Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results - a total of 31,954 changes - are incorporated in and made available through the UNITE database for molecular identification of fungi (including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.

Trapelioid fungi constitute a widespread groupof mostly crust-forming lichen mycobionts that are key tounderstanding the early evolutionary splits in theOstropomycetidae, the second-most species-rich subclassof lichenized Ascomycota. The uncertain phylogeneticresolution of the approximately 170 species referred tothis group contributes to a poorly resolved backbone forthe entire subclass. Based on a data set including 657newly generated sequences from four ribosomal and fourprotein-coding gene loci, we tested a series of a priori andnew evolutionary hypotheses regarding the relationshipsof trapelioid clades within Ostropomycetidae. We foundstrong support for a monophyletic group of nine coretrapelioid genera but no statistical support to reject thelong-standing hypothesis that trapelioid genera are sisterto Baeomycetaceae or Hymeneliaceae. However, we canreject a sister group relationship to Ostropales with highconfidence. Our data also shed light on several longstandingquestions, recovering Anamylopsoraceae nestedwithin Baeomycetaceae, elucidating two major monophyleticgroups within trapelioids (recognized here asTrapeliaceae and Xylographaceae), and rejecting themonophyly of the genus Rimularia. We transfer elevenspecies of the latter genus to Lambiella and describe thegenus Parainoa to accommodate a previously misunderstoodspecies of Trapeliopsis. Past phylogenetic studies inOstropomycetidae have invoked Bdivergence order^ fordrawing taxonomic conclusions on higher level taxa.Our data show that if backbone support is lacking, contrastingsolutions may be recovered with different oradded data. We accordingly urge caution in concludingevolutionary relationships from unresolved phylogenies.

The phylogeny of the Acarosporaceae (Lecanoromycetes, Acarosporomycetidae, Acarosporales) is investigated using data from three molecular markers; nuclear ITS-LSU rDNA, mitochondrial SSU and β-tubulin. Acarosporaceae is shown to be constituted by six main clades; Myriospora, Timdalia, Pleopsidium, a clade composed by Acarospora rhizobola and A. terricola, the poorly supported Sarcogyne clade (including several Polysporina and Acarospora species) and the Acarospora clade (including the type of Polysporina, P. simplex, and several other Polysporina species). The common ancestor of the Acarosporaceae did not produce strongly black pigmented (carbonized or melanized) ascomata, but this trait has arisen secondarily and independently numerous times in the evolution of the group. The number of changes in character states of both carbonized epihymenium and carbonized exciple are considerably more than the minimum number. The genera Sarcogyne and Polysporina—largely circumscribed based on the presence of black pigmented ascomata—are shown to be distinctly non-monophyletic. The presence of green algae in the ascoma margin (lecanorine or lecideine ascomata) may vary even within single species.