Browsing by Author "Fargette, Denis"

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    Distribution and diversity of local strains of rice yellow motile virus in Tanzania
    (2006-12) Kanyeka, Zakaria L.; Sangu, Emmanuel; Fargette, Denis; Galzi, Agnès P.; Hérbrard, E.
    Rice ( Oryza sativa ) is a key staple in Tanzania but its productivity is affected by disease infestation, primary among which is the rice yellow mottle virus (RYMV). Tanzania possesses high RYMV densities and several locations including the Eastern Arc Mountains provide suitable habitat fragmentation that facilitates the diversification process of the virus. However, the distribution pattern and diversity of the local strains of RYMV remain largely unknown and this hinders progress in designing interventions. Efforts were, therefore, made to study the pattern and distribution of RYMV. Collection of isolates was made in May; recovery of virus on a susceptible elite line viz. TXD 220-1-3-3-1 was in June-July and molecular analysis was done in September-December 2005. The sequences of the coat protein (CP) gene of 23 isolates, representative of the three strains of RYMV found in Tanzania, were selected from 52 isolates collected from three regions. The phylogenetic analyses of the CP sequences revealed high (14.8%) nucleotide divergence between strains. Strain S6 was the most divergent with an intra- strain nucleotide divergence of 8.8%; this was consistent with its wide distribution in the region and particularly the eastern part of the Tanzania. Isolates of strains S4 were recorded for the first time in the eastern Arc Mountain region. These formed a monophyletic group with the Lake Malawi strain S4 sub-lineage (percentage identity of 95.4 to 96.8%) and differed from the Lake Victoria strain S4 sub-lineage by 4.5%. Coexistence within the same field of S4, S5 and S6 isolates was observed in the eastern Arc Mountains region. Strong competition between strains of RYMV was suspected from the limited distribution and rarity of strain S5. This study confirm speculations that the Eastern Arc Mountain region is the centre of origin of RYMV. Thus, the high viral load in the Eastern Arc Mountain imply that it is a suitable location for strategic studies aimed at designing control interventions against RYMV.
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    Rate Of Substitution, Date of Emergence and Speed of Dispersal of Rice Yellow Mottle Virus in Africa
    (2008-12) Fatogoma, Sorho; Galzi, Agnès P.; Traore, Oumar; Rakotomalala, Mbolarinosy; Sangu, Emmanuel; Kanyeka, Zakaria L.; Hébrard, Eugénie; Konte, G.; Sere, Y.; Fargette, Denis; Ake, S.
    arallel evolution is the evolution of similar or identicalfeatures independently in related lineages when subjected tosimilar selection pressures [1,2]. Parallel evolution has beenreported extensively both in natural isolates and in exper-imental populations of many microbes, most often viruses [2–4], but also bacteria [5], yeast [6], and protozoa [7]. Withviruses, similar amino acid replacements often occurred inimmune or antiviral escape variants. This is usually inter-preted as the fixation of a mutation with a beneficial effect.However, differences in founding genotypes may result indivergent evolutionary trajectories [5]. So, patterns ofadaptation to selective constraints may also be dependenton intraspecific polymorphisms. This is well documented forHIV resistance to antiretroviral agents, where pathways ofviral evolution towards drug resistance may proceed throughdistinct steps and at different rates among different HIVsubtypes [8,9]. The objective of this article is to assess the
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    A Reassessment of the Epidemiology of Rice Yellow Mottle Virus Following Recent Advances In Field And Molecular Studies
    (Elsevier, 2009-02) Traore, Oumar; Galzi, Agnès P.; Fatogoma, Sorho; Sarra, Soungalo; Rakotomalala, Mbolarinosy; Sangu, Emmanuel; Kanyeka, Zakaria L.; Sere, Y.; Konaté, Gnissa; Fargette, Denis
    The available knowledge on the epidemiology of Rice yellow mottle virus (RYMV) is reassessed in the light of major advances in field and molecular studies of the disease it causes in rice. Previously un-described means of transmission by mammals and through leaf contact have been discovered recently. Several agricultural practices, including the use of seedbed nurseries, have also contributed to a massive build-up of RYMV inoculum. Phytosanitation is now known to be critical to reduce disease incidence in rice. A new model of the ecology of RYMV in which man plays a central role has emerged. Furthermore, estimates of the evolutionary rate of change of RYMV provided a time-frame for its epidemiology, the first attempt for a plant virus. Earlier interpretations of the patterns of virus diversity which assumed a long-term evolution, and assigned a major role to adaptive events had to be discarded. In contrast, a wave-like model of dispersal of RYMV, which postulates its initial diversification in East Africa, followed by westward spread across the continent, was developed, refined and dated. The most salient -- and largely unexpected -- finding is that RYMV emerged recently and subsequently spread rapidly throughout Africa in the last two centuries. Diversification and spread of RYMV has been concomitant with an extension of rice cultivation in Africa since the 19th century. This major agro-ecological change increased the encounters between primary hosts of RYMV and cultivated rice. It also modified the landscape ecology in ways that facilitated virus spread.
