Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Subterranean Clover Stunt Virus Revisited: Detection of Two Missing Genome Components.

ABSTRACT: Subterranean clover stunt virus (SCSV) is a type species of the genus Nanovirus in the family Nanoviridae. It was the first single-stranded DNA plant virus with a multipartite genome, of which genomic DNA sequences had been determined. All nanoviruses have eight genome components except SCSV, for which homologs of two genome components present in all other nanovirus genomes, DNA-U2 and DNA-U4, were lacking. We analysed archived and more recent samples from SCSV-infected legume plants to verify its genome composition and found the missing genome components. These results indicated that SCSV also has eight genome components and is a typical member of the genus Nanovirus.

SUBMITTER: Knierim D

PROVIDER: S-EPMC6410307 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Subterranean Clover Stunt Virus Revisited: Detection of Two Missing Genome Components.

Knierim Dennis D Barrière Quentin Q Grigoras Ioana I Winter Stephan S Vetten Heinrich-Josef HJ Schwinghamer Mark M Thomas John J Chu Paul P Gronenborn Bruno B Timchenko Tatiana T

Viruses 20190204 2

Subterranean clover stunt virus (SCSV) is a type species of the genus Nanovirus in the family Nanoviridae. It was the first single-stranded DNA plant virus with a multipartite genome, of which genomic DNA sequences had been determined. All nanoviruses have eight genome components except SCSV, for which homologs of two genome components present in all other nanovirus genomes, DNA-U2 and DNA-U4, were lacking. We analysed archived and more recent samples from SCSV-infected legume plan ...[more]

PMID: 30720711

Similar Datasets

Draft genome sequence of subterranean clover, a reference for genus Trifolium.

Project description:Clovers (genus Trifolium) are widely cultivated across the world as forage legumes and make a large contribution to livestock feed production and soil improvement. Subterranean clover (T. subterraneum L.) is well suited for genomic and genetic studies as a reference species in the Trifolium genus, because it is an annual with a simple genome structure (autogamous and diploid), unlike the other economically important perennial forage clovers, red clover (T. pratense) and white clover (T. repens). This report represents the first draft genome sequence of subterranean clover. The 471.8 Mb assembled sequence covers 85.4% of the subterranean clover genome and contains 42,706 genes. Eight pseudomolecules of 401.1 Mb in length were constructed, based on a linkage map consisting of 35,341 SNPs. The comparative genomic analysis revealed that different clover chromosomes showed different degrees of conservation with other Papilionoideae species. These results provide a reference for genetic and genomic analyses in the genus Trifolium and new insights into evolutionary divergence in Papilionoideae species.

| S-EPMC4992838 | biostudies-literature

Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping.

Project description:We selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The structural variations (SVs) discovered by Bionano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 regions containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome. Nucleotide-level validation is crucial to confirm and characterize SVs reported by optical mapping. The accuracy of SV detection by BOM is highly dependent on the quality of reference genomes and the density of selected nickases.

| S-EPMC6056659 | biostudies-literature

Complete genome sequences of two sweet potato chlorotic stunt virus isolates from china.

Project description:Sweet potato chlorotic stunt virus (SPCSV) was first detected in China in 2010, and several partial sequences have been determined for Chinese SPCSV isolates. This report describes the complete genome sequences of two SPCSV isolates from the Guangdong and Jiangsu provinces and will be valuable for understanding the characteristics of SPCSVs in China.

| S-EPMC3650446 | biostudies-literature

Complete Genome Sequence of Clover Yellow Mosaic Virus Isolated from White Clover in Japan.

Project description:Clover yellow mosaic virus (ClYMV) infecting white clover was isolated in Japan, and the complete genome sequence was determined.

| S-EPMC9202368 | biostudies-literature

Complete Genome Sequences of Seven Peanut Stunt Virus Strains from Japan.

Project description:We present the complete genomic RNA sequences of seven isolates of Peanut stunt virus discovered in diseased legume plants in various regions in Japan. These sequences and the published viral sequences were compared with respect to nucleotide percentages. Their phylogenetic analysis showed that all the isolates belong to subgroup IA.

| S-EPMC6256678 | biostudies-literature

An Improved Protocol for Agrobacterium-Mediated Transformation in Subterranean Clover (Trifolium subterraneum L.).

