Nucleotide sequence and genomic organization of a newly identified member of the genus Carmovirus, soybean yellow mottle mosaic virus, from soybean

RT-RPA Assay Combined with a Lateral Flow Strip to Detect Soybean Mosaic Virus

Soybean (Glycine max L.) is one of the most widely planted and used legumes in the world, being used for food, animal feed products, and industrial production. The soybean mosaic virus (SMV) is the most prevalent virus infecting soybean plants. This study developed a diagnostic method for the rapid and sensitive detection of SMV using a reverse transcription-recombinase polymerase amplification (RT-RPA) technique combined with a lateral flow strip (LFS). The RT-RPA and RT-RPA-LFS conditions to detect the SMV were optimized using the selected primer set that amplified part of the VPg protein gene. The optimized reaction temperature for the RT-RPA primer and RT-RPA-LFS primer used in this study was 38℃ for both, and the minimum reaction time was 10 min and 5 min, respectively. The RT-RPA-LFS was as sensitive as RT-PCR to detect SMV with 10 pg/μl of total RNA. The reliability of the developed RT-RPA-LFS assay was evaluated using leaves collected from soybean fields. The RT-RPA-LFS diagnostic method developed in this study will be useful as a diagnostic method that can quickly and precisely detect SMV in the epidemiological investigation of SMV, in the selection process of SMV-resistant varieties, on local farms with limited resources.

Complete genome sequence of seed-transmitted soybean yellow mottle mosaic virus from soybeans in Korea

Soybean yellow mottle mosaic virus (SYMMV), a member of the genus Gammacarmovirus, remains poorly understood in terms of its transmission pathway. This study reveals the complete genome sequence of a seed-transmitted isolate, ST-HB56, contributing to the understanding of SYMMV's ecological dynamics.

Molecular and biological characterization of soybean yellow mottle mosaic virus severe strain infecting soybean in India

The complete nucleotide sequence and genome organization of soybean yellow mottle mosaic virus severe strain causing bright yellow mosaic, mottling and puckering symptoms in soybean (Glycine max) from India was determined. The monopartite single stranded genomic RNA is 3974 nuclotides long and has the potential to encode six viral proteins viz., p25, p83, p8, p10, p39 and p25. The SYMMV-Sb isolate differed from mungbean strain with 69 nucleotides and nine aminoacids dispersed over the various ORFs. Comparative sequence analysis revealed that SYMMV-Sb shared 98% nt sequence identity at complete genome level and 96-100% at all ORFs level with SYMMV mungbean strain from India and 71-92% identity with SYMMV Korean soybean isolate, whereas it showed very low sequence identity with other tombusviridae members (2-53%). The phylogenetic analysis showed the clustering of SYMMV-Sb along with other members of genus Gammacarmovirus. The SYMMV-Sb isolate produced chlorotic blotches, mild and veinal mottling, necrosis and puckering symptoms in various leguminous host plants. The symptomatalogy of the soybean isolate was differed from mungbean strain as earlier induced severe symptoms on soybean and mild symptoms on mungbean.

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The online version contains supplementary material available at 10.1007/s13205-021-02925-2.

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

Soybean (Glycine max L.) is one of the most important crop plants in the Republic of Korea. Here, we conducted a soybean virome study. We harvested a total of 172 soybean leaf samples showing disease symptoms from major soybean-growing regions in the Republic of Korea. Individual samples were examined for virus infection by RT-PCR. Moreover, we generated eight libraries representing eight provinces by pooling samples and four libraries from single samples. RNA-seq followed by bioinformatics analyses revealed 10 different RNA viruses infecting soybean. The proportion of viral reads in each transcriptome ranged from 0.2 to 31.7%. Coinfection of different viruses in soybean plants was very common. There was a single dominant virus in each province, and this geographical difference might be related to the soybean seeds that transmit viruses. In this study, 32 viral genome sequences were assembled and successfully used to analyze the phylogenetic relationships and quasispecies nature of the identified RNA viruses. Moreover, RT-PCR with newly developed primers confirmed infection of the identified viruses in each library. Taken together, our soybean virome study provides a comprehensive overview of viruses infecting soybean in eight geographical regions in the Republic of Korea and four single soybean plants in detail.

