Genetic variation and population structure of an isolate of Citrus exocortis viroid (CEVd) and of the progenies of two infectious sequence variants

Archives of Virology

Volumn 150, Issue 10, 2005, Pages 1945-1957

  Gandia M ^a   Rubio, L ^a   Palacio, A ^a   Duran Vila, N ^a  

^a INSTITUTO VALENCIANO DE INVESTIGACIONES AGRARIAS IVIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; VIRUS DNA; VIRUS RNA;

ARTICLE; CHEMISTRY; CITRUS FRUIT; CONFORMATION; GENETIC VARIABILITY; GENETICS; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SINGLE STRAND CONFORMATION POLYMORPHISM; VIROID; VIROLOGY;

BASE SEQUENCE; CITRUS; DNA, COMPLEMENTARY; DNA, VIRAL; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; POLYMORPHISM, SINGLE-STRANDED CONFORMATIONAL; RNA, VIRAL; VARIATION (GENETICS); VIROIDS;

CITRUS; CITRUS EXOCORTIS VIROID; CITRUS MEDICA; VIROIDS;

EID: 25444509843     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-005-0570-5     Document Type: Article

References (46)

1. S Ambrós JC Desvignes G Llácer R Flores 1995 Pear blister canker viroid: sequence variability and causal role in pear blister canker disease. J Gen Virol 76 2625 2629
2. S Ambrós C Hernández JC Desvignes R Flores 1998 Genomic 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
3. S Ambrós C Hernández R Flores 1999 Rapid 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
4. MA Bracho A Moya E Barrio 1998 Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J Gen Virol 79 2921 2928
5. F Bussiére D Lafontaine JP Perrault 1996 Compilation and analysis of viroid and viroid-like RNA sequences. Nucleic Acids Res 24 1793 1798
6. P De Rijk R De Wachter 1997 RnaViz, a program for the visualization of RNA secondary structure. Nucleic Acids Res 25 4679 4684
7. AJ Dingley G Steger B Esters D Riesner S Grzesiek 2003 Structural characterization of the 69 nucleotide potato spindle tuber viroid left-terminal domain by NMR and thermodynamic analysis. J Mol Biol 334 751 767
8. E Domingo JJ Holland 1997 RNA virus mutations and fitness for survival. Annu Rev Microbiol 51 151 178
9. M Eigen 1971 Self-organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58 465 523
10. M Eigen 1993 The origin of genetic information: viruses as models. Gene 135 37 47
11. R Flores F Di Serio C Hernández 1997 Viroids: the noncoding genomes. Semin Virol 8 65 73
12. 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
13. X Foissac N Duran-Vila 2000 Characterisation of two citrus apscaviroids isolated in Spain. Arch Virol 145 1975 1983
14. M Gandía N Duran-Vila 2004 Variability of the progeny of a sequence variant of Citrus bent leaf viroid (CBLVd). Arch Virol 149 407 416
15. F García-Arenal F Fraile JM Malpica 2001 Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39 157 186
16. FU Gast D Kempe RL Spieker HL Sönger 1996 Secondary 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
17. A Góra T Candresse W Zagórski 1994 Analysis of the population structure of three phenotipically different PSTVd isolates. Arch Virol 138 233 245
18. A Góra-Sochacka A Kierzez T Candresse W Zagórski 1997 The genetic stability of potato spindle tuber viroid (PSTVd) molecular variants. RNA 3 68 74
19. HJ Gross G Krupp H Domdey M Raba P Jank C Lossow H Alberty K Ramm HL Sanger 1982 Nucleotide sequence and secondary structure of citrus exocortis and chrysanthemum stunt viroid. Eur J Biochem 121 249 257
20. PG Higgins PM Sharp 1989 Fast and sensitive multiple sequence alignment on a microcomputer. Comput Appl Biosci 5 151 153
21. JJ Holland K Spindler F Horodyski E Grabau S Nichol S Vanderpol 1982 Rapid evolution of RNA genomes. Science 215 1577 1585
