Correction: Deep-sequencing of the peach latent mosaic viroid reveals new aspects of population heterogeneity (PLoS ONE (2014) 9, 1 (e87297) DOI:10.1371/journal.pone.0087297);Deep-sequencing of the peach latent mosaic viroid reveals new aspects of population heterogeneity

PLoS ONE

Volumn 9, Issue 1, 2014, Pages

  Glouzon, Jean Pierre Sehi ^a,b   Bolduc, François ^b   Wang, Shengrui ^a   Najmanovich, Rafael J ^b   Perreault, Jean Pierre ^b  

^a UNIVERSITÉ DE SHERBROOKE   (Canada)

^b UNIVERSITY OF SHERBROOKE   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; MUTATION RATE; NONHUMAN; PEACH; PEACH LATENT MOSAIC VIROID; PHENOTYPE; POPULATION DYNAMICS; VIROID; VIROIDAL PLANT DISEASE; VIRUS MUTATION;

BASE SEQUENCE; FRUIT; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MOSAIC VIRUSES; MUTATION; PLANT DISEASES; PRUNUS; VIROIDS;

EID: 84899678349     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0096229     Document Type: Erratum

References (33)

1. Ding B (2009) The biology of viroid-host interactions. Annu Rev Phytopathol 47: 105-131.
2. Navarro B, Gisel A, Rodio ME, Delgado S, Flores R, et al. (2012) Small RNAs containing the pathogenic determinant of a chloroplast-replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing. Plant J 70: 991-1003.
3. Wang MB, Bian XY, Wu LM, Liu LX, Smith NA, et al. (2004) On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites. Proc Natl Acad Sci U S A 101: 3275-3280. (Pubitemid 38327771)
4. Shimura H, Pantaleo V, Ishihara T, Myojo N, Inaba J, et al. (2011) A viral satellite RNA induces yellow symptoms on tobacco by targeting a gene involved in chlorophyll biosynthesis using the RNA silencing machinery. PLoS Pathog 7: e1002021.
5. 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. (Pubitemid 352844032)
6. Takeda R, Petrov AI, Leontis NB, Ding B (2011) A three-dimensional RNA motif in Potato spindle tuber viroid mediates trafficking from palisade mesophyll to spongy mesophyll in Nicotiana benthamiana. Plant Cell 23: 258-272.
7. Diener TO (1971) Potato spindle tuber "virus". IV. A replicating, low molecular weight RNA. Virology 45: 411-428.
8. Rocheleau L, Pelchat M (2006) The Subviral RNA Database: a toolbox for viroids, the hepatitis delta virus and satellite RNAs research. BMC Microbiol 6: 24.
9. Gago S, Elena SF, Flores R, Sanjuan R (2009) Extremely high mutation rate of a hammerhead viroid. Science 323: 1308.
10. Pelchat M, Grenier C, Perreault JP (2002) Characterization of a viroid-derived RNA promoter for the DNA-dependent RNA polymerase from Escherichia coli. Biochemistry 41: 6561-6571. (Pubitemid 34526024)
11. Codoner FM, Daros JA, Sole RV, Elena SF (2006) The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens. PLoS Pathog 2: e136.
12. Ambros S, Hernandez C, Desvignes JC, Flores R (1998) Genomic structure of three phenotypically different isolates of peach latent mosaic viroid: implications of the existence of constraints limiting the heterogeneity of viroid quasispecies. J Virol 72: 7397-7406. (Pubitemid 28377871)
13. Ambros S, Hernandez C, Flores R (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 (Pt 8): 2239-2252. (Pubitemid 29389163)
14. Gilles A, Meglecz E, Pech N, Ferreira S, Malausa T, et al. (2011) Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12: 245.
15. Vrancken B, Lequime S, Theys K, Lemey P (2010) Covering all bases in HIV research: unveiling a hidden world of viral evolution. AIDS Rev 12: 89-102.
16. Fekih Hassen I, Massart S, Motard J, Roussel S, Parisi O, et al. (2007) Molecular features of new Peach Latent Mosaic Viroid variants suggest that recombination may have contributed to the evolution of this infectious RNA. Virology 360: 50-57.
17. Skums P, Dimitrova Z, Campo DS, Vaughan G, Rossi L, et al. (2012) Efficient error correction for next-generation sequencing of viral amplicons. BMC Bioinformatics 13 Suppl 10: S6-2105-13-S10-S6.
18. Ambros S, Flores R (1998) In vitro and in vivo self-cleavage of a viroid RNA with a mutation in the hammerhead catalytic pocket. Nucleic Acids Res 26: 1877-1883. (Pubitemid 28291719)
19. Przybilski R, Hammann C (2007) Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof. Biol Chem 388: 737-741. (Pubitemid 46934160)
20. Perreault J, Weinberg Z, Roth A, Popescu O, Chartrand P, et al. (2011) Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PLoS Comput Biol 7: e1002031.
21. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76: 5269-5273. (Pubitemid 10236121)
22. Xiong T, Wang S, Jiang Q, Huang JZ (2011) A New Markov Model for Clustering Categorical Sequences. Data Mining, IEEE International Conference on : 0 : 854-863.
23. Bicego M, Murino V, Figueiredo M (2003) Similarity-Based Clustering of Sequences Using Hidden Markov Models. In: Perner P, Rosenfeld A (eds) Machine Learning and Data Mining in Pattern Recognition. Springer Berlin Heidelberg, 86-95.
24. Jiong Yang, Wei Wang (2002) Towards automatic clustering of protein sequences. Bioinformatics Conference, 2002 Proceedings IEEE Computer Society: 175-186.
25. Yang J, Wang W (2003) CLUSEQ: efficient and effective sequence clustering. Data Engineering, 2003 Proceedings 19th International Conference on: 101-112.
26. Greenacre M, Blasius J (2006) Multiple correspondence analysis and related methods. Chapman & Hall/CRC.
27. Xiong T (2009) A New MCA-Based Divisive Hierarchical Algorithm for Clustering Categorical Data. Data Mining, IEEE International Conference on : 0 : 1058-1063.
28. 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. (Pubitemid 30117574)
29. Daros JA, Flores R (2004) Arabidopsis thaliana has the enzymatic machinery for replicating representative viroid species of the family Pospiviroidae. Proc Natl Acad Sci U S A 101: 6792-6797.
30. Matousek J, Orctova L, Steger G, Skopek J, Moors M, et al. (2004) Analysis of thermal stress-mediated PSTVd variation and biolistic inoculation of progeny of viroid "thermomutants" to tomato and Brassica species. Virology 323: 9-23. (Pubitemid 38681016)
31. Dubé A, Bolduc F, Bisaillon M, Perreault JP (2011) Mapping studies of the Peach latent mosaic viroid reveal novel structural features. Mol Plant Pathol 12: 688-701.
32. Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
33. Hertel KJ, Pardi A, Uhlenbeck OC, Koizumi M, Ohtsuka E, et al. (1992) Numbering system for the hammerhead. Nucleic Acids Res 20: 3252.