Abstract
A viroid-like RNA was detected from coleus (Coleus blumei) in China. It consisted of 274 nucleotides and had 66% sequence identity with a member of the closest known viroid species. The predicted secondary structure is rod-shaped with extensive base pairing, and it has the conserved region characteristic of the genus Coleviroid. Two terminal sequences that are highly conserved among some members of the genus were also identified. The viroid-like RNA was successfully transmitted to coleus by slash-inoculation. This viroid was identified as a new member of the genus Coleviroid, and we tentatively propose the name Coleus blumei viroid 5 (CbVd-5).
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References
Daròs J, Elena S, Flores R (2006) Viroids: an Ariadne’s thread into the RNA labyrinth. EMBO Rep 7:593–598
Diener TO (1986) Viroid processing: a model involving the central conserved region and hairpin I. Proc Natl Acad Sci USA 83:58–62
Diener TO (1987) The viroids. Plenum Press, New York
Diener TO (2001) The viroid: biological oddity or evolutionary fossil. Adv Virus Res 57:137–184
Fauquet CM, Mayo MA, Maniloff J (2005) Virus taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses, pp 1259
Flores R, Randles JW, Bar-Joseph M (1998) A proposed scheme for viroid classification and nomenclature. Arch Virol 143:623–629
Fonseca M, Boiteux L, Singh R (1989) A small viroid in Coleus species from Brazil. Fitopatol Bras 14:94–96
Fonseca ME, Marcellino LH, Kitajima EW (1994) Nucleotide sequence of the original Brazilian isolate of coleus yellow viroid from Solenostemon scutellarioides and infectivity of its complementary DNA. J Gen Virol 75:1447–1449
Gas ME, Hernandez C, Flores R, Daròs JA (2007) Processing of nuclear viroids in vivo: an interplay between RNA conformations. PLoS Pathog 3(11):e182. doi:10.1371/journal.ppat.0030182
Hadidi A, Semancik J, Flores R (2003) Viroids. In: Semancik J (ed) Viroid pathogenesis. CSIRO S P, USA, pp 61–65
Ishiguro A, Sano T, Harada Y (1996) Nucleotide sequence and host range of coleus viroid isolated from coleus (Coleus blumei Benth) in Japan. Ann Phytopathol Soc Jpn 62:84–86
Keese P, Symons R (1985) Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc Natl Acad Sci USA 82:4582–4586
Li SF, Onodera S, Sano T (1995) Gene diagnosis of viroids: Comparisons of return-PAGE and hybridization using DIG-labelled DNA and RNA probes for practical diagnosis of hop stunt, citrus exocortis and apple scar skin viroids in their natural host plants. Ann Phytopath Soc Japan 61:381–390
Li SF, Su Q, Guo R (2006) First report of Coleus blumei viroid from coleus in China. Plant Pathol 55:565
Machida S, Shibuya M, Sano T (2008) Enrichment of viroid small RNAs by hybridization selection using biotinylated RNA transcripts to analyze viroid induced RNA silencing. J Gen Pl Pathol 74:203–207
Sano T, Candresee T, Hammond R (1992) Identification of multiple structural domains regulating viroid pathogenicity. Proc Natl Acad Sci USA 89:10104–10108
Sano T, Ishiguro A (1998) Viability and pathogenicity of inter subgroup viroid chimeras suggest possible involvement of the terminal right region in replication. Virology 240:238–244
Schumacher J, Randles JW, Riesner D (1983) A two-dimensional electrophoretic technique for the detection of circular viroids and virusoids. Anal Biochem 135:288–295
Semancik J (1987) viroids and viroid-like pathogens. CRC press, Boca Raton
Singh R, Boucher A, Singh A (1991) High incidence of transmission and occurrence of viroid in commercial seeds of Coleus in Canada. Plant Dis 75:184–187
Spieker R (1996) A new sequence variant of Coleus blumei viroid 1 from the Coleus blumei cultivar “Rainbow Gold’. Arch Virol 141:2153–2161
Spieker R, Haas B, Charng Y (1990) Primary and secondary structure of a new viroid ‘species’ (CbVd 1) present in the Coleus blumei cultivar ‘Bienvenue’. Nucleic Acids Res 18:3998
Spieker R, Marinkovic S, Sanger H (1996) A new sequence variant of coleus blumei viroid 3 from the coleus blumei cultivar ‘Fairway Ruby’. Arch Virol 141:1377–1386
Spieker R (1996) In vitro-generated ‘inverse’ chimeric Coleus blumei viroids evolve in vivo into infectious RNA replicons. J Gen Virol 77:2839–2846
Su Q, Li SF, Sano T (2006) Detection and molecular characterization of coleus blumei viroid in China. Acta Phytopathologica Sinica 36:226–231
Yang YA, Wang HQ, Wu ZJ, Cheng ZM, Li SF (2008) Molecular variability of hop stunt viroid: identification of a unique variant with a tandem 15-nucleotide repeat from naturally infected plum tree. Biochem Genet 46:113–123
Acknowledgments
We thank Prof. Roger Hull for his critical reading of this manuscript, Ling-Xiao Mu, graduate student from Shenyang Agricultural University, for his valuable advice on artwork and Qian-Fu Su, graduate student from Jilin University, for his sample collection. This work was supported by grants from the National Basic Research and Development Program of China (973 Program) (No. 2006CB100203 and 2009CB119200), the Beijing Natural Science Foundation of China (No. 6072022), the National Natural Science Foundation of China (No. 30771403), and the Opening Project of State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences. This work was also supported in part by a Grant-in Aid for Scientific Research B18380028 from Japan Society for the Promotion of Science, and JSPS’s FY2008 Bilateral Joint Projects between Japan and China-NSFC (30811140157).
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T. Sano and S. Li have equally contributed to this work.
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Hou, WY., Sano, T., Li, F. et al. Identification and characterization of a new coleviroid (CbVd-5). Arch Virol 154, 315–320 (2009). https://doi.org/10.1007/s00705-008-0276-6
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DOI: https://doi.org/10.1007/s00705-008-0276-6