22. GL Igloi 1983 Silver stain for the detection of nanogram amounts of tRNA following two-dimensional electrophoresis. Ann Biochem 134 184 188
23. P Keese RH Symons 1985 Domains in viroids: evidence of intermolecular RNA rearrangements and their contribution to viroid evolution. Proc Natl Acad Sci USA 82 4582 4586
24. AM Koltunow MA Rezaian 1988 Grapevine yellow speckle viroid: structural features of a new viroid group. Nucleic Acids Res 16 849 864
25. P Kong L Rubio M Polek BW Falk 2000 Population structure and genetic diversity of California citrus tristeza virus (CTV) field isolates. Virus Genes 21 139 145
26. M Lynch TJ Crease 1990 The analysis of population survey data on DNA sequence variation. Mol Biol Evol 7 377 394
27. J Matousek J Patzak L Orctová J Schubert L Vrba G Steger D Riesner 2001 The variability of Hop Latent Viroid as induced upon heat treatment. Virology 287 349 358
28. RA Owens G Steger Y Hu A Fels RW Hammond D Riesner 1996 RNA structural features responsible for potato spindle tuber viroid pathogenicity. Virology 222 144 158
29. RA Owens G Yang D Gundersen-Rindal RW Hammond T Candresse M Bar-Joseph 2000 Both point mutation and RNA recombination contribute to the sequence diversity of Citrus Viroid III. Virus Genes 20 243 252
30. RA Owens SM Thomson M Kramer 2003 Identification of neutral mutants surrounding two naturally occurring variants of Potato spindle tuber viroid. J Gen Virol 84 751 756
31. A Palacio N Duran-Vila 1999 Single-strand conformation polymorphism (SSCP) analysis as a tool for viroid characterization. J Virol Methods 77 27 36
32. 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
33. A Palacio-Bielsa J Romero-Durbán N Duran-Vila 2004 Characterization of citrus HSVd isolate. Arch Virol 149 537 552
34. H Polivka U Staub HJ Gross 1996 Variation 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
35. J Rozas R Rozas 1999 DNASP version 3: an integrated program for molecular population genetic and molecular evolution analysis. Bioinformatics 15 174 175
36. L Rubio Y Abou-Jawdah HX Lin BW Falk 2001 Geographically 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
37. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory, New York. USA
38. JS Semancik LG Weathers 1972 Exocortis virus: an infectious free-nucleic acid plant virus with unusual properties. Virology 47 456 466
39. JS Semancik TJ Morris LG Weathers GF Rordorf DR Kearns 1975 Physical properties of a minimal infectious RNA (viroid) associated with the exocortis disease. Virology 63 160 167
40. Steger G, Riesner D (2003) Molecular characteristics. In: Hadidi A, Flores R, Randles JW, Semancik JS (eds), Viroids. CSIRO Publishing, Australia, pp 15-29
41. F Tajima 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123 585 595
42. C Vernière X Perrier C Dubois A Dubois L Botella C Chabrier JM Bové N Duran-Vila 2004 Citrus viroids: Symptom expression and effect on vegetative growth and yield on clementine trees grafted on trifoliate orange. Plant Dis 88 1189 1197
43. JE Visvader AR Gould GE Bruening RH Symons 1982 Citrus exocortis viroid: nucleotide sequence and secondary structure of an Australian isolate. FEBS Lett 137 288 292
44. JE Visvader RH Symons 1985 Eleven new sequence variants of citrus exocortis viroid and the correlation of sequence with pathogenicity. Nucleic Acids Res 13 2907 2920
45. MC Vives L Rubio L Galipienso L Navarro P Moreno J Guerri 2002 Low genetic variation between isolates of Citrus leaf blotch virus from different host species and different geographical origins. J Gen Virol 83 2587 2591
46. M Zuker 1989 On findings all suboptimal foldings of an RNA molecule. Science 244 48 52