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Open Access 01-12-2022 | Research

Detection and discovery of plant viruses in soybean by metagenomic sequencing

Authors: Manjula G. Elmore, Carol L. Groves, M. R. Hajimorad, Tracey P. Stewart, Mikaela A. Gaskill, Kiersten A. Wise, Edward Sikora, Nathan M. Kleczewski, Damon L. Smith, Daren S. Mueller, Steven A. Whitham

Published in: Virology Journal | Issue 1/2022

Abstract

Background

Viruses negatively impact soybean production by causing diseases that affect yield and seed quality. Newly emerging or re-emerging viruses can also threaten soybean production because current control measures may not be effective against them. Furthermore, detection and characterization of new plant viruses requires major efforts when no sequence or antibody-based resources are available.

Methods

In this study, soybean fields 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 workflow was used to identify and assemble known and unknown virus genomes.

Results

Several viruses were identified 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 identification of several viruses in field-grown soybean and can provide rapid information about expected viruses as well as viruses that were previously not detected in soybean.

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Title: Detection and discovery of plant viruses in soybean by metagenomic sequencing
Authors: Manjula G. Elmore
Carol L. Groves
M. R. Hajimorad
Tracey P. Stewart
Mikaela A. Gaskill
Kiersten A. Wise
Edward Sikora
Nathan M. Kleczewski
Damon L. Smith
Daren S. Mueller
Steven A. Whitham
Publication date: 01-12-2022
Publisher: BioMed Central
Published in: Virology Journal / Issue 1/2022
Electronic ISSN: 1743-422X
DOI: https://doi.org/10.1186/s12985-022-01872-5

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Detection and discovery of plant viruses in soybean by metagenomic sequencing

Abstract

Background

Methods

Results

Conclusions

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Abstract

Background

Methods

Results

Conclusions

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