Detection and discovery of plant viruses in soybean by metagenomic sequencing

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.

Metagenomic identification of novel viruses of maize and teosinte in North America

“…All assembled contigs were queried against the all-organism NCBI nucleotide and protein database through BLASTN and BLASTX searches with default parameters using Blastplus v2.7.1 [ 31 ]. A similar informatics pipeline has previously been proven capable of virus identification by our research group [ 32 ].…”

Evaluation of soybean genotypes for cowpea mild mottle virus resistance through phenotypic reaction and genotypic analysis

“…Among the many plant viruses infecting soybean, CPMMV is an emerging virus that causes significant yield losses in field conditions (Elmore et al, 2022). The most cost-effective and environmentally friendly approach to manage viral diseases is to develop resistant Molecular markers are a vital tool to assess the presence of genetic variation in germplasm.…”

“…The soybean crop can be affected by several biotic and abiotic stresses, causing significant yield and quality losses. Among biotic stresses, soybean can be infected by more than 100 plant viral species and natural field infections by at least 46 viral species have been detected (Elmore et al, 2022), causing yield losses of 10%-30% under normal conditions and 50%-100% yield losses under severe outbreaks (Song et al, 2016). Cowpea mild mottle virus (CPMMV), a member of the genus Carlavirus (family Betaflexiviridae), has emerged as a major biotic constraint in soybean crop production (Zanardo & Carvalho, 2017).CPMMV was first reported in cowpea (Vigna unguiculata) in Ghana (Brunt & Kenten, 1973).…”

Investigating Variability in Viral Presence and Abundance across Soybean Seed Development Stages Using Transcriptome Analysis

“…Soybean ( Glycine max L.) is one of the most important crops globally, providing a vital source of protein and oil for human consumption, livestock feed, and industrial applications [ 1 ]. As soybean production expands across diverse regions, the threat of viral diseases poses a significant challenge to sustainable cultivation and global food security [ 2 ].…”

“…In addition to SMV, several other RNA viruses have been identified in soybean, including soybean vein necrosis-associated virus (SVNaV), bean pod mottle virus (BPMV), soybean yellow mottle mosaic virus (SYMMV), soybean yellow common mosaic virus (SYCMV), peanut stunt virus (PSV), peanut mottle virus (PeMoV), and alfalfa mosaic virus (AMV) [ 2 , 3 ]. Furthermore, recent studies have uncovered the presence of novel geminiviruses infecting soybean; however, the disease symptoms caused by these geminiviruses in soybean plants are largely asymptomatic [ 9 , 10 ].…”