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. 2008 Apr;82(7):3584-9.
doi: 10.1128/JVI.02506-07. Epub 2008 Jan 16.

Rice yellow mottle virus, an RNA plant virus, evolves as rapidly as most RNA animal viruses

D Fargette  1 , A Pinel, M Rakotomalala, E Sangu, O Traoré, D Sérémé, F Sorho, S Issaka, E Hébrard, Y Séré, Z Kanyeka, G Konaté
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Rice yellow mottle virus, an RNA plant virus, evolves as rapidly as most RNA animal viruses

D Fargette et al. J Virol. 2008 Apr.

Abstract

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.

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Figures

FIG. 1.
FIG. 1.
Genetic distance (percent nucleotide difference) and sampling interval (number of years in absolute value) of each pair of isolates for each of the five groups and the regression line between the two variables. r, estimate of the evolution rate; R, correlation coefficient.
FIG. 2.
FIG. 2.
Overall (top) and synonymous (bottom) evolution rates of a range of 50 RNA animal viruses (Jenkins et al., 2002 [26]) and of the RYMV CP gene (solid bars and arrows). Horizontal dashed lines indicate the median and average evolution rates of the 50 RNA animal viruses.
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