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Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

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Abstract

We have used three independent phylogenomic approaches (concatenated alignments, single-, and multi-gene supertrees) to reconstruct the fungal tree of life (FTOL) using publicly available fungal genomes. This is the first time multi-gene families have been used in fungal supertree reconstruction and permits us to use up to 66% of the 1,001,217 genes in our fungal database. Our analyses show that different phylogenomic datasets derived from varying clustering criteria and alignment orientation do not have a major effect on phylogenomic supertree reconstruction. Overall the resultant phylogenomic trees are relatively congruent with one another and successfully recover the major fungal phyla, subphyla and classes. We find that where incongruences do occur, the inferences are usually poorly supported. Within the Ascomycota phylum, our phylogenies reconstruct monophyletic Saccharomycotina and Pezizomycotina subphyla clades and infer a sister group relationship between these to the exclusion of the Taphrinomycotina. Within the Pezizomycotina subphylum, all three phylogenies infer a sister group relationship between the Leotiomycetes and Sordariomycetes classes. However, there is conflict regarding the relationships with the Dothideomycetes and Eurotiomycetes classes. Within the Basidiomycota phylum, supertrees derived from single- and multi-gene families infer a sister group relationship between the Pucciniomycotina and Agaricomycotina subphyla while the concatenated phylogeny infers a poorly supported relationship between the Agaricomycotina and Ustilagomycotina. The reconstruction of a robust FTOL is important for future fungal comparative analyses. We illustrate this point by performing a preliminary investigation into the phyletic distribution of yeast prion-like proteins in the fungal kingdom.

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Acknowledgments

We wish to acknowledge the financial support of the Irish Health Research Board (HRB). We also wish to acknowledge the SFI/HEA Irish Centre for High-End Computing (ICHEC) for the provision of computational facilities and support. EMMT was funded through a SFI-UREKA summer school and would like to thank Dr James McInerney and Dr Davide Pisani. He also wishes to thank his academic advisor Prof. Silvia Restrepo.

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  1. Mycology and Phytopathology Laboratory, Universidad de Los Andes, Bogotá, Colombia

    Edgar M. Medina

  2. Department of Biology, Yeast Genetics Laboratory, The National University of Ireland Maynooth, Maynooth, County Kildare, Ireland

    Gary W. Jones

  3. Department of Biology, Genome Evolution Laboratory, The National University of Ireland Maynooth, Maynooth, County Kildare, Ireland

    David A. Fitzpatrick

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  1. Edgar M. Medina
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Correspondence to David A. Fitzpatrick.

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Medina, E.M., Jones, G.W. & Fitzpatrick, D.A. Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom. J Mol Evol 73, 116–133 (2011). https://doi.org/10.1007/s00239-011-9461-4

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