Gene, 123 (1993) 149-156 0 1993 Elsevier Science Publishers B.V. All rights reserved. 0378-I 119/93/$06.00 GENE 06912 149 Cloning and sequencing of potato virus Y (Hungarian isolate) genomic RNA (Recombinant DNA; plant virus; potyvirus; single-stranded messenger RNA; complete sequence; sequence comparison) Vera Thole, Tam& Dalmay, Jbzsef Burgyin and Ervin Balizs Agricultural Biotechnology Center, Institutefor Plant Sciences, H-2101 GiidBllii.Hungary Received by R. Padmanabhan: 2 July 1992; Revised/Accepted: 24 September/28 September 1992; Received at publishers: 29 October 1992 SUMMARY A sequence of 9703 nucleotides (nt) is reported for the genomic RNA of potato virus Y (Hungarian isolate, PVY-H), which causes necrotic rings around the buds on the tubers and mottling of leaves. The sequence contains one large open reading frame of 3061 amino acids (aa), a noncoding region of 189 nt at the 5’ end and a 330-nt 3’ nontranslated region. The nt sequence and the predicted aa sequence of the polyprotein of PVY-H were analysed pairwise with the only available complete sequence of PVY strain N (PVYn) and with the partial sequences of different PVY strains, as well as with other potyviruses and potyvirus-related plant viruses. The overall relationship between PVY-H and PVYn shows a nt sequence identity of 88.5% and an aa sequence identity of 94.2%. The lowest degree of homology was detected at the 5’ terminus of the genome, including the 5’ noncoding region (70.3%) and the 275-aa Pl protein (78%). A fivefold sequence repeat block of 5’-UUUCA was found in the 5’ noncoding region of PVY-H, which seems to be characteristic of PVY strains. INTRODUCTION Potato virus Y (PVY) is the type member of the potyvi- rus group, which constitutes the largest known and eco- nomically most important group of plant viruses (Hollings and Brunt, 1981). The single-stranded messen- ger-sense genomic RNA molecule of approximately 10 kb with a 5’-terminal genome-linked protein (VPg) and a poly(A) tract at the 3’ end is encapsidated into flexuous Correspondence to; Dr. V. Thole, Agricultural Biotechnology Center, Institute for Plant Sciences, Szent-GyBrgyi A. u.4, P.O.B. 170, H-2101 GiidB116, Hungary. Tel. (36-28)30539; Fax (36-28)30482; e-mail: h3782bal@ella.hu Abbreviations: aa, amino acid(s); bp, base pair(s); cDNA, DNA comple- mentary to RNA; CI, cylindrical inclusion protein; CP, coat protein; HC, helper component; HC-Pro, helper component-protease; kb, kilo- base(s) or 1000 bp; nt, nucleotide(s); 6K,, first 6-kDa peptide of the polyprotein precursor; 6K,, second 6-kDa peptide of the polyprotein precursor; NIa, small nuclear inclusion protein; Nib, large nuclear in- clusion protein; oligo, oligodeoxyribonucleotide; ORF, open reading rods 680 to 900 nm in length. The viral RNA of potyvi- ruses is translated into a large polyprotein precursor (340-360 kDa) which is co- and post-translationally pro- cessed by at least three viral-encoded proteases (Fig. la; see Riechmann et al., 1992, for a review). Among potyviruses the complete nt sequences of TEV (Allison et al., 1986), of TVMV (Domier et al., 1986), of four strains of PPV (PPV-RAN (Lam et al., 1989); PPV- NAT (Maiss et al., 1989); PPV-D (Teycheney et al., 1989); frame; p, plasmid; PCR, polymerase chain reaction; PPV, plum pox virus; PPV-D, D strain of PPV; PPV-NAT, NAT strain of PPV; PPV- RAN, RAN strain of PPV; PPV-SK68, SK68 strain of PPV, Pro, prote- ase; PVC, C strain of PVY; PVY, potato virus Y; PVY-D, D strain of PVY, PVY G016, GO16 strain of PVY; PVY-H, Hungarian isolate of PVY; PVY-MM, MM strain of PVY, PVYn and PVY-N’ and PVY- N’, three isolates of PVY strain N; PVY-0 and PVY-0’ and PVY-O’, three isolates of PVY strain 0; Pl protein, first protein of the polypro- tein precursor; P3, third protein of the polyprotein precursor; TEV, tobacco etch virus; TVMV, tobacco vein mottling virus; VPg, genome- linked protein.