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    Recombination, selection and clock-like evolution of Rice yellow mottle virus
    (Elsevier, 2009-09) Galzi, Agnès P.; Mpunami, Anatolia; Sangu, Emmanuel; Rakotomalala, Mbolarinosy; Traore, Oumar; Sereme, Drissa; Fatogoma, Sorho; Sere, Y.; Kanyeka, Zakaria L.; Konaté, Gnissa; Fargette, Denis
    The clock-like diversification of Rice yellow mottle virus (RYMV), a widespread RNA plant virus that infects rice in Africa, was tested following a three-step approach with (i) an exhaustive search of recombinants, (ii) a comprehensive assessment of the selective constraints over lineages, and (iii) a stepwise series of tests of the molecular clock hypothesis. The first evidence of recombination in RYMV was found in East Africa, in the region most favorable to co-infection. RYMV evolved under a pronounced purifying selection, but the selection pressure did vary among lineages. There was no phylogenetic evidence of transient deleterious mutations. ORF2b, which codes for the polymerase and is the most constrained ORF, tends to diversify clock-like. With the other ORFs and the full genome, the departure from the strict clock model was limited. This likely reflects the dominant conservative selection pressure and the clock-like fixation of synonymous mutations.
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    Rice Yellow Mottle Virus, an RNA Plant Virus, Evolves as Rapidly as Most RNA Animal Viruses
    (2008-04) Fargette, Denis; Pinel, A.; Rakotomalala, Mbolarinosy; Sangu, Emmanuel; Traore, Oumar; Sereme, Drissa; Fatogoma, Sorho; Issaka, S.; Hébrard, Eugénie; Sere, Y.; Kanyeka, Zakaria L.; Konaté, Gnissa
    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 × 10−4 and 8 × 10−4 nucleotides (nt)/site/year were obtained whatever method and model were applied. The synonymous evolution rate was between 8 × 10−4 and 11 × 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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    Theme and Variations in The Evolutionary Pathways to Virulence of an RNA Plant Virus Species
    (2007-01) Galzi, Agnès P.; Rakotomalala, Mbolarinosy; Sangu, Emmanuel; Fatogoma, Sorho; Kanyeka, Zakaria L.; Traore, Oumar; Sereme, Drissa; Poulicard, Nils; Rabenantoandro, Yvonne; Sere, Y.; Konaté, Gnissa; Ghesquière, Alain; Hébrard, Eugénie; Fargette, Denis
    The diversity of a highly variable RNA plant virus was considered to determine the range of virulence substitutions, the evolutionary pathways to virulence, and whether intraspecific diversity modulates virulence pathways and propensity. In all, 114 isolates representative of the genetic and geographic diversity of Rice yellow mottle virus (RYMV) in Africa were inoculated to several cultivars with eIF(iso)4G-mediated Rymv1-2 resistance. Altogether, 41 virulent variants generated from ten wild isolates were analyzed. Nonconservative amino acid replacements at five positions located within a stretch of 15 codons in the central region of the 79-aa-long protein VPg were associated with virulence. Virulence substitutions were fixed predominantly at codon 48 in most strains, whatever the host genetic background or the experimental conditions. There were one major and two isolate-specific mutational pathways conferring virulence at codon 48. In the prevalent mutational pathway I, arginine (AGA) was successively displaced by glycine (GGA) and glutamic acid (GAA). Substitutions in the other virulence codons were displaced when E48 was fixed. In the isolate-specific mutational pathway II, isoleucine (ATA) emerged and often later coexisted with valine (GTA). In mutational pathway III, arginine, with the specific S2/S3 strain codon usage AGG, was displaced by tryptophane (TGG). Mutational pathway I never arose in the widely spread West African S2/S3 strain because G48 was not infectious in the S2/S3 genetic context. Strain S2/S3 least frequently overcame resistance, whereas two geographically localized variants of the strain S4 had a high propensity to virulence. Codons 49 and 26 of the VPg, under diversifying selection, are candidate positions in modulating the genetic barriers to virulence. The theme and variations in the evolutionary pathways to virulence of RYMV illustrates the extent of parallel evolution within a highly variable RNA plant virus species.