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Journal of Clinical Microbiology, June 2005, p. 2816-2823, Vol. 43, No. 6
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.6.2816-2823.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Internal Transcribed Spacer rRNA Gene-Based Phylogenetic Reconstruction Using Algorithms with Local and Global Sequence Alignment for Black Yeasts and Their Relatives

R. B. Caligiorne,^1* P. Licinio,² J. Dupont,³ and G. S. de Hoog⁴

Laboratório de Pesquisas Clínicas, Centro de Pesquisas René Rachou, FIOCRUZ, Brasil, and Muséum National d'Histoire Naturelle, Paris, France,¹ Departamento de Física, Universidade Federal de Minas Gerais, Minas Gerais, Brazil,² Muséum National d'Histoire Naturelle, Paris, France,³ Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands, and Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands⁴

Received 18 November 2004/ Returned for modification 14 January 2005/ Accepted 23 February 2005

Sequences of rRNA gene internal transcribed spacer (ITS) of a standard set of black yeast-like fungal pathogens were compared using two methods: local and global alignments. The latter is based on DNA-walk divergence analysis. This method has become recently available as an algorithm (DNAWD program) which converts sequences into three-dimensional walks. The walks are compared with, or fit to, each other generating global alignments. The DNA-walk geometry defines a proper metric used to create a distance matrix appropriated for phylogenetic reconstruction. In this work, the analyses were carried out for species currently classified in Capronia, Cladophialophora, Exophiala, Fonsecaea, Phialophora, and Ramichloridium. Main groups were verified by small-subunit rRNA gene data. DNAWD applied to ITS2 alone enabled species recognition as well as phylogenetic reconstruction reflecting clades discriminated in small-subunit rRNA gene phylogeny, which was not possible with any other algorithm using local alignment for the same data set. It is concluded that DNAWD provides rapid insight into broader relationships between groups using genes that otherwise would be hardly usable for this purpose.

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* Corresponding author. Mailing address: Laboratório de Pesquisas Clínicas, Centro de Pesquisas René Rachou, FIOCRUZ, Brazil. Phone: 553132953566. Fax: 553132953566. E-mail: rachel{at}cpqrr.fiocruz.br.

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Journal of Clinical Microbiology, June 2005, p. 2816-2823, Vol. 43, No. 6
0095-1137/05/$08.00+0     doi:10.1128/JCM.43.6.2816-2823.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

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