Phylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment

The proposed monophyletic origin of a group of subviral plant pathogens (viroids and viroid-like satellite RNAs), as well as the phylogenetic relationships and the resulting taxonomy of these entities, has been recently questioned. The criticism comes from the (apparent) lack of sequence similarity...

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Bibliographic Details
Published in:Journal of molecular evolution 2001-08, Vol.53 (2), p.155-159
Main Authors: Elena, S F, Dopazo, J, de la Peña, M, Flores, R, Diener, T O, Moya, A
Format: Article
Language:English
Subjects:
Biological properties
Evolution, Molecular
Evolutionary biology
Genetics
Molecular biology
Phylogeny
Plant biology
Plant Viruses - genetics
Ribonucleic acid
RNA
RNA, Satellite - genetics
RNA, Viral - genetics
Viroids - genetics
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Summary:The proposed monophyletic origin of a group of subviral plant pathogens (viroids and viroid-like satellite RNAs), as well as the phylogenetic relationships and the resulting taxonomy of these entities, has been recently questioned. The criticism comes from the (apparent) lack of sequence similarity among these RNAs necessary to reliably infer a phylogeny. Here we show that, despite their low overall sequence similarity, a sequence alignment manually adjusted to take into account all the local similarities and the insertions/deletions and duplications/rearrangements described in the literature for viroids and viroid-like satellite RNA, along with the use of an appropriate estimator of genetic distances, constitutes a data set suitable for a phylogenetic reconstruction. When the likelihood-mapping method was applied to this data set, the tree-likeness obtained was higher than that corresponding to a sequence alignment that does not take into consideration the local similarities. In addition, bootstrap analysis also supports the major groups previously proposed and the reconstruction is consistent with the biological properties of this RNAs.
ISSN:0022-2844
1432-1432
DOI:10.1007/s002390010203