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The complete nucleotide sequence and genomic characterization of grapevine asteroid mosaic associated virus
- Source :
- Virus research. 227
- Publication Year :
- 2016
-
Abstract
- In analyzing grapevine clones infected with grapevine red blotch associated virus, we identified a small number of isometric particles of approximately 30 nm in diameter from an enriched fraction of leaf extract. A dominant protein of 25 kDa was isolated from this fraction using SDS-PAGE and was identified by mass spectrometry as belonging to grapevine asteroid mosaic associated virus (GAMaV). Using a combination of three methods RNA-Seq, sRNA-Seq, and Sanger sequencing of RT- and RACE-PCR products, we obtained a full-length genome sequence consisting of 6719 nucleotides without the poly(A) tail. The virus possesses all of the typical conserved functional domains concordant with the genus Marafivirus and lies evolutionarily between citrus sudden death associated virus and oat blue dwarf virus. A large shift in RNA-Seq coverage coincided with the predicted location of the subgenomic RNA involved in coat protein (CP) expression. Genus wide sequence alignments confirmed the cleavage motif LxG(G/A) to be dominant between the helicase and RNA dependent RNA polymerase (RdRp), and the RdRp and CP domains. A putative overlapping protein (OP) ORF lacking a canonical translational start codon was identified with a reading frame context more consistent with the putative OPs of tymoviruses and fig fleck associated virus than with those of marafiviruses. BLAST analysis of the predicted GAMaV OP showed a unique relatedness to the OPs of members of the genus Tymovirus .
- Subjects :
- 0301 basic medicine
Cancer Research
food.ingredient
Marafivirus
Amino Acid Motifs
RNA-dependent RNA polymerase
Genome, Viral
Oat blue dwarf virus
Virus
Tymoviridae
03 medical and health sciences
symbols.namesake
Open Reading Frames
Viral Proteins
food
Start codon
Protein Domains
Virology
Conserved Sequence
Phylogeny
Sanger sequencing
Genetics
biology
Base Sequence
Nucleic acid sequence
Sequence Analysis, DNA
biology.organism_classification
030104 developmental biology
Infectious Diseases
symbols
RNA, Viral
Subjects
Details
- ISSN :
- 18727492
- Volume :
- 227
- Database :
- OpenAIRE
- Journal :
- Virus research
- Accession number :
- edsair.doi.dedup.....4e0eda29b619a3cfb082f61ecf9cdab9