Seed transmission of a distinct soybean yellow mottle mosaic virus strain identified from India in natural and experimental hosts

Soybean yellow mottle mosaic virus (SYMMV) is a newly identified member of the genus Gammacarmovirus from grain legumes in India. As the modes of transmission of this virus have not been described, we assessed the possibility of SYMMV to be transmitted through seed collected from field infected mungbean plants and mechanically sap inoculated French bean plants using serological and molecular techniques followed by progeny assays. Direct antigen coated enzyme linked immunosorbent assay (DAC-ELISA) and reverse transcription polymerase chain reaction (RT-PCR) results are inconsistent with field infected mungbean seed tissues to ensure seed transmissibility irrespective of seed number used. Seed from mechanical sap inoculated French bean showed higher absorbance values in DAC-ELISA and amplification corresponding to replicase, movement and coat protein regions of SYMMV genome. The relative accumulation of SYMMV was higher in pod walls, immature seed and stamens and stigma of mechanical sap inoculated French bean. Progeny assays with infected seed revealed the seed transmissibility of SYMMV at the rate of 63.33% in mungbeanand 73.33% in French bean. Mechanical sap inoculation of mungbean progeny seedlings on French bean cv. Pusa Parvati produced characteristic symptoms of SYMMV. The results obtained from this study demonstrate that SYMMV is seed borne in nature and can be transmitted to next generation seedlings. This is the first report of seed transmission of SYMMV in mungbean and French bean.

Development of Soybean Yellow Mottle Mosaic Virus-Based Expression Vector for Heterologous Protein Expression in French Bean

Plant virus-based vectors provide attractive and valuable tools for rapid production of recombinant protein in large quantities as they produce systemic infections in differentiated plant tissues. In the present study, we engineered the Soybean yellow mottle mosaic virus (SYMMV) as a gene expression vector which is a promising candidate for systemic expression of foreign proteins in French bean plants. Full virus vector strategy was exploited for insertion of foreign gene by inserting MCS through PCR in the circular pJET-SYMMV clone. To examine the ability of the SYMMV vector system, GFP gene was cloned after the start codon of coat protein (CP) so that its expression was driven by the SYMMV-CP subgenomic promoter. When in vitro run off SYMMV-GFP transcript was mechanically inoculated to French bean leaves, good level of GFP expression was observed through confocal microscopy up to 40 dpi. Expression of heterologous protein was also confirmed through ISEM, DAC-ELISA and RT-PCR with specific primers at 20 dpi. The recombinant SYMMV construct was stable in in vitro runoff transcript inoculated plants but the inserted GFP was lost in progeny virion inoculated plants. The system developed here will be useful for further studies of SYMMV gene functions and exploitation of SYMMV as a gene expression vector.

Complete genome sequence of a lettuce chlorosis virus isolate from China and genome recombination/rearrangement analysis

We determined the complete genome sequence of a lettuce chlorosis crinivirus (LCV) from China (LCV-NJ). The bipartite genome of LCV-NJ consists of RNA1 and RNA2 which are 8165 and 8454 nucleotides (nt) in length, respectively. The genomic structure of LCV-NJ RNA1 resembles that of LCV-California, an isolate with four open reading frames (ORFs) in RNA1. Although the amino acid sequences of ORF 1a and 1b have 92 and 99% identity between LCV-NJ and LCV-California, ORF 2 and ORF3 of LCV-NJ share only 63 and 71% identity with those of LCV-California, respectively. In addition LCV-NJ RNA2 contains 9 ORFs, compared to 10 ORFs in LCV-California. ORF10 was missing due to the deletion of a 173-nt sequence within the 3'-terminal region of LCV-NJ RNA2. Insertion or deletion of sequences of varying lengths was also observed in RNA1 and other regions of RNA2. Based on these findings, we propose that LCV-NJ/LCV-California may have undergone genome recombination and/or rearrangement in RNA1 and RNA2.

