title: Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales.
abstract: Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5' end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our understanding of the ecological modes associated with particular clades, and provides a first estimation of their phylogenetic relationships in the Eurotiomycetes.
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA. Electronic address: ko.hsuan.chen@duke.edu.
authors.forename: Ko-Hsuan
authors.initials: KH
authors.lastname: Chen
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Jolanta
authors.initials: J
authors.lastname: Miadlikowska
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Katalin
authors.initials: K
authors.lastname: Molnár
authors.affiliation: School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: A Elizabeth
authors.initials: AE
authors.lastname: Arnold
authors.affiliation: School of Plant Sciences and Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Jana M
authors.initials: JM
authors.lastname: U'Ren
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: Ester
authors.initials: E
authors.lastname: Gaya
authors.affiliation: Australia National Herbarium, CSIRO, GPO Box 1600, Canberra, ACT 2601, Australia.
authors.forename: Cécile
authors.initials: C
authors.lastname: Gueidan
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708, USA.
authors.forename: François
authors.initials: F
authors.lastname: Lutzoni
mesh_terms: D001203:Ascomycota / Q000145:classification* / Q000235:genetics; D001499:Bayes Theorem; D005075:Biological Evolution; D004271:DNA, Fungal / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D060026:Endophytes / Q000145:classification*; D008011:Lichens / Q000382:microbiology; D016013:Likelihood Functions; D010641:Phenotype; D010802:Phylogeny; D010944:Plants / Q000382:microbiology; D054683:Ribosome Subunits, Large, Eukaryotic / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer
keywords: Cumulative supermatrix approach; Eurotiomycetes; Fungal endophytes; Lichens; Phaeomoniella; Phaeomoniellales ord. nov.