaic virus (DMV, [ 5 ]); six badnaviruses, Dioscorea bacilliform AL virus 2 (DBALV2, [ 6 ]), Dioscorea bacilliform ES virus (DBESV, [ 6 ]), Dioscorea bacilliform RT virus 1 (DBRTV1, [ 7 ]), Dioscorea bacilliform RT virus 2 (DBRTV2, [ 7 ]), Dioscorea bacilliform RT virus 3 (DBRTV3, [ 8 ]) and Dioscorea bacilliform TR virus (DBTRV, [ 9 ]); one sadwavirus, Dioscorea mosaic associated virus (DMaV, [ 10 ]); two macluraviruses, Yam chlorotic mosaic virus (YCMV, [ 11 ]) and Yam chlorotic necrosis virus (YCNV, [ 12 ]); two ampeloviruses, Air potato ampelovirus 1 (AiPoV1, [ 5 ]) and yam asymptomatic virus 1 (YaV1, [ 13 ]) and one virus belonging to the family Betaflexiviridae , yam virus Y (YVY, [ 14 ]).…”

Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution

“…For example, identification of CTV strains requires different sets of primers ( Roy et al., 2010 ) as recombination has played an important role in shaping CTV genome ( Martín et al., 2009 ). HTS can be useful to detect recombination since full-length or almost full-length viral genomes are sequenced rapidly, in a single analysis ( Akinyemi et al., 2016 ; Silva et al., 2019 ), unlike genome walking that requires successive steps of PCR, Sanger sequencing and primer design. Third-generation sequencing of single molecules seems more appropriate to identify recombination ( Viehweger et al., 2019 ) than second-generation sequencing methods that can produce recombinant artifacts, as genomic sequences are assembled from short sequences.…”

Post-COVID-19 Action: Guarding Africa’s Crops against Viral Epidemics Requires Research Capacity Building That Unifies a Trio of Transdisciplinary Interventions

“…In Africa, HTS has been used for the detection of viruses from crops such as common bean (Phaseolus vulgaris) [12][13][14][15][16], maize (Zea mays) [17][18][19], sweet potato (Ipomoea batatas) [20][21][22], papaya (Carica papaya) [23], pumpkin (Cucurbita pepo) [24,25], fluted pumpkin (Telfairia occidentalis) [26], cassava [27][28][29], yam (Dioscorea spp.) [30,31], cowpea (Vigna unguiculate) [32] and in Poaceae plants [33]. These forages into HTS have led to the detection of known viruses and the discovery of many novel virus species (Table 1).…”