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Title: Complete genomic sequence of a tobacco rattle virus isolate from Michigan-grown potatoes

Author
item Crosslin, James
item HAMM, P - Oregon State University
item KIRK, W - Michigan State University
item Hammond, Rosemarie

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/22/2009
Publication Date: 3/11/2010
Citation: Crosslin, J., Hamm, P.B., Kirk, W.W., Hammond, R. 2010. Complete genomic sequence of a tobacco rattle virus isolate from Michigan-grown potatoes. Archives of Virology. 155:621-625.

Interpretive Summary: Tobacco rattle virus (TRV), transmitted by stubby root nematodes, causes stem mottle on potato leaves and necrotic arcs and rings in potato tubers, known as corky ringspot disease. This disease can result in substantial economic losses to growers because of internal damage to the tuber. In Michigan, potato is the fourth most important agricultural crop, and TRV infection was recently found to be associated with corky ringspot disease in Michigan-grown potatoes. We report the purification of the Michigan isolate of TRV (TRV MI-1) and determination of the complete genomic sequence of this virus. We also found that TRV MI-1 and other North American isolates are different from the European isolates. TRV M1-1 is only the second North American isolate for which there is a complete sequence of the genome, and it is distinct from the North American isolate TRV ORY. Knowledge of the disease agent will allow use of appropriate control measures to reduce crop losses. This report will be of interest to an international audience of growers, plant pathologists and agronomists.

Technical Abstract: Tobacco rattle virus (TRV) causes stem mottle on potato leaves and necrotic arcs and rings in potato tubers, known as corky ringspot disease. Recently, TRV was reported in Michigan potato tubers cv. FL1879 exhibiting corky ringspot disease. Sequence analysis of the RNA-1-encoded 16 kDa gene of the isolate, designated MI-1, revealed homology to TRV isolates from Florida and Washington. Here, we report the complete genomic sequence of RNA-1 (6791 nt) and RNA-2 (3685 nt) of TRV MI-1. RNA-1 is predicted to contain four open reading frames and the genome structure and phylogenetic analyses of the RNA-1 nucleotide sequence revealed significant homologies to the known sequences of other TRV-1 isolates. The relationships based on the full-length nucleotide sequence were different from than those based on the 16 kDa gene encoded on genomic RNA-1, and reflect sequence variation within a 20-25 aa residue region of the 16 kDa protein. MI-1 RNA-2 is predicted to contain three ORFs, encoding the coat protein (CP, ORF 2a) a 37.6 kDa protein (ORF 2b), and a 33.6 kDa protein (ORF 2c). In addition, it contains a region of similarity to the 3' terminus of RNA-1, including a truncated portion of the 16 kDa cistron. Phylogenetic analysis of RNA-2, based on a comparison of nucleotide sequences with other members of the genus Tobravirus, indicates that TRV MI-1 and other North American isolates cluster as a distinct group. TRV M1-1 is only the second North American isolate for which there is a complete sequence of the genome, and it is distinct from the North American isolate TRV ORY. The relationship of TRV MI-1 isolate to other tobravirus isolates is discussed.