Complete genome analysis of a novel umbravirus-polerovirus combination isolated from Ixeridium dentatum

Two novel viruses, isolated in Bonghwa, Republic of Korea, from an Ixeridium dentatum plant with yellowing mottle symptoms, have been provisionally named Ixeridium yellow mottle-associated virus 1 (IxYMaV-1) and Ixeridium yellow mottle-associated virus 2 (IxYMaV-2). IxYMaV-1 has a genome of 6,017 nucleotides sharing a 56.4% sequence identity with that of cucurbit aphid-borne yellows virus (genus Polerovirus). The IxYMaV-2 genome of 4,196 nucleotides has a sequence identity of less than 48.3% with e other species classified within the genus Umbravirus. Genome properties and phylogenetic analysis suggested that IxYMaV-1 and -2 are representative isolates of new species classifiable within the genus Polerovirus and Umbravirus, respectively.

Complete genome sequence of rice virus A, a new member of the family Tombusviridae

An evaluation of the virus population in rice plants using next-generation sequencing technologies resulted in the discovery of a new RNA virus, tentatively named rice virus A (RVA). The complete RVA genome sequence was determined and analyzed, revealing a genome organization resembling that of viruses classified in the genera Aureusvirus, Tombusvirus and Zeavirus within the family Tombusviridae. With 4,832 nucleotides, the RVA genome may be the largest monopartite genome sequenced to date in the family Tombusviridae. The 453-amino acid RVA coat protein shares the highest identity with the gp3 protein of an unclassified carascovirus, SF1 (GenBank accession no. KF510027) isolated from San Francisco wastewater, rather than the coat protein of any known member of the family Tombusviridae. These novel characteristics represent a significant divergence from the genomes of viruses belonging to the sixteen existing genera of the family Tombusviridae, demonstrating that RVA is likely a new family member.

Genome characterization, infectivity assays of in vitro and in vivo infectious transcripts of soybean yellow mottle mosaic virus from India reveals a novel short mild genotype

Nucleotide sequence of a distinct soybean yellow mottle mosaic virusisolate from Vignaradiata (mungbean isolate, SYMMV-Mb) from India was determined and compared with othermembers of the family Tombusviridae. The complete monopartite single-stranded RNA genome of SYMMV-Mb consisted of 3974nt with six putative open reading frames and includes 5' and 3' untranslated regions of 35 and 254nt, respectively. SYMMV-Mb genome shared 75% nt sequence identity at complete genome level and 67-92% identity at all ORFs level with SYMMV Korean and USA isolates (soybean isolates) followed by CPMoV, whereas it shared very low identity with other tombusviridae members (5-41%). A full-length infectious cDNA clone of the SYMMV-Mb placed under the control of the T7 RNA polymerase and the CaMV35S promoters was generated and French bean plants on mechanical inoculation with in vitro RNA transcripts, p35SSYMMV-O4 plasmid and agroinoculation with p35SSYMMV-O4 showed symptoms typical of SYMMV-Mb infection. The infection was confirmed by DAC-ELISA, ISEM, RT-PCR and mechanical transmission to new plant species. Further testing of different plant species with agroinoculation of p35SSYMMV-O4 showed delay in symptoms but indistinguishable from mechanical sap inoculation and the infection was confirmed by DAC-ELISA, RT-PCR and mechanical transmission to new plants. The system developed here will be useful for further studies on pathogenecity, viral gene functions, plant-virus-vector interactions of SYMMV-Mb and to utilize it as a gene expression and silencing vector.

The complete genomic sequence of a tentative new polerovirus identified in barley in South Korea

The complete nucleotide sequence of a new barley polerovirus, tentatively named barley virus G (BVG), which was isolated in Gimje, South Korea, has been determined using an RNA sequencing technique combined with polymerase chain reaction methods. The viral genomic RNA of BVG is 5,620 nucleotides long and contains six typical open reading frames commonly observed in other poleroviruses. Sequence comparisons revealed that BVG is most closely related to maize yellow dwarf virus-RMV, with the highest amino acid identities being less than 90 % for all of the corresponding proteins. These results suggested that BVG is a member of a new species in the genus Polerovirus.

