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J. Virol. doi:10.1128/JVI.01929-07
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus Tomato yellow leaf curl virus (TYLCV)

Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802; Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA

^* To whom correspondence should be addressed. Email: smd16{at}psu.edu.

	Abstract

Geminiviruses are devastating viruses of plants that possess single-stranded (ss) DNA genomes. Despite the importance of this class of phytopathogen, there have been no estimates of the rate of nucleotide substitution in the geminiviruses. Herein we report the evolutionary rate of the tomato yellow leaf curl disease-causing viruses, an intensively studied group of monopartite begomoviruses. Sequences from GenBank, isolated from diseased plants between 1988 – 2006, were analyzed using Bayesian coalescent methods. The mean genomic substitution rate was estimated to be 2.88 x 10^-4 nucleotide substitutions per site, per year (subs/site/year), although this rate could be confounded by frequent recombination within TYLCV genomes. A recombinant-free data set comprising the coat protein (V1) gene in isolation yielded a similar mean rate (4.63 x 10^-4 subs/site/year), validating the order of magnitude of genomic substitution rate for protein-coding regions. The intergenic region, which is known to be more variable, was found to evolve even more rapidly, with a mean substitution rate of 1.56 x 10^-3 sub/site/year. Notably, these substitution rates, the first reported for a plant DNA virus, are in line with those estimated previously for mammalian ssDNA viruses and RNA viruses. Our results therefore suggest that the high evolutionary rate of the geminiviruses is not primarily due to frequent recombination and may explain their ability to emerge in novel hosts.

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