Summary.
The population structure and diversity within a Citrus exocortis viroid (CEVd) isolate was estimated by single strand conformation polymorphism (SSCP) and sequence analysis. A predominant sequence variant (V1) representing 52.8% of the overall population was identified. V1 and other additional variants presented a composition of the P domain characteristic of severe strains of CEVd. The nucleotide diversity of this CEVd population was lower than expected according to a model of neutral evolution, suggesting a strong negative selection. Citron plants were inoculated with dimeric clones of nine sequence variants and two resulted infectious inducing the severe symptoms characteristic of the original isolate. De novo populations were generated from these infectious variants and like in the original CEVd isolate, both populations presented V1 as the predominant variant but they evolved to a higher nucleotide diversity.
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References
S Ambrós JC Desvignes G Llácer R Flores (1995) ArticleTitlePear blister canker viroid: sequence variability and causal role in pear blister canker disease. J Gen Virol 76 2625–2629 Occurrence Handle7595369
S Ambrós C Hernández JC Desvignes R Flores (1998) ArticleTitleGenomic structure of three phenotipically different isolates of peach latent mosaic viroid: implications of the existence of constraints limiting the heterogeneity of viroid quasispecies. J Virol 72 7397–7406 Occurrence Handle9696836
S Ambrós C Hernández R Flores (1999) ArticleTitleRapid generation of genetic heterogeneity in progenies from individual cDNA clones of peach latent mosaic viroid in its natural host. J Gen Virol 80 2239–2252 Occurrence Handle10466824
MA Bracho A Moya E Barrio (1998) ArticleTitleContribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J Gen Virol 79 2921–2928 Occurrence Handle9880005
F Bussiére D Lafontaine JP Perrault (1996) ArticleTitleCompilation and analysis of viroid and viroid-like RNA sequences. Nucleic Acids Res 24 1793–1798 Occurrence Handle10.1093/nar/24.10.1793 Occurrence Handle8657556
P De Rijk R De Wachter (1997) ArticleTitleRnaViz, a program for the visualization of RNA secondary structure. Nucleic Acids Res 25 4679–4684 Occurrence Handle10.1093/nar/25.22.4679 Occurrence Handle9358182
AJ Dingley G Steger B Esters D Riesner S Grzesiek (2003) ArticleTitleStructural characterization of the 69 nucleotide potato spindle tuber viroid left-terminal domain by NMR and thermodynamic analysis. J Mol Biol 334 751–767 Occurrence Handle10.1016/j.jmb.2003.10.015 Occurrence Handle14636600
E Domingo JJ Holland (1997) ArticleTitleRNA virus mutations and fitness for survival. Annu Rev Microbiol 51 151–178 Occurrence Handle10.1146/annurev.micro.51.1.151 Occurrence Handle9343347
M Eigen (1971) ArticleTitleSelf-organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58 465–523 Occurrence Handle10.1007/BF00623322 Occurrence Handle4942363
M Eigen (1993) ArticleTitleThe origin of genetic information: viruses as models. Gene 135 37–47 Occurrence Handle10.1016/0378-1119(93)90047-7 Occurrence Handle8276276
R Flores F Di Serio C Hernández (1997) ArticleTitleViroids: the noncoding genomes. Semin Virol 8 65–73 Occurrence Handle10.1006/smvy.1997.0107
Flores R, Randles JW, Bar-Joseph M, Diener TO (2000) Viroids. In: van Regenmortel MHV, Fauquet CM, Bishop DHL, Carstens EB, Estes MK, Lemon SM, Maniloff J, Mayo MA, McGeoch DJ, Pringle CR, Wickner RB (eds), Virus taxonomy, 7th Rep Intern Com Taxon Viruses, Academic Press, San Diego CA USA, pp. 1009–1024
X Foissac N Duran-Vila (2000) ArticleTitleCharacterisation of two citrus apscaviroids isolated in Spain. Arch Virol 145 1975–1983 Occurrence Handle10.1007/s007050070070 Occurrence Handle11043955