Diagnosis of a new variant of soybean yellow mottle mosaic virus with extended host-range in India

Soybean yellow mottle mosaic virus (SYMMV, genus Carmovirus) was previously known to occur in South Korea and USA causing bright yellow mosaic in soybean. In this study, SYMMV (Car-Mb14 isolate) was isolated from mungbean (Vigna radiata) exhibiting mild mottling and puckering symptoms in the experimental field at Indian Agricultural Research Institute, New Delhi during 2012. The virus isolate, Car-Mb14 induced veinal mottling, mild mottling, chlorotic blotching, local and systemic necrosis in soybean, mungbean, blackgram, French bean and guar bean, respectively. The symptomatology of the present isolate of SYMMV was different from the previously reported South Korean isolate, as the later did not induce symptoms in any of the above legumes other than soybean. The present isolate was phylogenetically distinct and shared 90-93 % sequence identity in coat protein (CP) of 52 SYMMV isolates reported from Korea and USA. In order to know the serological relationships, the CP gene of the present isolate was over expressed as a 39 kDa protein in E. coli and an antiserum of 1:16,000 titer against the recombinant CP was produced. Serological cross reactivity analysis revealed that SYMMV was serologically related to blackgram mottle virus but not to cowpea mottle virus, the other legume infecting carmoviruses. The antiserum was used to detect prevalence of SYMMV in legume crops by ELISA. Out of 145 field samples of legumes (mungbean, blackgram, French bean and soybean) collected from different places in India, SYMMV was detected only in 16 samples of mungbean and one sample of blackgram. The natural infection of SYMMV in mungbean and blackgram was further confirmed based on CP gene sequence. This study provides evidence of occurrence of a new variant of SYMMV with distinct symptom phenotype and extended host-range in India.

The complete genome sequences of two isolates of cnidium vein yellowing virus, a tentative new member of the family Secoviridae

We determined the complete genome sequences of two isolates of cnidium vein yellowing virus (CnVYV-1 and -2) that co-infected all field samples collected from Cnidium officinale in Korea. Unlike CnVYV-2, however, CnVYV-1 was sap-transmissible to Nicotiana benthamiana. CnVYV-1 and -2 have bipartite genomes of 7,263 and 3,110 nucleotides and 7,278 and 3,112 nucleotides, respectively, excluding the poly(A) tails. Phylogenetic analysis of the CnVYV-1 and -2 sequences indicated close relationships to strawberry latent ringspot virus, an unassigned member of the family Secoviridae. CnVYV-1 and CnVYV-2 are closely related viruses that may represent a tentative new species of the family Secoviridae.

Nucleotide sequence and genome organization of a new proposed crinivirus, tetterwort vein chlorosis virus

The genome of tetterwort vein chlorosis virus (TVCV) from South Korea has been completely sequenced. Its genomic organization resembles those of other criniviruses, with several new features, indicating that TVCV is a member of a new species in the genus Crinivirus, family Closteroviridae. RNA1 contains 8467 nucleotides, with at least four opening reading frames (ORFs). ORF1a encodes a protein with predicted papain-like protease, methyltransferase, and helicase activities. ORF1b encodes a putative RNA-dependent RNA polymerase that is apparently expressed through a +1 ribosomal frameshift. RNA2 contains 8113 nucleotides encoding at least nine proteins, similar to most crinivirus RNA2s. The 3' untranslated regions of the bipartite RNA genome share 82.1% nucleotide sequence identity.

Nucleotide sequence and genome organization of atractylodes mottle virus, a new member of the genus Carlavirus

The complete genome sequence of a member of a distinct species of the genus Carlavirus in the family Betaflexiviridae, tentatively named atractylodes mottle virus (AtrMoV), has been determined. Analysis of its genomic organization indicates that it has a single-stranded, positive-sense genomic RNA of 8866 nucleotides, excluding the poly(A) tail, and consists of six open reading frames typical of members of the genus Carlavirus. The individual open reading frames of AtrMoV show moderately low sequence similarity to those of other carlaviruses at the nucleotide and amino acid sequence levels. Pairwise comparison and phylogenetic analysis suggest that AtrMoV is most closely related to chrysanthemum virus B.

