Time-sampled population sequencing reveals the interplay of selection and genetic drift in experimental evolution of Potato virus Y

[EN] RNA viruses are one of the fastest evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly-generated variation in the evolving viral lineages. A time-sampled approach allowed us to: (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less susceptible host (efficient in the accumulation of salicylicacid).This study was supported by the Slovenian Research Agency (grants L4-5525 and P4-0165 and Ph.D. grant to D.K.). Work in Valencia was supported by Spain Ministry of Economy and Competitiveness (grant BFU2015-65037-P to S.F.E.), and short-term scientific mission support was provided to D.K. in the frame of EU-funded COST action FA1407.Kutnjak, D.; Elena Fito, SF.; Ravnikar, M. (2017). Time-sampled population sequencing reveals the interplay of selection and genetic drift in experimental evolution of Potato virus Y. Journal of Virology. 91(16):1-17. https://doi.org/10.1128/JVI.00690-171179116Andino, R., & Domingo, E. (2015). Viral quasispecies. Virology, 479-480, 46-51. doi:10.1016/j.virol.2015.03.022Ohshima, K., Nomiyama, R., Mitoma, S., Honda, Y., Yasaka, R., & Tomimura, K. (2016). Evolutionary rates and genetic diversities of mixed potyviruses in Narcissus. Infection, Genetics and Evolution, 45, 213-223. doi:10.1016/j.meegid.2016.08.036Froissart, R., Roze, D., Uzest, M., Galibert, L., Blanc, S., & Michalakis, Y. (2005). 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