[en] Worldwide, barley/cereal yellow dwarf viruses (YDVs) are the most widespread and damaging group of cereal viruses. In this study, we applied high-throughput sequencing technologies (HTS) to perform a virus survey on symptomatic plants from 47 cereal fields in Estonia. HTS allowed the assembly of complete genome sequences for 22 isolates of cereal yellow dwarf virus RPS, barley yellow dwarf virus GAV, barley yellow dwarf virus PAS (BYDV-PAS), barley yellow dwarf virus PAV (BYDV-PAV), and barley yellow dwarf virus OYV (BYDV-OYV). We also assembled a near-complete genome of the putative novel species BYDV-OYV from Swedish samples of meadow fescue. Previously, partial sequencing of the central part of the coat protein gene indicated that BYDV-OYV represented a putative new species closely related to BYDV-PAV-CN, which currently is recognized as a subtype of BYDV-PAV. The present study found that whereas the 3'gene block of BYDV-OYV shares the closest relationship with BYDV-PAV-CN, the 5'gene block of BYDV-OYV shows the closest relationships to that of BYDV-PAS. Recombination detection analysis revealed that BYDV-OYV is a parental virus for both. Analysis of complete genome sequence data indicates that both BYDV-OYV and BYDV-PAV-CN meet the species criteria of genus Luteovirus. The study discusses BYDV phylogeny, and through a systematic in silico analysis of published primers for YDV detection, the existing gaps in current diagnostic practices for detection of YDVs, proposing primer pairs based on the most recent genomic information for the detection of different BYDV species. Thanks to the rising number of sequences available in databases, continuous updating of diagnostic primers can improve test specificity, e.g., inclusivity and exclusivity at species levels. This is needed to properly survey the geographical and host distribution of the different species of the YDV complex and their prevalence in cereal/barley yellow dwarf disease epidemics.
Disciplines :
Biotechnology
Author, co-author :
Sõmera, Merike; Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
Massart, Sébastien ; Université de Liège - ULiège > Département GxABT > Gestion durable des bio-agresseurs
Tamisier, Lucie; Laboratory of Integrated and Urban Phytopathology, Gembloux Agro-Bio Tech - University of Liège, Gembloux, Belgium
Sooväli, Pille; Department of Plant Protection, Estonian Crop Research Institute, Jõgeva, Estonia
Sathees, Kanitha; Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
Kvarnheden, Anders; Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden ; Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
Language :
English
Title :
A Survey Using High-Throughput Sequencing Suggests That the Diversity of Cereal and Barley Yellow Dwarf Viruses Is Underestimated.
This article was based upon collaboration from COST Action FA1407 (DIVAS), supported by COST (European Cooperation in Science and Technology). Research visit of MS to Swedish University of Agricultural Sciences was performed thanks to a Swedish Institute scholarship. Lundströms Stiftelse offered financial support for the sequence determination of the Swedish isolate. The Estonian field survey was performed as part of the Estonian Biotechnology Program “Breeding for disease resistance in plants” (2012–2015).MS is grateful to Erkki Truve (deceased in April 2020) for his collegial support and discussions. Anna Akkerman is appreciated for technical assistance with the Estonian samples, and Ingrid Eriksson is appreciated for technical assistance with analyses of the Swedish samples. Funding. This article was based upon collaboration from COST Action FA1407 (DIVAS), supported by COST (European Cooperation in Science and Technology). Research visit of MS to Swedish University of Agricultural Sciences was performed thanks to a Swedish Institute scholarship. Lundstr?ms Stiftelse offered financial support for the sequence determination of the Swedish isolate. The Estonian field survey was performed as part of the Estonian Biotechnology Program ?Breeding for disease resistance in plants? (2012?2015).
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