Characterization of a new apscaviroid from American persimmon
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ANNOTATED SEQUENCE RECORD
Characterization of a new apscaviroid from American persimmon Takao Ito • Koichi Suzaki • Masaaki Nakano Akihiko Sato
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Received: 24 April 2013 / Accepted: 19 May 2013 Ó Springer-Verlag Wien 2013
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 CVdVI, 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.
Viroids, the smallest known plant pathogens, consist of unencapsidated, circular, and single-stranded RNA of 246–401 nucleotides (nt). Three viroids in the genus Apscaviroid have been identified in Japanese persimmons (Diospyros kaki Thunb.): apple fruit crinkle viroid (AFCVd) and citrus viroid VI (CVd-VI, synonym: CVd-OS), which are also known to infect apple and hop (AFCVd) and citrus (CVd-VI), respectively, and a new viroid, persimmon latent viroid (PLVd, synonym: persimmon viroid) whose other hosts are unknown [7, 8]. The relationship of
T. Ito (&) K. Suzaki A. Sato Grape and Persimmon Research Station, National Institute of Fruit Tree Science (NIFTS), National Agriculture and Food Research Organization (NARO), Akitsu, Hiroshima 739-2494, Japan e-mail: [email protected] M. Nakano Okitsu Citrus Research Station, NIFTS, NARO, Okitsu, Shizuoka 424-0292, Japan
these viroids to symptom expression in Japanese persimmons is not clear. Japanese persimmon trees grafted onto American persimmon (D. virginiana L.) rootstocks often grow very poorly, showing several decline symptoms, suggesting the presence of a transmissible agent, both in the scion and the rootstock [1]. One American persimmon tree grafted onto a Japanese persimmon rootstock has been maintained in an orchard in the NIFTS but shows poor growth. To detect a transmissible agent, deep sequencing analysis [9] was performed using an Illumina Genome Analyzer II (Illumina, San Diego, CA, USA), using viral double-stranded RNAs isolated following the protocol of Diaz-Ruiz and Kaper [2] from leaf tissue of the American persimmon. Although the detailed analysis will be published in another paper, searches using BLASTN in the GenBank/EMBL/ DDBJ databases of contigs assembled using the Velvet program [12] from the obtained sequences detected some viroid-like molecules as well as virus-like ones. The viroidlike molecules had the highest sequence similarities, but with significant mismatches with CVd-VI and another citrus-infecting apscaviroid, citrus dwarfing viroid (CDVd, synonym: CVd-III). Because the presence of a new apscaviroid related to CVd-VI
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