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

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Abstract
To evaluate the genetic diversity and understand the evolution ofYam mosaic virus(YMV), a highly destructive pathogen of yam (Dioscoreasp.), sequencing was carried out of the C-terminal part of the replicase (NIb), the coat protein (CP) and the 3′-untranslated region (3′-UTR) of 27 YMV isolates collected from the three main cultivated species (Dioscoreaalata, the complexDioscoreacayenensis–DioscorearotundataandDioscoreatrifida). 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 3′-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 complexD.cayenensis–D.rotundata, followed by independent transfers toD.alataandD.trifidaduring virus evolution.