Abstract
A unique circular molecule of 358 nucleotides was detected in American persimmon (Diospyros virginiana L.). The molecule was graft-transmissible and had genetic characteristics of members of the genus Apscaviroid. It had the highest sequence similarity (72-73 %) to citrus viroid VI (CVd-VI) and formed a clade with CVd-VI, citrus dwarfing viroid, and apple dimple fruit viroid in a phylogenetic tree. The molecule was not detected in citrus, unlike CVd-VI, which infects citrus and persimmon, and it was genetically distant from persimmon latent viroid, which infects persimmon only. The genetic and biological features indicated that the molecule may be a member of a new apscaviroid species.
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References
Cohen Y, Gur A, Barkai Z, Blumenfeld A (1991) Decline of persimmon (Diospyros kaki L.) trees on Diospyros virginiana rootstocks. Sci Hortic 48:61–70
Diaz-Ruiz JR, Kaper JM (1978) Isolation of viral double-stranded RNAs using a LiCl fractionation procedure. Prep Biochem Biotechnol 8:1–17
Ito T, Ieki H, Ozaki K, Ito T (2001) Characterization of a new citrus viroid species tentatively termed Citrus viroid OS. Arch Virol 146:975–982
Ito T, Ohta S (2010) First report of Citrus viroid V in Japan. J Gen Plant Pathol 76:348–350
Keese P, Visvader JE, Symon RH (1988) Sequence variability in plant viroid RNAs. In: Domingo E, Holland JJ, Ahlquist P (eds) RNA genetics volume III. CRC Press, FL, pp 71–98
Nakaune R, Nakano M (2006) Efficient methods for sample processing and cDNA synthesis by RT-PCR for the detection of grapevine viruses and viroids. J Virol Methods 134:244–249
Nakaune R, Nakano M (2008) Identification of a new Apscaviroid from Japanese persimmon. Arch Virol 153:969–972
Owens RA, Flores R, Di Serio F, Li S-F, Pallás V, Randles JW, Sano T, Vidalakis G (2012) Viroids. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy, ninth report of the international committee on taxonomy of viruses. Academic Press, San Diego, CA, pp 1221–1234
Radford AD, Chapman D, Dixon L, Chantrey J, Darby AC, Hall N (2012) Application of next-generation sequencing technologies in virology. J Gen Virol 93:1853–1868
Shimizu S, Ito T, Miyoshi T, Tachibana Y, Ito T (2011) A broad spectrum, one-step RT-PCR to detect Satsuma dwarf virus variants using universal primers targeting both segmented RNAs 1 and 2. J Gen Plant Pathol 77:326–330
Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680
Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415
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The authors thank Dr. A. Kono for persimmons, and Dr. Nakaune for technical advice.
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Ito, T., Suzaki, K., Nakano, M. et al. Characterization of a new apscaviroid from American persimmon. Arch Virol 158, 2629–2631 (2013). https://doi.org/10.1007/s00705-013-1772-x
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DOI: https://doi.org/10.1007/s00705-013-1772-x