title: The nucleotide sequence and proposed genome organization of oat chlorotic stunt virus, a new soil-borne virus of cereals.
abstract: The complete genomic sequence of a new virus, first found infecting oats in Wales, UK, has been determined. The genome is a positive-sense ssRNA molecule, 4114 nucleotides in length, examination of which indicates the presence of four ORFs. The first ORF initiating at the 5' terminus (ORF1) encodes a protein with a predicted M(r) of 23476 (p23). ORF2 extends through the amber termination codon of ORF1 to give a protein with a predicted M(r) of 84355 (p84). The readthrough domain of p84 contains amino acid sequence similarities with a number of putative RNA-dependent RNA polymerases. ORF3 is in a different reading frame from ORF1/2 and encodes a protein with an M(r) of 48231 (p48), identified as the coat protein by direct peptide sequencing. ORF4 nests within ORF3 but is in a different frame from it and codes for a protein with a predicted M(r) of 8220 (p8). Comparisons of peptide sequence, particularly within the putative polymerase region and within the S domain of the coat protein, highlight similarities with members of both the tombusvirus and carmovirus groups. The coat protein region shows most similarity with members of the tombusvirus group, whilst the size and predicted strategy of the genome seem to be intermediate between that of the carmovirus and tombusvirus groups. These features highlight possible evolutionary links with each group whilst being distinct from both. We propose the name of oat chlorotic stunt for this new virus.
authors.affiliation: School of Biological Sciences, University of Birmingham, Edgbaston, UK.
authors.forename: N
authors.initials: N
authors.lastname: Boonham
authors.forename: C M
authors.initials: CM
authors.lastname: Henry
authors.forename: K R
authors.initials: KR
authors.lastname: Wood
mesh_terms: D000595:Amino Acid Sequence; D018554:Avena / Q000821:virology*; D001483:Base Sequence; D002213:Capsid / Q000235:genetics; D003001:Cloning, Molecular; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D010942:Plant Viruses / Q000145:classification* / Q000201:enzymology / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012988:Soil Microbiology; D017864:Tombusvirus / Q000235:genetics
chemical_list: D012367:RNA, Viral; D012324:RNA-Dependent RNA Polymerase