Top

Published in:

01-12-2013 | Annotated Sequence Record

Characterization of a new apscaviroid from American persimmon

Authors: Takao Ito, Koichi Suzaki, Masaaki Nakano, Akihiko Sato

Published in: Archives of Virology | Issue 12/2013

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 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.

Cohen Y, Gur A, Barkai Z, Blumenfeld A (1991) Decline of persimmon (Diospyros kaki L.) trees on Diospyros virginiana rootstocks. Sci Hortic 48:61–70CrossRef

Diaz-Ruiz JR, Kaper JM (1978) Isolation of viral double-stranded RNAs using a LiCl fractionation procedure. Prep Biochem Biotechnol 8:1–17CrossRef

Ito T, Ieki H, Ozaki K, Ito T (2001) Characterization of a new citrus viroid species tentatively termed Citrus viroid OS. Arch Virol 146:975–982PubMedCrossRef

Ito T, Ohta S (2010) First report of Citrus viroid V in Japan. J Gen Plant Pathol 76:348–350CrossRef

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 134:244–249PubMedCrossRef

Nakaune R, Nakano M (2008) Identification of a new Apscaviroid from Japanese persimmon. Arch Virol 153:969–972PubMedCrossRef

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 93:1853–1868PubMedCrossRef

10.

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 77:326–330CrossRef

11.

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 22:4673–4680PubMedCrossRef

12.

Zerbino DR, Birney E (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821–829PubMedCrossRef

13.

Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415PubMedCrossRef

Title: Characterization of a new apscaviroid from American persimmon
Authors: Takao Ito
Koichi Suzaki
Masaaki Nakano
Akihiko Sato
Publication date: 01-12-2013
Publisher: Springer Vienna
Published in: Archives of Virology / Issue 12/2013
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-013-1772-x

ACC 2024 Congress Coverage

Heart Failure Video

Keynote webinar | Spotlight on sleep in brain health

Springer Medicine

Characterization of a new apscaviroid from American persimmon

Abstract

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page

Keynote webinar | Spotlight on sleep in brain health

Springer Medicine

Abstract

Please log in to get access to this content

Other articles of this Issue 12/2013

In vitro binding and bimolecular fluorescence complementation assays suggest an interaction between tomato mosaic virus coat protein and tobacco chloroplast ferredoxin I

Complete genome sequence of a novel dsRNA mycovirus isolated from the phytopathogenic fungus Verticillium dahliae Kleb.

Genetic diversity and mutation of avian paramyxovirus serotype 1 (Newcastle disease virus) in wild birds and evidence for intercontinental spread

Matrix metalloproteinases and their tissue inhibitors in serum and cerebrospinal fluid of children with Japanese encephalitis virus infection

Protection of Chinese painted quails (Coturnix chinensis) against a highly pathogenic H5N1 avian influenza virus strain after vaccination

MiR-199a-5p promotes migration and tube formation of human cytomegalovirus-infected endothelial cells through downregulation of SIRT1 and eNOS

ACC 2024 Congress Coverage

Year in Review: Heart failure and cardiomyopathies

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

Incentivised to exercise

New intervention for STEMI-related cardiogenic shock

» View more highlights on the ACC 2024 congress hub page