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Validation of high rates of nucleotide substitution in geminiviruses: Phylogenetic evidence from East African cassava mosaic viruses

¹ Penn State University;
² The Pennsylvania State University

³ E-mail: smd16{at}psu.edu

Whitefly-transmitted geminiviruses are major pathogens of the important cassava crop in Africa. The intensive sampling and sequencing of cassava mosaic disease-causing viruses that occurred in the wake of a severe outbreak in Central Africa (1997-2002) allowed us to estimate the rate of evolution of this virus. East African cassava mosaic virus and related species are obligately bipartite (DNA-A and DNA-B segments), and these two genome segments have very different evolutionary histories. Despite these phylogenetic differences, we inferred high rates of nucleotide substitution in both segments: mean rates of 1.60 x 10-3 and 1.33 x 10-4 substitutions/site/year for DNA-A and DNA-B, respectively. While similarly high substitution rates were found in data sets free of detectable recombination, only that estimated for the coat protein (AV1), for which an additional DNA-A sequence isolated in 1995 was available, was statistically robust. These high substitution rates also confirm that those previously estimated for the monopartite Tomato yellow leaf curl virus (TYLCV) are representative of multiple begomoviruses. We also validated our rate estimates by comparing them to those depicting the emergence of TYLCV in North America. These results further support the notion that geminiviruses evolve as rapidly as many RNA viruses.

Received 30 November 2008; accepted 17 February 2009.

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