Phylogenomics of Fungi: Nuclearia is the deepest fungal divergence.
Emma Steenkamp (1), Yu Liu (2), B. Franz Lang (3)
(1) Department of Microbiology and Plant Pathology, University of Pretoria, Pretoria, 0001, South Africa; (2) Biochimie, Universite de Montreal, 2900, E. Montpetit, Montreal, H3C 3J7, Canada; (3) Canadian Institute for Advanced Research, Centre Robert Cedergren, Départment de Biochemie, Université de Montréal, 2900 Boulevard Edouard Montpetit, Montréal, Québec, H3T 1J4, Canada
It is now widely accepted that fungi and animals (grouped together in the supertaxon Opisthokonta) have a common evolutionary origin. Even so, little is known about protist species that branch close to the fungal-animal divergence. Phylogenomic studies have shown that Choanoflagellata and Ichthyosporea share origins with animals, but other candidates examined such as the flagellate Apusomonas, and amoeboids like Nuclearia and Capsaspora, have not yet been placed with significant support. Previous phylogenetic studies including these species were based on single or small numbers of gene sequences, which invariably produced alternative phylogenetic scenarios that could not be rejected in statistical tests. To overcome these limitations, we have sequenced several thousands ESTs from the protist Nuclearia simplex. We also work on the complete sequence of the mitochondrial DNA (mtDNA) of this bacterivorous protist, in order to obtain a second, independent dataset for phylogenetic inferences. Analyses of the EST dataset generate well-resolved phylogenies with significant statistical support, unequivocally placing Nuclearia at the base of the fungal branch. Nuclearia thus represents the only known protistan sistertaxon of Fungi. These findings suggest that similar approaches will reveal the definitive phylogenetic affinities of other enigmatic protists such as Apusomonas and Capsaspora.