Complete nucleotide sequence of the cucumber necrosis virus genome

Abstract

The complete nucleotide sequence of the cucumber necrosis virus (CNV) genome has been determined. The genome is 4701 nucleotides in length and contains five long open reading frames (ORF). ORF1 begins at the first AUG codon at the 5′ terminus and terminates at an amber codon. The predicted molecular weight of the polyprotein encoded by ORF1 is 33 kilodaltons (kDa). Readthrough of the ORF1 amber codon would yield a protein with a molecular weight of 92 kDa. Comparison of the amino acid sequence of the 92-kDa protein with the putative replicases of carnation mottle virus (CarMV) and barley yellow dwarf virus (BYDV) shows extensive sequence similarity. This suggests that the CNV 92kDa protein is the viral replicase and, furthermore, suggests a close evolutionary relationship between CNV, CarMV, and BYDV, members of the Tombus-, Carmo-, and Luteovirus groups, respectively. Immediately following the 92-kDa protein is ORF3 which can encode a 40-kDa protein. It is identified as the coat protein based on its similarity in amino acid composition to the previously determined CNV coat protein sequence ( J. H. Tremaine, 1972, Virology 48, 582–590 ) and on its amino acid sequence similarity with the tomato bushy stunt virus coat protein. Two nested ORFs (ORF4 and −5), in different frames, follow the coat protein gene. Although it is not known if both ORFs are expressed, they would encode proteins with predicted molecular weights of 21 and 20 kDa, respectively.