Al Rwahnih M, Daubert S, Golino D, Rowhani A (2009) Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology 387:395–401
Biebricher CK, Eigen M (2006) What is a quasispecies? Curr Top Microbiol Immunol 299:1–31
Bussière F, Ouellet J, Côté F, Lévesque D, Perreault JP (2000) Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex branched secondary structure. J Virol 74:2647–2654
[+]
Al Rwahnih M, Daubert S, Golino D, Rowhani A (2009) Deep sequencing analysis of RNAs from a grapevine showing Syrah decline symptoms reveals a multiple virus infection that includes a novel virus. Virology 387:395–401
Biebricher CK, Eigen M (2006) What is a quasispecies? Curr Top Microbiol Immunol 299:1–31
Bussière F, Ouellet J, Côté F, Lévesque D, Perreault JP (2000) Mapping in solution shows the peach latent mosaic viroid to possess a new pseudoknot in a complex branched secondary structure. J Virol 74:2647–2654
Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655
Chiumenti M, Torchetti EM, Di Serio F, Minafra A (2014) Identification and characterization of a viroid resembling Apple dimple fruit viroid in fig (Ficus carica L) by next generation sequencing of small RNAs. Virus Res. doi: 10.1016/jvirusres201403026 (in press)
Codoñer FM, Daròs JA, Solé RV, Elena SF (2006) The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens. PLoS Path 2:1187–1193
Di Serio F, Gisel A, Navarro B, Delgado S, Martínez de Alba AE, Donvito G, Flores R (2009) Deep sequencing of the small RNAs derived from two symptomatic variants of a chloroplastic viroid: implications for their genesis and for pathogenesis. PLoS One 4:e7539
Diener TO (1971) Potato spindle tuber “virus” IV. A replicating low molecular weight RNA. Virology 45:411–428
Diener TO (1989) Circular RNAs: relics of precellular evolution? Proc Natl Acad Sci USA 86:9370–9374
Ding B (2009) The biology of viroid-host interactions. Annu Rev Phytopathol 47:105–131
EFSA Panel on Plant Health (PLH) (2011) Scientific Opinion on the assessment of the risk of solanaceous pospiviroids for the EU territory and the identification and evaluation of risk management options. EFSA J 9:2330. doi: 10.2903/j.efsa.2012.3027 [133 pp]
Elena SF, Dopazo J, De la Peña M, Flores R, Diener TO, Moya A (2001) Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment. J Mol Evol 53:155–159
Elena SF, Dopazo J, Flores R, Diener TO, Moya A (1991) Phylogeny of viroids and viroid-like satellite RNAs and the viroid-like domain of hepatitis δ virus RNA. Proc Natl Acad Sci USA 88:5631–5634
Fadda Z, Daròs JA, Flores R, Duran-Vila N (2003) Identification in eggplant of a variant of citrus exocortis viroid (CEVd) with a 96 nucleotide duplication in the right terminal region of the rod-like secondary structure. Virus Res 97:145–149
Flores R (1995) Subviral agents: viroids In: Murphy FA, Fauquet CM, Bishop DHL, Ghabrial SA, Jarvis AW, Martelli GP, Mayo MA, Summers MD (eds) Virus taxonomy, 6th report of the International Committee on Taxonomy of Viruses, Archives of Virology, Supplement 10, Springer, Vienna AT pp 495–497
Flores R, Di Serio F, Navarro B, Duran-Vila N, Owens RA (2011) Viroids and viroid diseases of plants. In: Hurst CJ (ed) Studies in viral ecology 1 microbial and botanical host systems. Wiley & Sons Inc Hoboken, New Jersey USA, pp 307–342
Flores R, Daròs JA, Hernández C, Di Serio F (2011b) Viroids. In: Encyclopedia of life sciences. Wiley, Chichester, [ http://www.els.net/ ]. doi: 10.1002/9780470015902.a0000434.pub3
Flores R, Di Serio F, Hernández C (1997) Viroids: The non-coding genomes. Semin Virol 8:65–73
Flores R, Hernández C, Martínez de Alba AE, Daròs JA, Di Serio F (2005) Viroids and viroid-host interactions. Annu Rev Phytopathol 43:117–139
Flores R, Randles JW, Owens RA, Bar-Joseph M, Diener TO (2005b) Viroids In: Fauquet CM, Mayo MA, Maniloff J, Desselberger U, Ball AL (eds) Virus taxonomy classification and nomenclature VIIII report of the International Committee on Taxonomy of Viruses, Elsevier/Academic Press, London UK, pp 1145–1159
