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Recombination analysis of Soybean mosaic virus sequences reveals evidence of RNA recombination between distinct pathotypes

Alla G Gagarinova124, Mohan Babu1, Martina V Strömvik3 and Aiming Wang12*

Author Affiliations

1 Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, 1391 Sandford St., London, Ontario, N5V 4T3, Canada

2 Department of Biology, The University of Western Ontario, Biological & Geological Building, 1151 Richmond St., London, Ontario, N6A 5B7, Canada

3 Department of Plant Science, McGill University, 21111 Lakeshore Rd., Ste. Anne de Bellevue, Québec, H9X 3V9, Canada

4 Department of Molecular Genetics, The University of Toronto, Toronto, M5S 1A8, Canada

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Virology Journal 2008, 5:143  doi:10.1186/1743-422X-5-143

Published: 26 November 2008

Abstract

RNA recombination is one of the two major factors that create RNA genome variability. Assessing its incidence in plant RNA viruses helps understand the formation of new isolates and evaluate the effectiveness of crop protection strategies. To search for recombination in Soybean mosaic virus (SMV), the causal agent of a worldwide seed-borne, aphid-transmitted viral soybean disease, we obtained all full-length genome sequences of SMV as well as partial sequences encoding the N-terminal most (P1 protease) and the C-terminal most (capsid protein; CP) viral protein. The sequences were analyzed for possible recombination events using a variety of automatic and manual recombination detection and verification approaches. Automatic scanning identified 3, 10, and 17 recombination sites in the P1, CP, and full-length sequences, respectively. Manual analyses confirmed 10 recombination sites in three full-length SMV sequences. To our knowledge, this is the first report of recombination between distinct SMV pathotypes. These data imply that different SMV pathotypes can simultaneously infect a host cell and exchange genetic materials through recombination. The high incidence of SMV recombination suggests that recombination plays an important role in SMV evolution. Obtaining additional full-length sequences will help elucidate this role.