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Characterization of a distinct variant of hop stunt viroid and a new apscaviroid detected in grapevines

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Abstract

Using next-generation sequencing, we detected a novel variant of hop stunt viroid (HSVd) in grapevine ‘Chenin blanc’ (Vitis vinifera L.) and a new viroid species in ‘Nachubearmarie’ (Vitis labrusca L. × V. vinifera). The HSVd variant termed HSVd-CB has 296 nucleotides with up to 82% sequence identity with other HSVd variants such as HSVd-AP1 (Genbank accession EF523826). Many nucleotide changes, deletions, and insertions were sporadically found in HSVd-CB relative to HSVd-AP1 in the pathogenic and variable domains. Although several variations were also found in the central domain, few variations were found in the terminal left and right domains, including no variations in the terminal conserved hairpin. The new viroid, tentatively termed Japanese grapevine viroid (JGVd), has 367 nucleotides and has genetic features characteristic of the genus Apscaviroid. JGVd shared the highest nucleotide sequence identity (68%) with a persimmon latent viroid (PLVd) in its overall genome. However, the JGVd sequence shows chimerism with the partial genomes of other apscaviroids from apple, grapevine, and citrus. Phylogenetic analyses showed that only HSVd-CB formed a distinct branch from the cluster of the other HSVd variants and JGVd and PLVd formed a distinct branch from all other grapevine-infecting apscaviroids.

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Acknowledgements

We thank Dr. Akihiko Sato for useful advice and all those who provided samples. This study was funded by National Agriculture and Food Research Organization (NARO).

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Authors and Affiliations

  1. Grape and Persimmon Research Station, Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO), Akitsu, Higashihiroshima, Hiroshima, 739-2494, Japan

    Yuya Chiaki & Takao Ito

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  1. Yuya Chiaki
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  2. Takao Ito
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Contributions

Conceptualization: TI, Methodology: TI and YC; Formal analysis and investigation: YC and TI; Writing—original draft preparation: YC; Writing—review and editing: TI.

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Correspondence to Takao Ito.

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Both authors belong to NARO. The authors declare that they have no conflict of interest.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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Informed consent was obtained from all individual participants included in the study.

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Edited by Karel Petrzik.

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Chiaki, Y., Ito, T. Characterization of a distinct variant of hop stunt viroid and a new apscaviroid detected in grapevines. Virus Genes 56, 260–265 (2020). https://doi.org/10.1007/s11262-019-01728-1

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