title: The complete nucleotide sequence and genomic characterization of grapevine asteroid mosaic associated virus.
abstract: In analyzing grapevine clones infected with grapevine red blotch associated virus, we identified a small number of isometric particles of approximately 30nm in diameter from an enriched fraction of leaf extract. A dominant protein of 25kDa 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.
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: José
authors.initials: J
authors.lastname: Vargas-Asencio
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Klaudia
authors.initials: K
authors.lastname: Wojciechowska
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Maia
authors.initials: M
authors.lastname: Baskerville
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Annika L
authors.initials: AL
authors.lastname: Gomez
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Keith L
authors.initials: KL
authors.lastname: Perry
authors.affiliation: Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA. Electronic address: jrt36@cornell.edu.
authors.forename: Jeremy R
authors.initials: JR
authors.lastname: Thompson
mesh_terms: D020816:Amino Acid Motifs; D001483:Base Sequence; D017124:Conserved Sequence; D016679:Genome, Viral; D016366:Open Reading Frames; D010802:Phylogeny; D000072417:Protein Domains; D012367:RNA, Viral; D017422:Sequence Analysis, DNA; D046830:Tymoviridae / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification / Q000648:ultrastructure; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins
keywords: MS-MS; Marafivirus; RNA-Seq; Tymoviridae; sRNA-Seq library