Flores R, Randles JW, Bar-Joseph M, Diener TO (1998) A proposed scheme for viroid classification and nomenclature. Arch Virol 143:623–629
Flores R, Randles JW, Owens RA, Bar-Joseph M, Diener TO (2000) Subviral agents: Viroids In: van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, Mc Geoch DJ, Maniloff J, Mayo MA, Pringle CR, Wickner RB (eds) Virus taxonomy, seventh report of the International Committee on Taxonomy of Viruses, Academic Press, San Diego USA, pp 1009–1024
Flores R, Serra P, Minoia S, Di Serio F, Navarro B (2012) Viroids: from genotype to phenotype just relying on RNA sequence and structural motifs. Frontiers Microbiol 3:1–13
Flores R, Ruiz-Ruiz S, Serra P (2012) Viroids and hepatitis delta virus. Semin Liver Dis 32:201–210
Gas ME, Hernández C, Flores R, Daròs JA (2007) Processing of nuclear viroids in vivo: An interplay between RNA conformations. PLoS Pathog 3:1813–1826
Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, La Notte P, Terlizzi F, Credi R, Saldarelli P (2012) A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in cv Pinot gris. Virus Res 163:262–268
Gomez G, Martinez G, Pallás V (2009) Interplay between viroid-induced pathogenesis and RNA silencing pathways. Trends Plant Sci 14:264–269
Gozmanova M, Denti MA, Minkov IN, Tsagris M, Tabler M (2003) Characterization of the RNA motif responsible for the specific interaction of potato spindle tuber viroid RNA (PSTVd) and the tomato protein Virp1. Nucleic Acids Res 31:5534–5543
Gross HJ, Domdey H, Lossow C, Jank P, Raba M, Alberty H, Sänger HL (1978) Nucleotide sequence and secondary structure of potato spindle tuber viroid. Nature 273:203–208
Hammann C, Steger G (2012) Viroid-specific small RNA in plant disease. RNA Biol 9:809–819
Hammond R, Smith DR, Diener TO (1989) Nucleotide sequence and proposed secondary structure of Columnea latent viroid: a natural mosaic of viroid sequences. Nucleic Acids Res 17:10083–10094
Haseloff J, Mohamed NA, Symons RH (1982) Viroid RNAs of cadang-cadang disease of coconuts. Nature 299:316–321
Hernández C, Flores R (1992) Plus and minus RNAs of peach latent mosaic viroid self-cleave in vitro via hammerhead structures. Proc Natl Acad Sci USA 89:3711–3715
Hou WY, Sano T, Li SF, Li F, Li L, Wu ZJ (2009) Identification and characterization of a new Coleviroid (CbVd-5). Arch Virol 154:315–320
Hou WY, Li SF, Wu ZJ, Jiang DM, Sano T (2009) Coleus blumei viroid 6: a new tentative member of the genus Coleviroid derived from natural genome shuffling. Arch Virol 154:993–997
Ito T, Suzaki K, Nakano M, Sato A (2013) Characterization of a new apscaviroid from American persimmon. Arch Virol 158:2629–2631
Itaya A, Zhong X, Bundschuh R, Qi Y, Wang Y, Takeda R, Harris AR, Molina C, Nelson RS, Ding B (2007) A structured viroid RNA is substrate for Dicer-like cleavage to produce biologically active small RNAs but is resistant to RISC-mediated degradation. J Virol 81:2980–2994
Jiang D, Gao R, Qin L, Wu Z, Xie L, Hou W, Li S-F (2014) Infectious cDNA clones of four viroids in Coleus blumei and molecular characterization of their progeny. Virus Res 180:97–101
Jenkins GM, Woelk CH, Rambaut A, Holmes EC (2000) Testing the extent of sequence similarity among viroids satellite RNAs and the hepatitis delta virus. J Mol Evol 50:98–102
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism. Academic Press, New York, pp 21–132
Keese P, Symons RH (1985) Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc Natl Acad Sci USA 82:4582–4586
Ling K-S, Zhang W (2009) First report of a natural infection by Mexican papita viroid and Tomato chlorotic dwarf viroid on greenhouse tomatoes in Mexico. Plant Dis 93:1216
Machida S, Yamahata N, Watanuki H, Owens RA, Sano T (2007) Successive accumulation of two size classes of viroid-specific small RNA in potato spindle tuber viroid-infected tomato plants. J Gen Virol 88:3452–3457
