Detection and discovery of plant viruses in soybean by metagenomic sequencing

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

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

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.

Original languageEnglish
Article number149
JournalVirology Journal
Volume19
Issue number1
DOIs
StatePublished - Dec 2022

Bibliographical note

Funding Information:
We thank the Iowa State University DNA Facility for sequencing, Jim Specht (University of Nebraska) for seed from NAM lines, Ed Zaworski, Stith Wiggs for Acre Edge seed, Christian Montes-Serey, Pulkit Kanodia for technical advice, and Zach Lozier for advice on constructing phylogenetic trees.

Funding Information:
This project was funded by the Iowa Soybean Association, the Iowa State University Plant Sciences Institute, Wisconsin Soybean Marketing Board, North Central Soybean Research Program, and the USDA National Institute of Food and Agriculture Hatch project 4308. The funding bodies had no role in the design of this study, collection of materials, data analysis and interpretation of data and in the writing of the manuscript.

Publisher Copyright:
© 2022, The Author(s).

Keywords

  • Broad bean
  • Clover yellow vein virus
  • High-throughput sequencing
  • Ilarvirus
  • Mixed infection
  • Nicotiana benthamiana
  • Soybean
  • Virus identification

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

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