01950nas a2200229   4500008004100000245009500041210006900136300001000205490000700215520116100222653001401383653005301397653002801450653003701478100001801515700001501533700001901548700001501567700001901582700001301601856010601614       2001                        eng d00aPhylogenetic analysis of viroid and viroid-like satellite RNAs from plants: a reassessment0 aPhylogenetic analysis of viroid and viroidlike satellite RNAs fr  a155-90 v533 aThe 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.10aEvolution10aMolecular *Phylogeny Plant Viruses/*genetics RNA10aSatellite/*genetics RNA10aViral/genetics Viroids/*genetics1 aElena, S., F.1 aDopazo, J.1 ade la Pena, M.1 aFlores, R.1 aDiener, T., O.1 aMoya, A.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11479686