Evolutionary rates and genetic diversities of mixed potyviruses in Narcissus

Ohshima, Kazusato; Nomiyama, Rei; Mitoma, Shinichiro; Honda, Yuki; Yasaka, Ryosuke; Tomimura, Kenta

doi:10.1016/j.meegid.2016.08.036

Cited by 23 publications

(38 citation statements)

References 73 publications

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“…The varied d N /d S ratios obtained from Chinese, South Korean, German, Singaporean, Indonesian and Japanese subpopulations, also indicating that the ORSV CP gene is under different evolutionary constraints according to the geography. Analogously, there has been reported in several plant viruses where strong selection against amino acid change in the CP gene (Ge et al, 2014; He et al, 2014, 2016; Ogawa et al, 2008; Ohshima et al, 2016; Wei et al, 2009). …”

Section: Discussionsupporting

confidence: 61%

“…Our analysis showed that ORSV had similar evolutionary rates with these narcissus viruses, but slightly faster than TMV. TMRCAs of ORSV was similar to Narcissus degeneration virus and TMV, but younger than Narcissus late season yellows virus , Narcissus yellow stripe virus , Cyrtanthus elatus virus A , and Narcissus latent virus (Gao et al, 2019; Ohshima et al, 2016). …”

Section: Discussionmentioning

confidence: 86%

“…Recently, the evolutionary rates and the most recent common ancestors (TMRCAs) have been analyzed for Tobacco mosaic virus (TMV) (Gao et al, 2019), and flowers plant viruses (Ohshima et al, 2016). We estimated evolutionary rates and TMRCAs for ORSV.…”

Section: Discussionmentioning

confidence: 99%

“…We estimated evolutionary rates and TMRCAs for ORSV. Ohshima et al (2016) analyzed the evolutionary rates of five narcissus viruses were 1.33–7.15 × 10 −3 nt/site/y, while the four genes evolutionary rates of TMV were 3.92–4.38 × 10 −4 (Gao et al, 2019). Our analysis showed that ORSV had similar evolutionary rates with these narcissus viruses, but slightly faster than TMV.…”

Section: Discussionmentioning

confidence: 99%

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Evolutionary Rates and Phylogeographical Analysis of Odontoglossum Ringspot Virus Based on the 166 Coat Protein Gene Sequences

Dong

et al. 2019

Plant Pathol J

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Section: Discussionsupporting

confidence: 61%

Section: Discussionmentioning

confidence: 86%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

See 2 more Smart Citations

Evolutionary Rates and Phylogeographical Analysis of Odontoglossum Ringspot Virus Based on the 166 Coat Protein Gene Sequences

Dong

et al. 2019

Plant Pathol J

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“…Due to their error-prone replication, RNA viruses mutate rapidly and thus exist within hosts as mutant swarms (also referred to as quasispecies), derived from ancestral infecting genomes (1, 2). Fast replication, coupled with high mutation and recombination rates (3–5) and large populations, enables RNA viruses to quickly adapt to changing environments.…”

Section: Introductionmentioning

confidence: 99%

Time-Sampled Population Sequencing Reveals the Interplay of Selection and Genetic Drift in Experimental Evolution of Potato Virus Y

Kutnjak

Elena

Ravnikar

2017

J Virol

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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 variations 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 salicylic acid).IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes.

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