High genetic diversity, distant phylogenetic relationships and intraspecies recombination events among natural populations of Yam mosaic virus: a contribution to understanding potyvirus evolution

Abstract

To evaluate the genetic diversity and understand the evolution of Yam mosaic virus (YMV), a highly destructive pathogen of yam (Dioscorea sp.), sequencing was carried out of the C-terminal part of the replicase (NIb), the coat protein (CP) and the 3h-untranslated region (3h-UTR) of 27 YMV isolates collected from the three main cultivated species (Dioscorea alata, the complex Dioscorea cayenensis-Dioscorea rotundata and Dioscorea trifida). YMV showed the most variable CP relative to eight other potyviruses. This high variability was structured into nine distant molecular groups, as revealed by phylogenetic analyses and validated by assessment of the molecular evolutionary noise. No correlation was observed between the CP and 3h-UTR diversities and phylogenies. The most diversified and divergent groups included isolates from Africa. The remaining groups clustered in a single clade and a geographical distinction between isolates from the Caribbean, South America and Africa was observed. The role of the host in the selection of particular isolates was illustrated by the case of a divergent cultivar from Burkina Faso. Phylogenetic topological incongruence and complementary statistical tests highlighted the fact that recombination events, with single and multiple crossover sites, largely contributed to the evolution of YMV. We hypothesise an African origin of YMV from the yam complex D. cayenensis-D. rotundata, followed by independent transfers to D. alata and D. trifida during virus evolution.

Genetic Variation of Citrus Tristeza Virus Isolates from California and Spain: Evidence for Mixed Infections and Recombination

“…Recombination in natural populations has been reported for other plant viruses (5,10). It has been proposed that recombination can be advantageous for RNA viruses.…”

An attempt to identify recombinants between two sobemoviruses in doubly infected oat plants

“…Spatial separation patterns with very few cells expressing both viruses have been documented for different potyvirus species -PPV, TVMV and Clover yellow vein virus (CIYVV) (Dietrich and Maiss, 2003). However, there is substantial evidence for intra-and interspecific recombination between potyviruses derived from sequencing and phylogenetic analysis of natural virus populations (Bousalem et al, 2000;Cervera et al, 1993;Chare and Holmes, 2006;Desbiez and Lecoq, 2004;Fanigliulo et al, 2005;Ohshima et al, 2002;Tan et al, 2004;Zhong et al, 2005).…”

“…The recombination potential of TBSV, Turnip mosaic virus (TuMV), Yam mosaic virus (YMV) and BMV has been shown to depend on the host (Bousalem et al, 2000;Desvoyes and Scholthof, 2002;Dzianott and Bujarski, 2004;Ohshima et al, 2002). Screening the recombination efficiency of TBSV using a yeast single-knockout library revealed that host genes involved in RNA degradation were suppressing the generation of new viral RNA recombinants.…”

Efficient In Vitro System of Homologous Recombination in Brome Mosaic Bromovirus

“…RNA recombination is one of the fundamental aspects of the life cycle and evolution of RNA viruses and contributes significantly to a high level of variation in viral RNAs, as demonstrated by sequencing of virus populations (6,7,32,34,45,50,58) and with experimental in vivo systems for animal viruses (19,31,44,51,54), plant viruses (1,2,12,15,25,35,41,53,55,59), bacteriophages (38), and retroviruses (40). In vitro recombination assays (reviewed in reference 21) revealed either a nonreplicative (breakage-religation) (22) or replicative (template switch) (3,28,30,36) mechanism of crossover.…”