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Secondary structure of ITS2 rRNA provides taxonomic characters for systematic studies--a case in Lycoperdaceae (Basidiomycota).
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Secondary structure of ITS2 rRNA provides taxonomic characters for systematic studies--a case in Lycoperdaceae (Basidiomycota).

Author: D Krüger Affiliation: The Botany Department, University of Wisconsin, 430 Lincoln Drive, Madison, WI 53706, USA. dirk.krueger@ufz.de; A Gargas
Edition/Format: Article Article : English
Publication:Mycological research, 2008 Mar; 112 Pt 3: 316-30
Other Databases: WorldCatWorldCat
Summary:
The secondary structure of the ITS2 rDNA transcript (pre-rRNA) could provide information for identifying homologous nucleotide characters useful for cladistic inference of relationships. Such structure data could become taxonomic characters. This work compares the effect of several modern nucleotide alignment strategies, including those making use of structure data, on phylogenetic inference. From both the  Read more...
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Document Type: Article
All Authors / Contributors: D Krüger Affiliation: The Botany Department, University of Wisconsin, 430 Lincoln Drive, Madison, WI 53706, USA. dirk.krueger@ufz.de; A Gargas
ISSN:0953-7562
Language Note: English
Unique Identifier: 264105638
Awards:

Abstract:

The secondary structure of the ITS2 rDNA transcript (pre-rRNA) could provide information for identifying homologous nucleotide characters useful for cladistic inference of relationships. Such structure data could become taxonomic characters. This work compares the effect of several modern nucleotide alignment strategies, including those making use of structure data, on phylogenetic inference. From both the phylogenetic analyses and comparative secondary structure, implications for taxonomy and evolution of puffball fungi are discussed. Lycoperdaceae remain insufficiently resolved with present taxon and data sampling. Neither alignment allows statistically robust phylogenetic hypotheses under any current optimality criterion. The secondary structure data at this time are best used as accessory taxonomic characters as their phylogenetic resolving power and confidence in validity is limited compared with underlying nucleotide characters. We introduce a preliminary nomenclature convention to describe secondary structure for defining consensus features. These consensus structures are illustrated for the clades /Calvatia, /Handkea-Echinatum, /Vascellum, /Morganella, and /Plumbea-Paludosa (Bovista).

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