The first survey using high-throughput sequencing of cereal and barley yellow dwarf viruses in Irish spring and winter barley crops

Abstract

Yellow dwarf viruses (YDVs) are the most economically important plant viruses impacting cereal production worldwide and include viruses from the genus Luteovirus (e.g., barely yellow dwarf virus (BYDV)-PAV, BYDV-PAS, BYDV-MAV, BYDV-kerII, BYDV-kerIII) and Polerovirus (e.g., cereal yellow dwarf virus (CYDV)-RPV, CYDV-RPS). Until now, much of our knowledge on YDVs infecting Irish barley crops (Hordeum vulgare L.) has come from serological assays; however, due to cross-reactivity it can be difficult to discriminate between viruses of different species. In this study, we have carried out a high-throughput sequencing survey of symptomatic crops, positive with serological assays, to identify YDVs infecting Irish spring and winter barley crops and establish reference genomes to support further development of molecular surveillance tools. In total, RNA was extracted from 45 symptomatic crop samples that were collected across Ireland over 2 yr and sequenced following rRNA depletion. Three samples of barley plants from BYDV-infected aphid colonies were also included. BYDV-MAV was identified in all field samples sequenced. This confirms previous evidence based on serological assays that BYDV-MAV is the dominant YDV in Irish barley crops. We have also identified BYDV-PAS in 29% of symptomatic field samples, the first report of this species in Ireland. In addition, BYDV-PAV was also found, and crop samples with mixed infections were common; although in mixed infections the greatest proportion of YDV reads originated from BYDV-MAV. Finally, CYDV-RPS, the more severe variant of CYDV-RPV belonging to the genus Polerovirus, was identified in a single sample. The complete genomes, assembled from this first sequence-based survey, will enable the development of molecular surveillance tools with greater virus specificity, to further support the Irish aphid and YDV monitoring network.