Identification of plant viruses in soybean by metagenomic sequencing

Viruses negatively impact soybean production by causing disease 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. In this study, soybean fields were scouted for virus-like disease symptoms during 2018 and 2019 growing seasons. Total RNA was extracted from symptomatic soybean tissues collected individually. cDNA libraries were prepared and RNA sequencing was performed using next-generation sequencing (NGS) Illumina HiSeq3000 (Illumina, https://www.illumina.com/) to generate paired-end reads (HiSeq: 2 * 150 bp, 2 lanes). After removal of soybean reads, the short-reads were de novo assembled using the Trinity assembler. Through metagenomics approaches, several viruses were detected and identified as single or mixed infections in soybean. De novo assemblies generated full- or nearly full-length genomes in soybean. Taken together, the results of this study showed that NGS-based technology is a valuable diagnostic tool for the identification of several viruses in field-grown soybean, and can provide rapid information about plant viruses that were previously not detected in soybean fields.