Nucleotide sequence of the coat protein gene of a necrotic strain of potato virus Y from New Zealand

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Abstract
The sequence of the 3′-terminal 1,134 nucleotides of the genome of a New Zealand isolate of a necrotic strain of potato virus Y (PVYN) has been determined. This sequence contains one large open reading frame of 796 nucleotides, the start of which was not identified, which is capable of encoding a protein of 264 amino acid residues with a molecular weight of 29,631. Comparison of the amino acid sequence with a published coat protein sequence of another strain, PVY-D, and with the amino acid sequence deduced from PeMV cDNA sequence data, confirms that the 3′ cistron encodes the viral coat protein in PVYN. Adjacent to the 3′ end of the coding region there is an untranslatable sequence of 326 nucleotides terminating in a polyadenylate tract. An alignment of the PVYN amino acid sequence with the coat protein sequences of six other potyviruses revealed significant sequence similarities in the internal and carboxy terminal regions. Much amino acid sequence similarity was found between PVYN, PVY-D, and PeMV (91–93%), suggesting that PeMV should be regarded as a PVY strain. An analysis of the 3′-untranslated region of the six potyviruses revealed PVYN and PeMV as the only viruses displaying sequence similarity in this region. The 3′-untranslated sequences of PVYN and PeMV were further examined for secondary structure.