caa a22 4500 445820837 CHVBK 20180317145243.0 cr unu---uuuuu 170323e20111001xx s 000 0 eng 10.1007/s00239-011-9461-4 doi (NATIONALLICENCE)springer-10.1007/s00239-011-9461-4 Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom [Elektronische Daten] [Edgar Medina, Gary Jones, David Fitzpatrick] 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. Springer Science+Business Media, LLC, 2011 Fungal tree of life nationallicence Fungal phylogeny nationallicence Supertree nationallicence Supermatrix nationallicence Markovian clustering nationallicence Fungal prions nationallicence Medina Edgar Mycology and Phytopathology Laboratory, Universidad de Los Andes, Bogotá, Colombia aut Jones Gary Department of Biology, Yeast Genetics Laboratory, The National University of Ireland Maynooth, Maynooth, County Kildare, Ireland aut Fitzpatrick David Department of Biology, Genome Evolution Laboratory, The National University of Ireland Maynooth, Maynooth, County Kildare, Ireland aut Journal of Molecular Evolution Springer-Verlag 73/3-4(2011-10-01), 116-133 0022-2844 73:3-4<116 2011 73 239 https://doi.org/10.1007/s00239-011-9461-4 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s00239-011-9461-4 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Medina Edgar Mycology and Phytopathology Laboratory, Universidad de Los Andes, Bogotá, Colombia aut NATIONALLICENCE 700 1- Jones Gary Department of Biology, Yeast Genetics Laboratory, The National University of Ireland Maynooth, Maynooth, County Kildare, Ireland aut NATIONALLICENCE 700 1- Fitzpatrick David Department of Biology, Genome Evolution Laboratory, The National University of Ireland Maynooth, Maynooth, County Kildare, Ireland aut NATIONALLICENCE 773 0- Journal of Molecular Evolution Springer-Verlag 73/3-4(2011-10-01), 116-133 0022-2844 73:3-4<116 2011 73 239 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer