I. the origin of species by means of natural selection

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

http://web.stanford.edu/~kpeay/papers/Koljalg_2013_MEC.pdf

Towards a unified paradigm for sequence-based identification of fungi

https://cbs.umn.edu/sites/cbs.umn.edu/files/public/downloads/Nguyenetal2015b.pdf

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

Summary 1 Summary All plants in natural ecosystems appear to be symbiotic with fungal endophytes. This highly diverse group of fungi can have profound impacts on plant communities through increasing fitness by conferring abiotic and biotic stress tolerance, increasing biomass and decreasing water consumption, or decreasing fitness by altering resource allocation. Despite more than 100 yr of research resulting in thousands of journal articles, the ecological significance of these fungi remains poorly characterized. Historically, two endophytic groups (clavicipitaceous (C) and nonclavicipitaceous (NC)) have been discriminated based on phylogeny and life history traits. Here, we show that NC-endophytes represent three distinct functional groups based on host colonization and transmission, in planta biodiversity and fitness benefits conferred to hosts. Using this framework, we contrast the life histories, interactions with hosts and potential roles in plant ecophysiology of C- and NC-endophytes, and highlight several key questions for future work in endophyte biology.

https://courses.washington.edu/cfr523/documents/2009TansleyReview.pdf

Fungal endophytes: diversity and functional roles.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-8137.2009.03160.x

The UNITE database for molecular identification of fungi - recent updates and future perspectives

Vertinoid Polyketides from the Saltwater Culture of the Fungus Trichoderma longibrachiatum Separated from a Haliclona Marine Sponge.

Hypocrea brevipes, H. poronioidea and H. capitata, a new species, were grown in pure culture from individual part-ascospores. Each produced a Trichoderma anamorph, but none of the anamorphs were re...

Three species of Hypocrea with stipitate stromata and Trichoderma anamorphs

Helminthosphaeria, a genus of pyrenomy- cetes, is monographed. Its members occur on basi- diomata of species of the Aphyllophorales. The fol- lowing species are included: H. clavariarum, the type, H. odontiae, H. corticiorum, and the new species H. hyphodermiae. A new family, Helminthosphaeriaceae, is proposed for the genus. Litschaueria is found to be a synonym of Helminthosphaeria.

/pdf/fungicolous-pyrenomycetes-1-helminthosphaeria-and-the-new-stiqhxejbm.pdf

Fungicolous pyrenomycetes 1. Helminthosphaeria and the new family Helminthosphaeriaceae.

The aphyllophoricolous species of Hypo- myces that have pallid, KOH-negative perithecia and Cladobotryum anamorphs form the biggest subset within the genus. Twelve holomorphic members and one asexual member of this group that occur in tem- perate regions of the northern hemisphere are dis- cussed. Several new European collections are report- ed for H. albidus, H. orthosporus, H. polyporinus and H. semitranslucens. Hypomyces pseudopolyporinus, H. sympodiophorus and H. viridigriseus are presented from Europe for the first time. Two new species, H. corticiicola and H. rostratus, are described from Eu- rope. Cladobotryum stereicola, for which no teleo- morph is known, is not the anamorph of H. sympo- diophorus, as has been reported. The new combina- tion Cladobotryum uniseptatum is proposed for the anamorph of H. sympodiophorus. A previously un- known Cladobotryum anamorph is found associated with the teleomorph of H. tegillum in herbarium ma- terial from Central and South America. Hypomyces si- birinae, previously known only from its type location in Indonesia, is reported from North America. The role of anamorphic vs. teleomorphic characters and the use of ascospore measurements in delimitation of species and identification of specimens is discussed in the group of KOH- aphyllophoricolous Hypomyces.

Gary J. Samuels

Papers

Vertinoid Polyketides from the Saltwater Culture of the Fungus Trichoderma longibrachiatum Separated from a Haliclona Marine Sponge.

Three species of Hypocrea with stipitate stromata and Trichoderma anamorphs

Fungicolous pyrenomycetes 1. Helminthosphaeria and the new family Helminthosphaeriaceae.

Aphyllophoricolous species of Hypomyces with KOH-negative perithecia

Revision of Schizoparme (Diaporthales, Melanconidaceae)