This Article Full Text Full Text (PDF) Supplemental material Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Reprints and Permissions Copyright Information Books from ASM Press MicrobeWorld Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Fargette, D. Articles by Konaté, G. Search for Related Content PubMed PubMed Citation Articles by Fargette, D. Articles by Konaté, G.

 Previous Article  |  Next Article 

Journal of Virology, April 2008, p. 3584-3589, Vol. 82, No. 7
0022-538X/08/$08.00+0     doi:10.1128/JVI.02506-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Rice Yellow Mottle Virus, an RNA Plant Virus, Evolves as Rapidly as Most RNA Animal Viruses ^,

D. Fargette,^1* A. Pinel,¹ M. Rakotomalala,² E. Sangu,³ O. Traoré,⁴ D. Sérémé,⁴ F. Sorho,¹ S. Issaka,⁵ E. Hébrard,¹ Y. Séré,⁶ Z. Kanyeka,³ and G. Konaté⁴

Institut de Recherche pour le Développement (IRD), UMR RPB, BP 64501, 34394 Montpellier cedex 5, France,¹ Centre National de la Recherche Appliquée au Développement Rural (FOFIFA), BP 289, Mahajanga 401, Madagascar,² Botany Department, Dar es Salaam University, P.O. Box 35091, Dar es Salaam, Tanzania,³ Institut de l'Environnement et de Recherches Agricoles (INERA), Laboratoire de Biotechnologie et de Virologie Végétale, 01 BP 476, Kamboinsé, Ouagadougou, Burkina Faso,⁴ Institut de Recherche Agronomique du Niger, BP 60, Kollo, Niger,⁵ Africa Rice Center (WARDA), 01 BP 2031, Cotonou, Bénin⁶

Received 22 November 2007/ Accepted 4 January 2008

The rate of evolution of an RNA plant virus has never been estimated using temporally spaced sequence data, by contrast to the information available on an increasing range of animal viruses. Accordingly, the evolution rate of Rice yellow mottle virus (RYMV) was calculated from sequences of the coat protein gene of isolates collected from rice over a 40-year period in different parts of Africa. The evolution rate of RYMV was estimated by pairwise distance linear regression on five phylogeographically defined groups comprising a total of 135 isolates. It was further assessed from 253 isolates collected all over Africa by Bayesian coalescent methods under strict and relaxed molecular clock models and under constant size and skyline population genetic models. Consistent estimates of the evolution rate between 4 x 10^–4 and 8 x 10^–4 nucleotides (nt)/site/year were obtained whatever method and model were applied. The synonymous evolution rate was between 8 x 10^–4 and 11 x 10^–4 nt/site/year. The overall and synonymous evolution rates of RYMV were within the range of the rates of 50 RNA animal viruses, below the average but above the distribution median. Experimentally, in host change studies, substitutions accumulated at an even higher rate. The results show that an RNA plant virus such as RYMV evolves as rapidly as most RNA animal viruses. Knowledge of the molecular clock of plant viruses provides methods for testing a wide range of biological hypotheses.

---

* Corresponding author. Mailing address: IRD, BP 64501, 34394 Montpellier cedex 5, France. Phone: 33-467416227. Fax: 33-467416330. E-mail: Denis.Fargette{at}mpl.ird.fr

Published ahead of print on 16 January 2008.

Supplemental material for this article may be found at http://jvi.asm.org/.

---

Journal of Virology, April 2008, p. 3584-3589, Vol. 82, No. 7
0022-538X/08/$08.00+0     doi:10.1128/JVI.02506-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

This article has been cited by other articles:

• Sanjuan, R., Agudelo-Romero, P., Elena, S. F. (2009). Upper-limit mutation rate estimation for a plant RNA virus. Biol Lett 5: 394-396 [Abstract] [Full Text]  
• Duffy, S., Holmes, E. C. (2009). Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J. Gen. Virol. 90: 1539-1547 [Abstract] [Full Text]