المقالات العلميةفيروسات Virus

Detection and discovery of plant viruses in soybean by metagenomic sequencing

Elmore, M.G., Groves, C.L., Hajimorad, M.R. et al. Detection and discovery of plant viruses in soybean by metagenomic sequencing. Virol J 19, 149 (2022).

Abstract
Background: Viruses negatively impact soybean production by causing diseases that afect yield and seed quality. Newly emerging or re-emerging viruses can also threaten soybean production because current control measures may not be efective against them. Furthermore, detection and characterization of new plant viruses requires major eforts when no sequence or antibody-based resources are available.
Methods: In this study, soybean felds were scouted for virus-like disease symptoms during the 2016–2019 growing seasons. Total RNA was extracted from symptomatic soybean parts, cDNA libraries were prepared, and RNA sequencing was performed using high-throughput sequencing (HTS). A custom bioinformatic workfow was used to identify and assemble known and unknown virus genomes.
Results: Several viruses were identifed in single or mixed infections. Full- or nearly full-length genomes were generated for tobacco streak virus (TSV), alfalfa mosaic virus (AMV), tobacco ringspot virus (TRSV), soybean dwarf virus (SbDV), bean pod mottle virus (BPMV), soybean vein necrosis virus (SVNV), clover yellow vein virus (ClYVV), and a novel virus named soybean ilarvirus 1 (SIlV1). Two distinct ClYVV isolates were recovered, and their biological properties were investigated in Nicotiana benthamiana, broad bean, and soybean. In addition to infections by individual viruses, we also found that mixed viral infections in various combinations were quite common.
Conclusions: Taken together, the results of this study showed that HTS-based technology is a valuable diagnostic tool for the identifcation of several viruses in feld-grown soybean and can provide rapid information about expected viruses as well as viruses that were previously not detected in soybean.
Keywords: Soybean, High-throughput sequencing, Virus identifcation, Clover yellow vein virus, Nicotiana benthamiana, Broad bean, Mixed infection, Ilarvirus

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