Molecular features of new Peach Latent Mosaic Viroid variants suggest that recombination may have contributed to the evolution of this infectious RNA

• Published in: Virology (New York, N.Y.) Vol. 360; no. 1; pp. 50 - 57
• Main Authors: Fekih Hassen, I, Massart, S, Motard, J, Roussel, S, Parisi, O, Kummert, J, Fakhfakh, H, Marrakchi, M, Perreault, J.P, Jijakli, M.H
• Format: Journal Article Web Resource
• Language: English
• Published: United States Elsevier Inc 30-03-2007; Elsevier
• Subjects: almonds; Base Sequence; Biologie végétale (sciences végétales, sylviculture, mycologie...); evolution; Evolution, Molecular; fruit trees; genetic polymorphism; genetic recombination; Genetic Variation; Hammerhead self-cleavage; Infectious Disease; Life sciences; Molecular Sequence Data; Mosaic Viruses - genetics; Nucleic Acid Conformation; Peach latent mosaic viroid; peaches; pears; Phytobiology (plant sciences, forestry, mycology...); Plant Diseases - virology; Prunus; Prunus - virology; Prunus dulcis; Prunus persica; Pyrus communis; Recombination; RNA, Viral; Sciences du vivant; Secondary structure; Sequence variation; Viroid; Viroids - genetics; Tunisia; Recombination; Hammerhead self-cleavage; Secondary structure; Sequence variation; Viroid
• ISSN: 0042-6822; 1096-0341; 1096-0341
• DOI: 10.1016/j.virol.2006.10.021

Abstract Nucleotide sequences of a broad range of Peach Latent Mosaic Viroid (PLMVd) variants were determined. The variants were isolated from peach, pear, and almond tree samples collected in Tunisia. Sequence analysis confirmed the high variability of PLMVd, as no less than 119 new variants were identified. Variations included new polymorphic positions, insertions of 11 to 14 nucleotides, and new mutations within the hammerhead self-cleavage motifs. We provide the first covariation-based evidence for certain stems within the proposed secondary structure. Our covariation analysis also strengthens the view that a pseudoknot closes the replication domain. On the basis of phylogenetic tree studies and informative positions, PLMVd variants are proposed to cluster into groups and subgroups likely to have resulted from recombination events. PLMVd thus emerges as a suitable viroid for retracing the evolution of an RNA genome.