Nucleotide Sequences of the 3' Regions of Two Major Viruses from Mosaic-Diseased Garlic: Molecular Evidence of Mixed Infection by a Potyvirus and a Carlavirus

Abstract

Garlic viruses from 289 mosaic-diseased garlic plants, cultivar Howaitoroppen, were purified, and two different flexuous, rod-shaped viruses, one with a 33-kDa coat protein (CP) and the other with a 36-kDa CP, appeared to be the most common. We determined the partial amino acid sequences of these two CPs and obtained cDNA clones. The 1,413 nucleotides of the 3' region of garlic virus 1 had a genome structure conserved in carlaviruses: a coding region for the 36-kDa CP and the 3' open reading frame (ORF) for a 14.2-kDa putative protein followed by 51 nucleotides of the 3' noncoding region. Phylogenetic comparison of the CP sequences between this virus and known carlaviruses and protexviruses suggested that the virus belongs to the carlavirus group. The 1,974 nucleotides of the 3' terminal region of garlic virus 2 has one large ORF, 597 nucleotides of the 3' noncoding region, and a genome structure characteristic of the Potyviridae. The ORF codes for the C terminal 1/3 region of nuclear inclusion protein b (NIb) and the full length of the 33-kDa CP, which have high homologies to NIb and CP of known potyviruses. Comparison of the amino acid sequence at the NIb-CP junction revealed phylogenetic conservation of S/A residues at the P'1 position as well as the F/L/H residues at the P2 position