M Gandía N Duran-Vila (2004) ArticleTitleVariability of the progeny of a sequence variant of Citrus bent leaf viroid (CBLVd). Arch Virol 149 407–416 Occurrence Handle10.1007/s00705-003-0219-1 Occurrence Handle14745604
F García-Arenal F Fraile JM Malpica (2001) ArticleTitleVariability and genetic structure of plant virus populations. Annu Rev Phytopathol 39 157–186 Occurrence Handle10.1146/annurev.phyto.39.1.157 Occurrence Handle11701863
FU Gast D Kempe RL Spieker HL Sönger (1996) ArticleTitleSecondary structure probing of potato spindle tuber viroid (PSTVd) and sequence comparison with other small pathogenic RNA replicons provides evidence for central non-canonical base-pairs, large A-rich loops, and a terminal branch. J Mol Biol 262 652–670 Occurrence Handle10.1006/jmbi.1996.0543 Occurrence Handle8876645
A Góra T Candresse W Zagórski (1994) ArticleTitleAnalysis of the population structure of three phenotipically different PSTVd isolates. Arch Virol 138 233–245 Occurrence Handle10.1007/BF01379128 Occurrence Handle7998831
A Góra-Sochacka A Kierzez T Candresse W Zagórski (1997) ArticleTitleThe genetic stability of potato spindle tuber viroid (PSTVd) molecular variants. RNA 3 68–74 Occurrence Handle8990400
HJ Gross G Krupp H Domdey M Raba P Jank C Lossow H Alberty K Ramm HL Sanger (1982) ArticleTitleNucleotide sequence and secondary structure of citrus exocortis and chrysanthemum stunt viroid. Eur J Biochem 121 249–257 Occurrence Handle10.1111/j.1432-1033.1982.tb05779.x Occurrence Handle7060550
PG Higgins PM Sharp (1989) ArticleTitleFast and sensitive multiple sequence alignment on a microcomputer. Comput Appl Biosci 5 151–153 Occurrence Handle2720464
JJ Holland K Spindler F Horodyski E Grabau S Nichol S Vanderpol (1982) ArticleTitleRapid evolution of RNA genomes. Science 215 1577–1585 Occurrence Handle7041255
GL Igloi (1983) ArticleTitleSilver stain for the detection of nanogram amounts of tRNA following two-dimensional electrophoresis. Ann Biochem 134 184–188 Occurrence Handle10.1016/0003-2697(83)90281-6
P Keese RH Symons (1985) ArticleTitleDomains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc Natl Acad Sci USA 82 4582–4586 Occurrence Handle3860809
AM Koltunow MA Rezaian (1988) ArticleTitleGrapevine yellow speckle viroid: structural features of a new viroid group. Nucleic Acids Res 16 849–864 Occurrence Handle3344221
P Kong L Rubio M Polek BW Falk (2000) ArticleTitlePopulation structure and genetic diversity of California citrus tristeza virus (CTV) field isolates. Virus Genes 21 139–145 Occurrence Handle10.1023/A:1008198311398 Occurrence Handle11129629
M Lynch TJ Crease (1990) ArticleTitleThe analysis of population survey data on DNA sequence variation. Mol Biol Evol 7 377–394 Occurrence Handle1974693
J Matousek J Patzak L Orctová J Schubert L Vrba G Steger D Riesner (2001) ArticleTitleThe variability of Hop Latent Viroid as induced upon heat treatment. Virology 287 349–358 Occurrence Handle10.1006/viro.2001.1044 Occurrence Handle11531412
RA Owens G Steger Y Hu A Fels RW Hammond D Riesner (1996) ArticleTitleRNA structural features responsible for potato spindle tuber viroid pathogenicity. Virology 222 144–158 Occurrence Handle10.1006/viro.1996.0405 Occurrence Handle8806495
RA Owens G Yang D Gundersen-Rindal RW Hammond T Candresse M Bar-Joseph (2000) ArticleTitleBoth point mutation and RNA recombination contribute to the sequence diversity of Citrus Viroid III. Virus Genes 20 243–252 Occurrence Handle10.1023/A:1008144712837 Occurrence Handle10949952
RA Owens SM Thomson M Kramer (2003) ArticleTitleIdentification of neutral mutants surrounding two naturally occurring variants of Potato spindle tuber viroid. J Gen Virol 84 751–756 Occurrence Handle10.1099/vir.0.18755-0 Occurrence Handle12604828
