Soybean Viromes in the Republic of Korea Revealed by RT-PCR and Next-Generation Sequencing

Jo, Yeonhwa; Yoon, Yisang; Jang, Yunwoo; Choi, Hoseong; Lee, Yeonghoon; Kim, Sang-Min; Choi, Seok Reyol; Lee, Bong Choon; Cho, Won Kyong

doi:10.3390/microorganisms8111777

Cited by 14 publications

(22 citation statements)

References 44 publications

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“…Other groups have used HTS for identifying viruses in soybean and other crops. For instance, soybean leaf materials collected from 172 plants throughout Korea [ 42 ] exhibited virus-like symptoms. This study performed RT-PCR using primers that could detect five viruses SMV, soybean yellow mottle mosaic virus (SYMMV), soybean yellow common mosaic virus (SYCMV), PeMoV, and peanut stunt virus (PSV).…”

Section: Discussionmentioning

confidence: 99%

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Detection and discovery of plant viruses in soybean by metagenomic sequencing

Elmore

Groves

Hajimorad

et al. 2022

Virol J

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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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Section: Discussionmentioning

confidence: 99%

“…In addition, HTS has been extensively used for plant virome studies [ 36 – 40 ]. Furthermore, HTS was successfully used to identify viruses and other pathogens in soybean vegetative parts [ 25 , 41 , 42 ], seeds [ 43 ], or in arthropod vectors that transmit them to soybean [ 44 ].…”

Section: Introductionmentioning

confidence: 99%

Detection and discovery of plant viruses in soybean by metagenomic sequencing

Elmore

Groves

Hajimorad

et al. 2022

Virol J

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“…The same amount of fine powder from each sample of leaf tissue was pooled and subjected to total RNA extraction using the RNeasy Microarray Tissue Mini Kit, according to the manufacturer's instructions (Qiagen, Hilden, Germany). The total RNA was used for the RNA-sequencing library preparation, which was carried out using the TruSeq RNA Library Preparation Kit v2 (Illumina, San Diego, CA, USA), as described previously [14]. The library was paired-end sequenced by Illumina's HiSeq2000 system (Macrogen, Seoul, Korea).…”

Section: Library Preparation and Rna-sequencingmentioning

confidence: 99%

“…Of these, the soybean mosaic virus (SMV), the soybean yellow mottle mosaic virus (SYMMV), and the soybean yellow common mosaic virus (SYCMV) have been identified as major viruses infecting soybean in Korea [7]. Other viruses infecting soybean in Korea include the peanut mottle virus (PeMV), the soybean dwarf virus, the clover yellow vein virus, the bean common mosaic virus, the peanut stunt virus, the tomato spotted wilt virus, and the bean common mosaic necrosis virus [8][9][10][11][12][13][14]. Although various RNA viruses infecting soybean have been identified, none of the DNA viruses infecting soybean have been reported in Korea.…”

Section: Introductionmentioning

confidence: 99%

Complete Genome Sequence of a Novel Monopartite Mastrevirus, Soybean Geminivirus B, Isolated from Soybean (Glycine max (L.) Merrill)

Choi

Hong

et al. 2022

Plants

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Soybean is one of the most important crops in Korea. To identify the viruses infecting soybean, we conducted RNA sequencing with samples displaying symptoms of viral disease. A contig displaying sequence similarity to the known Geminivirus was identified. A polymerase chain reaction (PCR) using two different pairs of back-to-back primers and rolling circle amplification (RCA) confirmed the complete genome of a novel virus named soybean geminivirus B (SGVB), consisting of a circular monopartite DNA genome measuring 2616 nucleotides (nt) in length. SGVB contains four open reading frames (ORFs) and three intergenic regions (IRs). IR1 includes a nonanucleotide origin of replication in the stem-loop structure. Phylogenetic and BLAST analyses demonstrated that SGVB could be a novel virus belonging to the genus Mastrevirus in the family Geminiviridae. We generated infectious clones for SGVB by adding a copy of the IR1 region of SGVB, comparing the V-ori in addition to the full-length genome of SGVB. Using the infectious clones, we observed chlorosis and leaf curling with a latent infection in the inoculated Nicotiana benthamiana plants, while none of the inoculated soybean plants showed any visible symptoms of disease. This study provides the complete genome sequence and infectious clones of a novel Mastrevirus referred to as SGVB from soybean in Korea.

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“…The whole genome sequence of soybean has been published. Transcriptomic technologies have been applied in various aspects of soybean research, including seed coat color research, material synthesis pathway, identification of transcription factors (TFs), and determination of stress, disease, and insect resistances [18][19][20][21][22]. However, studies on the direct effects of sulfur on soybean transcriptome are limited, moreover, compared with nitrogen and phosphate nutrition, plant sulfur nutrition has not been extensively studied [23].…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analysis of Soybean in Response to Different Sulfur Concentrations

Wang¹,

Li²,

Wu³

et al. 2022

Phyton

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Sulfur is an indispensable nutrient for plant growth and development, and is important in the synthesis of sulfurcontaining amino acids. Although several studies on the effects of some macronutrients, including nitrogen and phosphorus, have been conducted on the performance of several crops at the genomic level, studies on the effect of sulfur on crop performance are limited. Therefore, this study aimed to examine the effect of different sulfur concentration on the transcriptome of soybean. Additionally, soybean yield parameters were also examined. Two soybean varieties, DND252 and HN84, were exposed to low and high concentrations of sulfur, and differentially expressed genes (DEGs) were identified using transcriptome analysis. The study results showed that the DEGs identified in the DND252 variety were involved in stimuli response, DNA binding and cell periphery under low sulfur concentrations. Also, the DEGs identified under high sulfur concentration were involved in membrane and membrane parts. Additionally, DEGs identified in the HN84 variety under low sulfur concentrations had similar functions as those identified in DND252 under high sulfur concentrations, indicating that HN84 was more sensitive to sulfur concentration changes than DND252. However, under higher sulfur concentrations, the DEGs identified in HN84 were primarily involved in membrane and membrane parts, indicating that high sulfur can cause cell membrane damage. Furthermore, soybean grown using 2.0 mmol/L sulfur had the best yield. The findings of this study identified candidate genes for the breeding and development of sulfur-efficient soybean varieties.

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Soybean Viromes in the Republic of Korea Revealed by RT-PCR and Next-Generation Sequencing

Cited by 14 publications

References 44 publications

Detection and discovery of plant viruses in soybean by metagenomic sequencing

Detection and discovery of plant viruses in soybean by metagenomic sequencing

Complete Genome Sequence of a Novel Monopartite Mastrevirus, Soybean Geminivirus B, Isolated from Soybean (Glycine max (L.) Merrill)

Transcriptome Analysis of Soybean in Response to Different Sulfur Concentrations

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