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Journal of Virology, April 2004, p. 3252-3261, Vol. 78, No. 7
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.7.3252-3261.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.

Inferring the Evolutionary History of Rice Yellow Mottle Virus from Genomic, Phylogenetic, and Phylogeographic Studies

Denis Fargette,1* Agnès Pinel,1 Zakia Abubakar,2 Oumar Traoré,3 Christophe Brugidou,1 Sorho Fatogoma,4 Eugénie Hébrard,1 Marc Choisy,1 Yacouba Séré,4 Claude Fauquet,5 and Gnissa Konaté3

IRD, 34394 Montpellier cedex 5, France,1 ZARC, Zanzibar, Tanzania,2 INERA, Ouagadougou, Burkina-Faso,3 ADRAO, Abidjan 01, Côte d'Ivoire,4 International Laboratory for Tropical Agricultural Biotechnology, St. Louis, Missouri 631325

Received 25 August 2003/ Accepted 9 December 2003

Fourteen isolates of Rice yellow mottle virus (RYMV) were selected as representative of the genetic variability of the virus in Africa from a total set of 320 isolates serologically typed or partially sequenced. The 14 isolates were fully sequenced and analyzed together with two previously reported sequences. RYMV had a genomic organization similar to that of Cocksfoot mottle sobemovirus. The average nucleotide diversity among the 16 isolates of RYMV was 7%, and the maximum diversity between any two isolates was 10%. A strong conservative selection was apparent on both synonymous and nonsynonymous substitutions, through the amino acid replacement pattern, on the genome size, and through the limited number of indel events. Furthermore, there was a lack of positive selection on single amino acid sites and no evidence of recombination events. RYMV diversity had a pronounced and characteristic geographic structure. The branching order of the clades correlated with the geographic origin of the isolates along an east-to-west transect across Africa, and there was a marked decrease in nucleotide diversity moving westward across the continent. The insertion-deletion polymorphism was related to virus phylogeny. There was a partial phylogenetic incongruence between the coat protein gene and the rest of the genome. Overall, our results support the hypothesis that RYMV originated in East Africa and then dispersed and differentiated gradually from the east to the west of the continent.

* Corresponding author. Mailing address: IRD, BP 64501, 34394 Montpellier cedex 5, France. Phone: 33 4 67 41 62 27. Fax: 33 4 67 41 63 30. E-mail: Denis.Fargette{at}mpl.ird.fr.

Journal of Virology, April 2004, p. 3252-3261, Vol. 78, No. 7
0022-538X/04/$08.00+0     DOI: 10.1128/JVI.78.7.3252-3261.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.



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