Abstract
Fungi in the class Leotiomycetes are ecologically diverse, including mycorrhizas, endophytes of roots and leaves, plant pathogens, aquatic and aero-aquatic hyphomycetes, mammalian pathogens, and saprobes. These fungi are commonly detected in cultures from diseased tissue and from environmental DNA extracts. The identification of specimens from such character-poor samples increasingly relies on DNA sequencing. However, the current classification of Leotiomycetes is still largely based on morphologically defined taxa, especially at higher taxonomic levels. Consequently, the formal Leotiomycetes classification is frequently poorly congruent with the relationships suggested by DNA sequencing studies. Previous class-wide phylogenies of Leotiomycetes have been based on ribosomal DNA markers, with most of the published multi-gene studies being focussed on particular genera or families. In this paper we collate data available from specimens representing both sexual and asexual morphs from across the genetic breadth of the class, with a focus on generic type species, to present a phylogeny based on up to 15 concatenated genes across 279 specimens. Included in the dataset are genes that were extracted from 72 of the genomes available for the class, including 10 new genomes released with this study. To test the statistical support for the deepest branches in the phylogeny, an additional phylogeny based on 3156 genes from 51 selected genomes is also presented. To fill some of the taxonomic gaps in the 15-gene phylogeny, we further present an ITS gene tree, particularly targeting ex-type specimens of generic type species. A small number of novel taxa are proposed: Marthamycetales ord. nov., and Drepanopezizaceae and Mniaeciaceae fams. nov. The formal taxonomic changes are limited in part because of the ad hoc nature of taxon and specimen selection, based purely on the availability of data. The phylogeny constitutes a framework for enabling future taxonomically targeted studies using deliberate specimen selection. Such studies will ideally include designation of epitypes for the type species of those genera for which DNA is not able to be extracted from the original type specimen, and consideration of morphological characters whenever genetically defined clades are recognized as formal taxa within a classification.
Highlights
The class Leotiomycetes was erected when the superclass Leotiomyceta was split into seven classes by Eriksson and Winka (1997)
Three sets of phylogenetic analyses were undertaken, one based on several thousand genes that were selected from 51 genomes, including the 10 new Leotiomycetes genomes released here; a second based on up to 15 genes for a set of specimens selected to represent as widely as possible the genetic diversity across the class Leotiomycetes as understood from current ribosomal DNA (rDNA)-based class-wide phylogenies (e.g. Wang et al 2007) and to include taxa known from both asexual and sexual morphs (e.g. Baschien et al 2013); and a third, based on Ribosomal DNA internal transcribed spacer region (ITS) sequences alone, which includes many taxa that were not represented in the other more data-rich analyses
Gene selection The genes targeted for the 15-gene analysis were the ribosomal genes (SSU, 5.8S, Ribosomal DNA large subunit region (LSU)), and genes commonly used in recent multi-gene studies that include Leotiomycetes — β-tubulin, Elongation factor 1-alpha gene (EF1a), Minichromosome maintenance complex component 7 gene (MCM7), Mitochondrial small subunit gene (mtSSU), DNA-directed RNA polymerase II subunit 1 gene (RPB1) and DNA-directed RNA polymerase II subunit (RPB2) (e.g. Baral et al 2009; Chen et al 2016; Crous et al 2014; Han et al 2014; Hosoya et al 2010, 2011; Hustad and Miller 2011; Iturriaga et al 2017; Lorch et al 2013; Malloch et al 2016; Pärtel et al 2017; Sanoamuang et al 2013; Schoch et al 2009; Spatafora et al 2006; Zhao et al 2012)
Summary
The class Leotiomycetes was erected when the superclass Leotiomyceta was split into seven classes by Eriksson and Winka (1997). No recent estimates of the diversity of the entire Leotiomycetes have been made, but Hawksworth (2001) provided estimates for Erysiphales (10,000 spp.), a moderately well-studied order of Leotiomycetes, and Helotiales (70,000 spp.), a poorly studied order. Using these numbers as rough guides, we can expect a minimum of 80,000 species for the class. The class comprises non-lichenized ascomycetes, with those species that form a sexual morph historically referred to as “inoperculate discomycetes” They are characterized by the production of an open ascoma (apothecium) and unitunicate asci generally opening by a pore (Eriksson 2005). These include vascular pathogens such as Cadophora, Phialocephala and Collophorina (Gams 2000; Damm et al 2010; Day et al 2012), the aquatic hyphomycetes (Baschien et al 2013), mycorrhizal species, and root-inhabiting dark septate endophytes (Grünig et al 2011)
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