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Journal of Molecular Evolution

, Volume 53, Issue 2, pp 155–159 | Cite as

Phylogenetic Analysis of Viroid and Viroid-Like Satellite RNAs from Plants: A Reassessment

  • Santiago F. Elena
  • Joaquín Dopazo
  • Marcos de la Peña
  • Ricardo Flores
  • Theodor O. Diener
  • Andrés Moya
Article

Abstract

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.

Key words: Likelihood-mapping — Molecular phylogeny — Tree-likeness — Viroid — Viroid-like satellite RNA 

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Copyright information

© Springer-Verlag New York Inc. 2001

Authors and Affiliations

  • Santiago F. Elena
    • 1
  • Joaquín Dopazo
    • 2
  • Marcos de la Peña
    • 3
  • Ricardo Flores
    • 3
  • Theodor O. Diener
    • 4
  • Andrés Moya
    • 1
  1. 1.Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de València, Apartat 2085, 46071 València, SpainSpain
  2. 2.Unidad de Bioinformática, Centro Nacional de Investigaciones Oncológicas Carlos III, Carretera Majadahonda-Pozuelo Km 2, 28220 Majadahonda, Madrid, SpainSpain
  3. 3.Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Avenida de los Naranjos, 46022 Valencia, SpainSpain
  4. 4.Center for Agricultural Biotechnology, University of Maryland Biotechnology Institute, College Park, MD 20742, USAUS

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