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Comparative Genomic Analysis of Pathogenic Yeasts and the Evolution of Virulence

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Pathogenic Yeasts

Part of the book series: The Yeast Handbook ((YEASTHDB))

Abstract

The increased availability of molecular data has had a major impact on phylogenetic studies in general, and on the study of fungal phylogeny in particular. To date, more than 60 fungal genomes have been completely sequenced, ranging from the Chytridiomycota to the Ascomycota. There have been several attempts to reconstruct aspects of the fungal Tree of Life, using a variety of approaches (Fitzpatrick et al. 2006; James et al. 2006; Kuramae et al. 2006; Robbertse et al. 2006; Marcet-Houben and Gabaldon 2009).

Because the use of single genes to infer phylogenetic relationships can generate a number of different topologies, it has become increasingly common to use several genes, often concatenating information. A very thorough analysis was carried out by James et al. (2006), who used six genes from 200 species. This analysis supports a monophyletic origin for the Ascomycota, Basidiomycota, and Glomeromycota. The study also addressed the relationship of the Microsporidia, intracellular animal parasites whose phylogenetic origin has long been controversial. James et al. (2006) place the Microsporidia on the earliest diverging fungal branch.

The analysis of Fitzpatrick et al. (2006) used information from 4,805 single-gene families from 42 fully sequenced fungal genomes. A robust phylogeny was generated, supporting the major phyla (Zygomycota, Basidiomycota, and Ascomycota) (Fig. 1.1). The subphyla within the Ascomycota (Taphrinomycotina, Pezizomycotina, and Saccharomycotina) are strongly supported. At the time the analysis was performed few basidiomycete sequences were available, but the monophyletic origin of the Hymenomycetes is clear. The overall structure of the fungal tree is supported by several additional phylogenomic analyzes (Kuramae et al. 2006; Robbertse et al. 2006; Marcet-Houben and Gabaldon 2009).

Phylogenetic relation of fungal species. A maximum likelihood phylogeny was constructed using a concatenated alignment of 153 fungal genes from 42 species. Taken from Fitzpatrick et al. (2006)

The majority of fungi associated with human disease are ascomycetes, from either the subphyla Pezizomycotina (e.g., Aspergilli) or Saccharomycotina (e.g., Candida). This may explain why most available genome sequences are from these groups.

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Authors and Affiliations

  1. Genome Evolution Laboratory, Department of Biology, National University of Ireland Maynooth, Maynooth, Co. Kildare, Ireland

    David A. Fitzpatrick

  2. UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

    Geraldine Butler

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  1. Old Medical School, Leeds General Infirmary, Leeds, LS1 3EX, United Kingdom

    Ruth Ashbee

  2. Div. Investigative Science, Imperial College London, South Kensington Campus, London , SW7 2AZ, United Kingdom

    Elaine M. Bignell

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Fitzpatrick, D.A., Butler, G. (2010). Comparative Genomic Analysis of Pathogenic Yeasts and the Evolution of Virulence. In: Ashbee, R., Bignell, E. (eds) Pathogenic Yeasts. The Yeast Handbook. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03150-2_1

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