Nucleotide Sequence of RNA from the Sobemovirus Found in Infected Cocksfoot Shows a Luteovirus-Like Arrangement of the Putative Replicase and Protease Genes

Abstract

A virus found in naturally infected cocksfoot plants had a host range, symptom expression characteristics, and a particle morphology similar to those of cocksfoot mottle sobemovirus (CoMV). The viral RNA was cloned and sequenced (GeneBank accession number L40905). Computer-assisted analysis of the 4,083-nt RNA sequence revealed four open reading frames (ORFs) flanked by 5'- and 3'-untranslated regions of 69 and 228 nt, respectively. The 3'-proximal ORF putatively coded for a 27.6-kDa product that was obviously homologous to the coat proteins of southern bean mosaic sobemovirus (SBMV) and rice yellow mottle sobemovirus (RYMV), which agrees with the identification of this virus as a Russian isolate of CoMV. This virus genome is closely related to that of a recently sequenced Norwegian isolate of CoMV. The 5' end of the subgenomic RNA was mapped 35 nt upstream of the coat-protein ORF initiation codon. Despite the considerable sequence similarity of the CoMV coat protein, putative RNA-dependent RNA polymerase (RDRP), and protease with the analogous proteins of SBMV and RYMV, CoMV differed from other sobemoviruses in the arrangement and expression of the RDRP and protease ORFs. The CoMV genome organization resembled those of the luteovirus genomes, i.e., the two ORFs overlap out of frame and are hypothesized to yield a frameshift fusion product.