Martín R, Arenas C, Daròs JA, Covarrubias A, Reyes JL, Chua NH (2007) Characterization of small RNAs derived from citrus exocortis viroid (CEVd) in infected tomato plants. Virology 367:135–146
Martinez G, Donaire L, Llave C, Pallas V, Gomez G (2010) High-throughput sequencing of Hop stunt viroid-derived small RNAs from cucumber leaves and phloem. Mol Plant Pathol 11:347–359
Martínez-Soriano JP, Galindo-Alonso J, Maroon CJ, Yucel I, Smith DR, Diener TO (1996) Mexican papita viroid: putative ancestor of crop viroids. Proc Natl Acad Sci USA 93:9397–9401
Navarro B, Gisel A, Rodio ME, Delgado S, Flores R, Di Serio F (2012) Viroids: how to infect a host and cause disease without encoding proteins. Biochimie 94:1474–1480
Navarro B, Pantaleo V, Gisel A, Moxon S, Dalmay T, Bisztray G, Di Serio F, Burgyan J (2009) Deep sequencing of viroid-derived small RNAs from grapevine provides new insights on the role of RNA silencing in plant-viroid interaction. PLoS One 4:e7686
Nohales MA, Flores R, Daròs JA (2012) A viroid RNA redirects host DNA ligase 1 to act as an RNA ligase. Proc Natl Acad Sci USA 109:13805–13810
Owens RA (2007) Potato spindle tuber viroid: the simplicity paradox resolved? Mol Plant Pathol 8:549–560
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, Elsevier/Academic Press, London UK, pp 1221–1234
Rezaian MA (1990) Australian grapevine viroid—evidence for extensive recombination between viroids. Nucleic Acids Res 18:1813–1818
Rubino L, Di Serio F, Martelli GP (2003) Viroid-like RNAs. In: Hadidi A, Flores R, Randles JW, Semancik JS (eds) Viroids. CSIRO Publishing, Collingwood, pp 76–86
Sano T, Candresse T, Hammond RW, Diener TO, Owens RA (1992) Identification of multiple structural domains regulating viroid pathogenicity. Proc Natl Acad Sci USA 89:10104–10108
Schmitz A, Riesner D (1998) Correlation between bending of the VM region and pathogenicity of different potato spindle tuber viroid strains. RNA 4:1295–1303
Semanicik JS, Vidalakis G (2005) The question of Citrus viroid IV as a cocadviroid. Arch. Virol 150:1059–1067
Szychowski JA, Vidalakis G, Semancik JS (2005) Host-directed processing of Citrus exocortis viroid. J Gen Virol 86:473–477
Singh RP, Dilworth AD (2009) Tomato chlorotic dwarf viroid in the ornamental plant Vinca minor and its transmission through tomato seed. Eur J Plant Pathol 123:111–116
Singh RP, Nie X, Singh M (1999) Tomato chlorotic dwarf viroid: an evolutionary link in the origin of viroids. J Gen Virol 80:2823–2828
Spieker RL (1996) In vitro-generated “inverse” chimeric Coleus blumei viroids evolve in vivo into infectious RNA replicons. J Gen Virol 77:2839–2846
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Tsagris EM, Martinez de Alba AE, Gozmanova M, Kalanditis K (2008) Viroids. Cell Microbiol 10:2168–2179
Verhoeven JT, Meekes ET, Roenhorst JW, Flores R, Serra P (2013) Dahlia latent viroid: a recombinant new species of the family Pospiviroidae posing intriguing questions about its origin and classification. J Gen Virol 94:711–719
Verhoeven JThJ, Jansen CCC, Botermans M, Roenhorst JW (2010) Epidemiological evidence that vegetatively propagated solanaceous plant species act as sources of Potato spindle tuber viroid inoculum for tomato. Plant Pathol 59:3–12
Verhoeven JThJ (2010) Identification and epidemiology of pospiviroids Thesis, Wageningen University, pp 136
Verhoeven JThJ, Roenhorst JW, Owens RA (2011) Mexican papita viroid and Tomato planta macho viroid belong to a single species in the genus Pospiviroid. Arch Virol 156:1433–1437
Wu Q, Wang Y, Cao M, Pantaleo V, Burgyan J, Li W-X, Ding S-W (2012) Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm. Proc Natl Acad Sci USA 109:3938–3943
Zhang Y, Singh K, Kaur R, Qiu W (2011) Association of a novel DNA virus with the grapevine vein-clearing and vine decline syndrome. Phytopathology 101:1081–1090
Zhong X, Archual AJ, Amin AA, Ding B (2008) A genomic map of viroid RNA motifs critical for replication and systemic trafficking. Plant Cell 20:35–47
[-]