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

http://www.ascofrance.fr/uploads/forum_file/1-s2.0-S0953756209804097-main-0001.pdf

Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences

Genera of Bionectriaceae, Hypocreaceae and Nectriaceae (Hypocreales, Ascomycetes)

https://repository.si.edu/bitstream/handle/10088/12054/stri_Mejia_et_al_including_Van_Bael_2008.pdf?sequence=1

Endophytic fungi as biocontrol agents of Theobroma cacao pathogens

Trichoderma: a review of biology and systematics of the genus

Trichoderma aggressivum sp. nov. and T. aggressivum f. europaeum f. nov. are described. These forms cause the green mold epidemic in commercially grown Agaricus bisporus in North America and Europe, respectively. In the literature they have been reported as T. harzianum biotypes Th 4 and Th 2, respectively. They are strongly separated from their closest relative, T. harzianum, in sequences of the ITS-1 region of nuclear rDNA and an approximately 689 bp fragment of the protein coding translation elongation factor gene (EF-1α). They are distinguished from the morphologically similar T. harzianum and T. atroviride (the latter also known as biotype Th 3) most readily by rate of growth. Of these, only T. harzianum grows well and sporulates at 35 C, while T. atroviride is the slowest growing. Trichoderma aggressivum f. aggressivum and f. europaeum are effectively indistinguishable morphologically although they have subtly different growth rates at 25 C on SNA and statistically significant micromorphological differences. Based on findings of this study, descriptions of T. harzianum and T. atroviride are expanded. A key to Trichoderma species commonly found associated with commercially grown A. bisporus is provided.

Gary J. Samuels

Papers

Taxonomy and phylogeny of Gliocladium analysed from nuclear large subunit ribosomal DNA sequences

Genera of Bionectriaceae, Hypocreaceae and Nectriaceae (Hypocreales, Ascomycetes)

Endophytic fungi as biocontrol agents of Theobroma cacao pathogens

Trichoderma: a review of biology and systematics of the genus

Trichoderma species associated with the green mold epidemic of commercially grown Agaricus bisporus.