title: Genome characterization of a Korean isolate of cymbidium mosaic virus.
abstract: The complete nucleotide sequence of the genomic RNA of a Korean isolate of cymbidium mosaic virus (CymMV-K2) was determined. The genomic RNA is 6227 nucleotides in length, excluding the poly(A) tail. It contains a 5'-noncoding region (NCR) of 73 nucleotides, five open reading frames (ORFs 1 to 5) which encode proteins with M(r) 160 kDa RNA-dependent RNA polymerase (ORF1), 26 kDa movement protein 1 (ORF2), 13 kDa movement protein 2 (ORF3), 10 kDa movement protein 3 (ORF4), 24 kDa coat protein (OFR5), and a 3' NCR of 76 nucleotides. The 5'-end of the CymMV-K2 genome initiates with GGAAAA which contrasts to GAAAA at the 5'-ends of other potexviruses, including a Singapore isolate of CymMV (CymMV-S2). When compared with CymMV-S2, 171 base substitutions were observed in the CymMV-K2 genome. Substitutions in the overlapping ORFs (ORFs 2 to 4) occurred more frequently than those in 5' NCR, ORF1, and 3' NCR. In addition to substitutions, two single-base deletions, one in the intercistronic region between ORF1 and ORF2 and the other in the ORF2, were found on the CymMV-K2 genome. The deletion in the ORF2 induced a frameshift which altered the C-terminal domain of movement protein 1. ORF3 and ORF4 of the CymMV-K2 genome are partially different from those of another Singapore CymMV genome (CymMV-S1) which has four frameshifts due to nucleotide deletions within these ORFs. Interestingly, the frameshifts resulted in no change in the conserved sequences of the movement proteins but reconstructed their transmembrane domains.
authors.affiliation: Department of Microbiology, College of Natural Sciences, Inje University, Kimhae, Korea.
authors.forename: J D
authors.initials: JD
authors.lastname: Kim
authors.forename: Y B
authors.initials: YB
authors.lastname: Koo
authors.forename: M U
authors.initials: MU
authors.lastname: Chang
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D003001:Cloning, Molecular; D017124:Conserved Sequence / Q000235:genetics; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D005814:Genes, Viral / Q000235:genetics; D016679:Genome, Viral; D007723:Korea; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D053830:Plant Viral Movement Proteins; D010944:Plants / Q000821:virology; D017863:Potexvirus / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D012367:RNA, Viral / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D014764:Viral Proteins / Q000235:genetics; D015678:Viral Structural Proteins / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D053830:Plant Viral Movement Proteins; D012367:RNA, Viral; D014764:Viral Proteins; D015678:Viral Structural Proteins