Complete genome sequence and construction of infectious full-length cDNA clones of tobacco ringspot Nepovirus, a viral pathogen causing bud blight in soybean

Tobacco ringspot virus (TRSV, genus Nepovirus), causes severe diseases in soybean and tobacco plants. TRSV-induced bud blight disease significantly reduced both the yield and quality of soybeans. The function of the encoded viral gene product involved in TRSV infection was unclear due to the limitation of reverse genetics studies on the viral genome. Here, we represent the successful construction of infectious full-length cDNA clones of TRSV genome (RNA1 and RNA2). The cDNAs of TRSV RNA1 and RNA2 were cloned into the binary vector pPZP211 immediately downstream of a double cauliflower mosaic virus 35S promoter and upstream of the nopaline synthase terminator. Seven days after agrobacterium-mediated co-inoculation of these two constructs, Nicotiana benthamiana plants developed a systemic infection with necrotic ringspot symptoms and weak stunting of the leaves, similar to that induced by natural TRSV. The systemic infection was confirmed by transmission electron microscopy and Western blot analysis. Simultaneously, soybean, tomato, and Arabidopsis ecotype Estland were mechanically inoculated with sap prepared from TRSV-agroinfiltrated N. benthamiana leaves, showing typical symptoms of bud blight, necrotic spots, and lethal systemic necrosis, respectively. The system developed herein will be an appealing way to determine TRSV viral gene functions and study host-TRSV interactions.

Complete genome sequence of a South Korean isolate of Brugmansia mosaic virus

We determined the complete genome sequence of a South Korean (SK) isolate of Brugmansia mosaic virus (BruMV), which has recently been proposed to be a member of a new species in the genus Potyvirus. The genomic RNA of BruMV isolate SK is 9781 nucleotides in length (excluding the 3'-terminal poly (A)) and shares complete nucleotide and polyprotein amino acid sequence identities of 85.6 % and 93.1 %, respectively, with the type isolate (D-437) of BruMV described in the USA. To our knowledge, this is the first report providing evidence of considerable sequence variation in BruMV.

Biological and molecular characterization of Soybean yellow common mosaic virus, a new species in the genus Sobemovirus

A novel soybean-infecting sobemovirus termed Soybean yellow common mosaic virus (SYCMV) was characterized. The virus has a single, positive-strand RNA genome of 4152 nucleotides. The virus contains four putative open reading frames encoding P1 (78-566 nt), polyprotein ORF2a (524-2248 nt), polymerase domain ORF2b (1852-3417 nt), and CP (3227-4030 nt). The entire nucleotide sequence of SYCMV showed 31.2-71.3% nucleotide identity with the previously known eleven species of sobemovirus. In host range analysis of SYCMV, in which twenty one species and three different Nicotiana tabacum cultivars belonging to seven families were inoculated with the virus, SYCMV had a narrow host range, infecting only Glycine max and G. soja. Based on the obtained sequence, full-length clones of SYCMV were constructed. Symptoms produced by inoculation with clones were indistinguishable from those produced by inoculation with sap from symptomatic plants. Viral RNA accumulation of SYCMV was detected in the upper leaves by Northern blotting. This indicated that full-length clones of SYCMV were sufficient to produce disease symptoms. Genomic organization, the predicted amino acid sequence, and phylogenetic analyses with known sobemoviruses confirmed the assignment of SYCMV as a new member of the genus Sobemovirus.

Molecular characterization of a new Tospovirus infecting soybean

A new, widespread disease was recently observed in soybean in the United States. The disease, named Soybean vein necrosis, is manifested by intraveinal chlorosis and necrosis, and has been found in almost all of the 50 fields visited over a period of 3 years in the midwest and midsouth part of the United States. A virus was isolated from symptomatic material, and detection protocols were developed. More than 150 symptomatic specimens collected from seven US States were tested, and all were found positive for the virus unlike 75 asymptomatic samples, revealing the absolute association between virus and disease. Protein pairwise comparisons coupled with phylogenetic analyses indicate that the virus is a new member of the genus Tospovirus.