A Palacio N Duran-Vila (1999) ArticleTitleSingle-strand conformation polymorphism (SSCP) analysis as a tool for viroid characterization. J Virol Methods 77 27–36 Occurrence Handle10.1016/S0166-0934(98)00121-9 Occurrence Handle10029322
Palacio A, Foissac X, Duran-Vila N (2000) Indexing of citrus viroids by imprint hybridization: comparision with other detection methods. In: Proc, 14th Conference of the International Organization of Citrus Virologists, International Organization of Citrus Virologists, Riverside, CA. pp. 294–301
A Palacio-Bielsa J Romero-Durbán N Duran-Vila (2004) ArticleTitleCharacterization of citrus HSVd isolate. Arch Virol 149 537–552 Occurrence Handle10.1007/s00705-003-0223-5 Occurrence Handle14991442
H Polivka U Staub HJ Gross (1996) ArticleTitleVariation of viroid profiles in individual grapevine plants: novel grapevine yellow speckle viroid 1 mutants show alterations of hairpin I. J Gen Virol 77 155–161 Occurrence Handle8558124
J Rozas R Rozas (1999) ArticleTitleDNASP version 3: an integrated program for molecular population genetic and molecular evolution analysis. Bioinformatics 15 174–175 Occurrence Handle10089204
L Rubio Y Abou-Jawdah HX Lin BW Falk (2001) ArticleTitleGeographically distant isolates of the crinivirus Cucurbit yellow stunting disorder virus show very long genetic diversity in the coat protein gene. J Gen Virol 82 929–933 Occurrence Handle11257199
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory, New York. USA
JS Semancik LG Weathers (1972) ArticleTitleExocortis virus: an infectious free-nucleic acid plant virus with unusual properties. Virology 47 456–466 Occurrence Handle10.1016/0042-6822(72)90281-4 Occurrence Handle4333740
JS Semancik TJ Morris LG Weathers GF Rordorf DR Kearns (1975) ArticleTitlePhysical properties of a minimal infectious RNA (viroid) associated with the exocortis disease. Virology 63 160–167 Occurrence Handle10.1016/0042-6822(75)90381-5 Occurrence Handle1111210
Steger G, Riesner D (2003) Molecular characteristics. In: Hadidi A, Flores R, Randles JW, Semancik JS (eds), Viroids. CSIRO Publishing, Australia, pp 15–29
F Tajima (1989) ArticleTitleStatistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 585–595 Occurrence Handle2513255
C Vernière X Perrier C Dubois A Dubois L Botella C Chabrier JM Bové N Duran-Vila (2004) ArticleTitleCitrus viroids: Symptom expression and effect on vegetative growth and yield on clementine trees grafted on trifoliate orange. Plant Dis 88 1189–1197
JE Visvader AR Gould GE Bruening RH Symons (1982) ArticleTitleCitrus exocortis viroid: nucleotide sequence and secondary structure of an Australian isolate. FEBS Lett 137 288–292 Occurrence Handle10.1016/0014-5793(82)80369-4 Occurrence Handle15768484
JE Visvader RH Symons (1985) ArticleTitleEleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity. Nucleic Acids Res 13 2907–2920 Occurrence Handle2582367
MC Vives L Rubio L Galipienso L Navarro P Moreno J Guerri (2002) ArticleTitleLow genetic variation between isolates of Citrus leaf blotch virus from different host species and different geographical origins. J Gen Virol 83 2587–2591 Occurrence Handle12237442
M Zuker (1989) ArticleTitleOn findings all suboptimal foldings of an RNA molecule. Science 244 48–52 Occurrence Handle2468181 Occurrence HandleMR989985
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Gandía, M., Rubio, L., Palacio, A. et al. Genetic variation and population structure of an isolate of Citrus exocortis viroid (CEVd) and of the progenies of two infectious sequence variants. Arch Virol 150, 1945–1957 (2005). https://doi.org/10.1007/s00705-005-0570-5
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DOI: https://doi.org/10.1007/s00705-005-0570-5