The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
Systematic Biology (Impact Factor: 14.39). 04/2009; 58(2):224-39. DOI: 10.1093/sysbio/syp020
Source: PubMed


We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

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    • "Within Chaetothyriomycetidae, four orders (Celotheliales ad int., Chaetothyriales, Pyrenulales, and Verrucariales) and seven families (Chaetothyriaceae, Celotheliaceae, Cyphellophoraceae, Herpotrichiellaceae, Pyrenulaceae (including Requienellaceae), Trichomeriaceae, and Verrucariaceae) were represented, although our taxon sampling focused mostly on the poorly delimited order Chaetothyriales (56 taxa). Sequences for these taxa were produced in various studies (e.g., Del Prado et al. 2006; Crous et al. 2007; Little and Currie 2007; Gueidan et al. 2008; Mayer and Volgmayr 2009; Schoch et al. 2009; Damm et al. 2010; Rossman et al. 2010; Stenroos et al. 2010; Voglmayr et al. 2011; Chomnunti et al. 2012a, b) and made available in GenBank (Table 1). Four gene regions were used as phylogenetic markers: the small (nuSSU) and the large (nuLSU) subunits of the nuclear ribosomal RNA gene, the small subunit Table 1 Taxon and gene sampling used for this study. "
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    ABSTRACT: The subclass Chaetothyriomycetidae (Eurotiomycetes, Ascomycota) is an assemblage of ecologically diverse species, ranging from mutualistic lichenised fungi to human opportunistic pathogens. Recent contributions from molecular studies have changed our understanding of the composition of this subclass. Among others, ant-associated fungi, deep-sea fungi and bryophilous fungi were also shown to belong to this group of ascomycetes. The delimitation of orders and families within this subclass has not previously been re-assessed using a broad phylogenetic study and the phylogenetic position of some taxa such as the lichenised family Celotheliaceae or the Chaetothyrialean bryophilous fungi is still unclear. In our study, we assemble new and published sequences from 132 taxa and reconstruct phylogenetic relationships using four markers (nuLSU, nuSSU, mtSSU and RPB1). Results highlight several shortfalls in the current classification of this subclass, mainly due to un-assigned paraphyletic taxa. The family Epibryaceae is therefore described to circumscribe a previously un-assigned lineage. Celotheliales ad int. is suggested for the lineage including the lichen genus Celothelium and various plant pathogens. The delimitation of the family Trichomeriaceae is also broadened to include the genus Knufia and some anamorphic taxa. As defined here, Chaetothyriomycetidae includes four orders (Celotheliales ad int., Chaetothyriales, Pyrenulales, and Verrucariales) and ten families (Adelococcaceae, Celotheliaceae, Chaetothyriaceae, Cyphellophoraceae, Epibryaceae fam. nov., Herpotrichiellaceae, Pyrenulaceae, Requienellaceae, Trichomeriaceae, and Verrucariaceae).
    Mycological Progress 11/2014; 13(4). DOI:10.1007/s11557-014-0990-2 · 1.91 Impact Factor
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    • "In phylogenetic studies, the need to study several loci in order to improve reliability and resolution power of phylogenies is widely recognized [9], [10], therefore several alternative marker genes have been proposed in this context also for the Glomeromycota. The largest subunit of RNA polymerase II (RPB1) gene stood out for several reasons: it has several variable regions useful for species discrimination; according to present knowledge it is a single-copy gene in fungi, avoiding problems with paralogues. "
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    PLoS ONE 10/2014; 9(10). DOI:10.1371/journal.pone.0107783 · 3.23 Impact Factor
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    • "Other orders of Ascomycota that were frequent in this study (e.g. the Microascales and Hypocreales) are generally known as wood-inhabiting or soil-borne saprotrophs and An investigation of thermophilic fungi in composts 141 plant pathogens (Moore et al. 2011). They are highly versatile, able to utilise a wide range of carbon sources and are often reported to be efficient cellulolytic organisms (Webster & Weber, 2007; Schoch et al. 2009). The Basidiomycota do not seem to be as abundant in the composts that we studied as they are in soils, in which next-generation sequencing studies of fungal communities have revealed this group to be frequent (Buee et al. 2009; Lim et al. 2010). "
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    ABSTRACT: In this study, the biodiversity of thermophilous fungi in two different commercial composts was investigated using culture-based methods, denaturing gradient gel electrophoresis (DGGE) and tag-encoded pyrosequencing. 454 pyrosequencing of the internal transcribed spacer (ITS) region recovered a total of 175 OTUs between the two composts. The Ascomycota was the dominant phylum in both composts (90 % of all sequences recovered) with the thermophilic-rich orders Sordariales and Eurotiales being the most numerous. Molecular studies demonstrated the frequent presence of several thermophilic (Scytalidium thermophilum, Myriococcum thermophilum) and thermotolerant (Pseudallescheria boydii, Corynascus verrucosus and Coprinopsis sp.) fungi in the composts, despite the absence of these species from the culture-based analysis. Conversely, Aspergillus fumigatus and Mycocladus corymbifer, which were the dominant species in cultivation analyses, had very low representation in molecular studies. The results show that the previous picture of the dominant thermophilous fungi in compost communities derived from culture-based analysis has been biased, and that composting environments represent a potentially rich resource of novel fungi.
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