Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Complete genome sequence of a new circular DNA virus from grapevine.

ABSTRACT: A novel circular DNA virus sequence is reported from grapevine. The corresponding genomic organization, coding potential, and conserved origin of replication are similar to those of members of the family Geminiviridae, but the genome of 3,206 nucleotides is 4% larger than the largest reported geminiviral genome and shares only 50% overall sequence identity.

SUBMITTER: Krenz B

PROVIDER: S-EPMC3416304 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Complete genome sequence of a new circular DNA virus from grapevine.

Krenz Björn B Thompson Jeremy R JR Fuchs Marc M Perry Keith L KL

Journal of virology 20120701 14

A novel circular DNA virus sequence is reported from grapevine. The corresponding genomic organization, coding potential, and conserved origin of replication are similar to those of members of the family Geminiviridae, but the genome of 3,206 nucleotides is 4% larger than the largest reported geminiviral genome and shares only 50% overall sequence identity. ...[more]

PMID: 22733880

Similar Datasets

Complete Sequence, Genome Organization and Molecular Detection of Grapevine Line Pattern Virus, a New Putative Anulavirus Infecting Grapevine.

Project description:: Grapevine line pattern virus (GLPV) was first described 30 years ago in Hungary. The lack of its genomic sequences and of an available antiserum made its detection impossible in other parts of the world. Three different high-throughput sequencing (HTS) protocols applied on a GLPV-infected vine allowed the construction of the full genome sequence of this virus. It includes three RNA segments, encoding four proteins: methyltransferase-helicase (1a), RNA-dependent RNA polymerase (2a), movement protein (3a) and coat protein (3b). The obtained sequences were used to design specific primers for its detection by RT-PCR and Northern blot hybridization, respectively. These diagnostic methods were used to test the presence of GLPV in graft-inoculated plants and in 220 grapevine accessions of different Mediterranean origins. The three RNAs-encoding proteins of GLPV shared a very high amino acid identity with those of hop yellow virus, a tentative member of the Anulavirus genus, leaving no doubt that both are two isolates of the same viral species. A circular RNA originating from the RNA2 was found, for which an alternative silencing suppressor role is hypothesized. Further investigation is needed to determine this possibility and also the host range and pathological significance of the virus.

| S-EPMC7354484 | biostudies-literature

Genome Sequence of Grapevine Virus K, a Novel Vitivirus Infecting Grapevine.

Project description:Here, we report the genome sequence of grapevine virus K (GVK), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVK is 7,476 nucleotides in length and encodes 5 open reading frames. GVK is a putative member of the genus Vitivirus in the family Betaflexiviridae.

| S-EPMC5597770 | biostudies-literature

Genome Sequence of Grapevine Virus T, a Novel Foveavirus Infecting Grapevine.

Project description:Here, we report the genome sequence of grapevine virus T (GVT), a novel single-stranded RNA virus identified from a transcriptome of grapevine. The genome of GVT is 8,701 nucleotides in length and encodes five open reading frames. GVT is a putative member of the genus Foveavirus in the family Betaflexiviridae.

| S-EPMC5597771 | biostudies-literature

Complete genome sequence of a novel vitivirus isolated from grapevine.

Project description:A novel virus-like sequence from grapevine was identified by Illumina sequencing. The complete genome is 7,551 nucleotides in length, with polyadenylation at the 3' end. Translation of the sequence revealed five open reading frames (ORFs). The genomic organization was most similar to those of vitiviruses. The polymerase (ORF1) and coat protein (ORF4) genes shared 31 to 49% nucleotide and 40 to 70% amino acid sequence identities, respectively, with other grapevine vitiviruses. The virus was tentatively named grapevine virus F (GVF).

| S-EPMC3416117 | biostudies-literature

Complete Genome Sequence of the Naegleria fowleri (Strain LEE) Closed Circular Extrachromosomal Ribosomal DNA Element.

Project description:The circular extrachromosomal ribosomal DNA (rDNA) element of Naegleria fowleri strain LEE was molecularly cloned and fully sequenced. The element comprises 15,786?bp and contains a single copy of the organism's rDNA cistron. The nonribosomal sequence contains five potential open reading frames, two large direct repeat sequences, and numerous smaller repeated-sequence regions.

| S-EPMC7714845 | biostudies-literature

Complete Genome Sequence of the Circular Extrachromosomal Element of Naegleria gruberi Strain EGB Ribosomal DNA.

Project description:The circular extrachromosomal element of Naegleria gruberi strain EGB was linearized, molecularly cloned, and fully sequenced. The sequence comprises 14,007 bp and encodes the organism's rRNA genes, two potential open reading frames, and numerous repeated sequence regions.

| S-EPMC5805870 | biostudies-literature

Complete Genome Sequences of Grapevine Red Globe Virus in Japan.

Project description:Two complete and three partial genome sequences of grapevine red globe virus (GRGV) from grapevines (Vitis spp.) in Japan were determined.

| S-EPMC9753726 | biostudies-literature

Complete genome sequence of trivittatus virus.

Project description:Trivittatus virus (family Bunyaviridae, genus Orthobunyavirus) represents an important genetic intermediate between the California encephalitis group and the Bwamba/Pongola and Nyando groups. Here, we report the first complete genome sequence of the prototype (Eklund) strain, isolated in 1948, which, interestingly, shows only a few differences when compared to partial sequences of modern strains.

| S-EPMC4591928 | biostudies-literature

Complete Genome Sequence of Buffalopox Virus.

Project description:The first complete genome assembly of buffalopox virus isolate Karachi 2005, with a length of 195,630 bp, is presented here. Phylogenetic analysis shows the virus to cluster within Vaccinia species, and the genome contains 177 protein-coding sequences.

| S-EPMC5968727 | biostudies-literature

Complete genome sequence of Tacaribe virus.

Project description:Tacaribe virus (TCRV) is the prototype of the New World arenaviruses (also known as TCRV serocomplex viruses). While TCRV is not itself a human pathogen, many closely related members of this group cause hemorrhagic fever, and thus TCRV has long served as an important BSL2 system for research into diverse areas of arenavirus biology. Due to its widespread use, a coding-complete sequence for both the S and L segments of the bipartite genome has been publically available for almost 30 years. However, more recently, this sequence has been found to contain significant discrepancies compared to other samples of the same original strain (i.e., TRVL-11573). Further, it is incomplete with respect to the genome ends, which contain critical regulatory elements for RNA synthesis. In order to rectify these issues we now present the first complete genome sequence for this important prototype arenavirus. In addition to completing the S segment 5' end, we identified an apparent error in the L segment 3' end as well as substantial discrepancies in the S segment intergenic region likely to affect folding. Comparison of this sequence with existing partial sequences confirmed a 12-amino-acid deletion in GP, including putative glycosylation sites, and a 4-amino-acid exchange flanking the exonuclease domain of NP. Accounting for these corrections, the TRVL-11573 strain appears to be nearly identical to that isolated in Florida in 2012. The availability of this information provides a solid basis for future molecular and genetic work on this important prototype arenavirus.

| S-EPMC7351806 | 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