Nucleotide sequence of sweet clover necrotic mosaic dianthovirus RNA-1.

The complete nucleotide sequence of sweet clover necrotic mosaic dianthovirus (SCNMV) RNA-1 has been determined. RNA-1 consists of 3876 nucleotides in length, containing three large open reading frames (ORFs). The 5'-proximal, internal and 3'-terminal ORFs potentially encode 27-kDa, 57-kDa and 37-kDa proteins, respectively. The frameshift event between the C-terminus of the 27-kDa protein and extension of the N-terminus of the 57-kDa protein may result in the formation of a 88-kDa protein which is presumed to be a replicase. The 37-kDa coat protein ORF is located immediately downstream of the 57-kDa ORF. The same genome organization and high similarity (80-92%) of both the nucleotide sequences and the deduced amino acid sequences between red clover necrotic mosaic dianthovirus and SCNMV suggest that they originate from a common progenitor, but have divergent evolution later. Striking similarity was detected between the putative RNA-dependent RNA polymerase of SCNMV and that of the tombus-, carmo-, necro-, machlomo- and luteoviruses, supporting a proposal that they belong to the same virus supergroup although there is a relatively low degree of coat protein sequence similarity in these viruses.