Project description:Subterranean clover (Trifolium subterraneum) is the most widely grown annual pasture legume in southern Australia. With the advent of advanced sequencing and genome editing technologies, a simple and efficient gene transfer protocol mediated by Agrobacterium tumefaciens was developed to overcome the hurdle of genetic manipulation in subterranean clover. In vitro tissue culture and Agrobacterium transformation play a central role in testing the link between specific genes and agronomic traits. In this paper, we investigate a variety of factors affecting the transformation in subterranean clover to increase the transformation efficiency. In vitro culture was optimised by including cefotaxime during seed sterilisation and testing the best antibiotic concentration to select recombinant explants. The concentrations for the combination of antibiotics obtained were as follows: 40 mg L-1 hygromycin, 100 mg L-1 kanamycin and 200 mg L-1 cefotaxime. Additionally, 200 mg L-1 cefotaxime increased shoot regeneration by two-fold. Different plant hormone combinations were tested to analyse the best rooting media. Roots were obtained in a medium supplemented with 1.2 µM IAA. Plasmid pH35 containing a hygromycin-resistant gene and GUS gene was inoculated into the explants with Agrobacterium tumefaciens strain AGL0 for transformation. Overall, the transformation efficiency was improved from the 1% previously reported to 5.2%, tested at explant level with Cefotaxime showing a positive effect on shooting regeneration. Other variables in addition to antibiotic and hormone combinations such as bacterial OD, time of infection and incubation temperature may be further tested to enhance the transformation even more. This improved transformation study presents an opportunity to increase the feeding value, persistence, and nutritive value of the key Australian pasture.

| S-EPMC8073064 | biostudies-literature

Characterization of components of resistance to Corn Stunt disease.

Project description:Corn Stunt is an important disease in the Americas due to it high prevalence and the yield reductions that can cause when present. However, changes in the presence of this disease across years hampers the effective identification of resistant genotypes to this disease. To avoid the limitations of phenotypic selection under natural pressure, this research aimed to devise an effective strategy to screen disease-resistant genotypes in the absence of high and constant natural pressures. To do so, we investigated the presence of antixenosis and antibiosis as components of resistance to the vector Dalbulus maidis as well as resistance to the pathogen Spiroplasma kunkelii under artificial inoculation conditions in four maize hybrids. The hybrids shown differences in their levels of resistance and target organisms, either the insect vector or the pathogen. Antixenosis and antibiosis to D. maidis were observed in DK72-10. Resistance to S. kunkelii by DK79-10 was seen as a delayed onset of symptoms, and DKB390 showed antixenosis to D. maidis and resistance to S. kunkelii. An association between symptom severity and yield reduction was found, but not between accumulation of pathogen S. kunkelii and symptom severity nor yield. In conclusion, the proposed methodology was efficacious and can aid in the screening of resistant genotypes in breeding programs to reduce the impact of Corn Stunt disease, ensuring that hybrids with good resistance level will be planted by farmers whenever disease occurs.

| S-EPMC7571704 | biostudies-literature

Transcription profiling of white clover plants following infection by white clover mosaic virus

Project description:White clover mosaic virus (WCMV) is a major pathogen of white clover (Trifolium repens L.), with significant effects on yield and persistence. Due to the absence of natural sources of WCMV resistance a transgenic strategy has been employed to produce plants constitutively expressing WCMV replicase gene derivatives, designed to inhibit the propagation of WCMV through an RNA silencing mechanism. A 12,000 feature oligonucleotide microarray has been used to identify global changes in host plant, in addition to virus genome-encoded gene expression associated with WCMV infection in non-transgenic and transgenic WCMV-resistant white clover. Pairwise comparison between the transcriptome of mock-inoculated non-transgenic and WCMV-inoculated transgenic plants provides clear evidence for substantial equivalence between these two genotype/treatments, and demonstrate the efficacy of the transgenic strategy. WCMV- inoculated non-transgenic plants exhibit elevated abundance of many virus-encoded, and host immune response-specific transcripts compared to the transgenic resistant plants or mock-inoculated non-transgenic plants. By contrast, relative to inoculated sensitive plants, the majority of significantly up-regulated genes in mock-inoculated non-transgenic plants or WCMV-inoculated transgenic plants are markers of healthy cellular function. These results, and the occurrence of levels of WCMV-encoded transcripts in inoculated transgenic plants equivalent to those in virus-free plants, confirm the validity of the transgenic RNA silencing approach.

2010-06-30 | E-MEXP-1688 | biostudies-arrayexpress

Complete Genome Sequence of a Soybean Dwarf Virus Isolate from White Clover in Germany.

Project description:In this study, we present the complete genome of a new isolate of soybean dwarf virus (SbDV) (genus Luteovirus, family Luteoviridae) from white clover in Germany. The complete genome of the isolate (JKI ID 23556) consists of 5,858 nucleotides and displays 94.98% nucleotide identity to its most similar SbDV relative (GenBank accession number MN412736).

| S-EPMC7348027 | biostudies-literature

Evaluation of two molecular methods for the detection of Yellow fever virus genome.

Project description:Yellow fever virus (YFV), a member of the family Flaviviridae, genus Flavivirus is endemic to tropical areas of Africa and South America and is among the arboviruses that pose a threat to public health. Recent outbreaks in Brazil, Bolivia, and Paraguay and the observation that vectors capable of transmitting YFV are presenting in urban areas underscore the urgency of improving surveillance and diagnostic methods. Two novel methods (RT-hemi-nested-PCR and SYBR(®) Green qRT-PCR) for efficient detection of YFV strains circulating in South America have been developed. The methods were validated using samples obtained from golden hamsters infected experimentally with wild-type YFV strains as well as human serum and tissue samples with acute disease.

| S-EPMC4109279 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data