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Genetic Diversity of Tobacco rattle virus isolates from Potato in the USA

Lindani Moyo: Department of Plant Pathology, Washington State University

<div><em>Tobacco rattle virus</em> (TRV), an important pathogen of potato, tobacco and ornamental bulbs, consists a segmented, positive sense RNA genome (RNA1, 6.79 kb and RNA2, 3.86 kb). It causes corky ringspot disease characterized by concentric rings and necrotic and brown spots in potato tubers. Virus population dynamics shift frequently due to genetic drift, migration, mutation, natural selection and recombination. This could result in increased genetic diversity and emergence of more virulent and resistance-breaking strains. To elucidate the genetic diversity of TRV, whose first report in USA was in 1946 in Florida, the whole genome of 4 RNA1 and 5 RNA2 TRV isolates from potatoes in different states in the USA were cloned and sequenced to assess its population structure, evolutionary and epidemiological dynamics. Phylogenetic analyses based on nucleotide sequences of the coat protein (CP) and nematode transmission (2b) genes, in RNA2, showed geographical clustering of the US isolates with previously known American isolates, while the European isolates formed a distinct cluster. Low genetic diversity among the American isolates was noticed compared to those from Europe. This was further corroborated by the observed high purifying selection pressure acting on the CP and 2b genes, genetic differentiation and infrequent gene flow between American and European isolates. Based on these sequence analyses, TRV did not seem to have significantly diverged in the USA. Phylogenetic groupings based on RdRp, 1a and 1b genes in RNA1 were consistent with geographical clustering of the isolates. This study provided new insights into the genetic diversity of TRV in the USA.</div>