Additions to Dendrodacrys and outline of taxa with branched hyphidia in Dacrymycetes (Basidiomycota)

The genus Dendrodacrys is a monophyletic group that belongs to Dacrymycetes (Agaricomycotina, Basidiomycota) and accommodates species distinguished by strongly branched hyphidia in combination with 3-septate basidiospores. While the original circumscription mainly treated European taxa, here we shift the focus to tropical and sub-tropical material and uncover wider variation in morphology within Dendrodacrys. Still united by hyphidia shape and basidiospore septation, the genus is expanded with 10 taxa having pustulate, cerebriform, or stipitate basidiocarps of yellow to dark brown colours, cylindrical to ovoid basidiospores, and hyphal septa with or without clamps. Monophyly of the amended Dendrodacrys is confirmed with a phylogeny based on six markers (SSU, ITS, LSU, TEF1-α, RPB1, and RPB2). As a result, we describe two new species (De. laetum and De. rigoratum), transfer three existing species to Dendrodacrys (De. brasiliense, De. dendrocalami, and De. pezizoideum), and raise one variety to the species level (De. kennedyae ≡ Dacrymyces enatus var. macrosporus). In addition, we provide descriptions for the earlier combined De. paraphysatum and four new informal taxa. Lastly, we present illustrations, a character table, and an identification key that addresses all known dacrymycetes with branched hyphidia.Peer reviewe

Red List of Estonian Fungi – 2019 update

In 2019 the conservation status of 214 fungal species in Estonia was assessed according to IUCN criteria and an IUCN category was assigned to each taxon. Altogether 94 species were categorized as threatened (CR, EN, VU), 42 least concern (LC), 60 near threatened (NT), three regionally extinct (RE) and six as data deficient (DD). Changes compared to the previous red list and threats to the species are discussed.   Eesti seente Punane nimestik – 2019. aasta uuendus 2019. aastal hinnati 214 seeneliigi ohustatust Eestis kasutades IUCN kategooriaid ja kriteeriume. Hinnatud liikidest kuulus 94 ohustatuse kategooriatesse CR, EN ja VU, 42 hinnati kui soodsas seisundis (LC), 60 ohulähedased (NT), 3 piirkonnas välja surnud (RE) ja 6 puuduliku andmestikuga (DD). Artikkel käsitleb muudatusi võrreldes eelmise punase nimestikuga ja olulisemate seeneliikide ohutegureid

Towards a unified paradigm for sequence-based identification of fungi

Kõljalg, Urmas et al.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.The North European Forest Mycologists network is acknowledged for support. Urmas Kõljalg and Kessy Abarenkov are supported by the Estonian Research Council grant no 8235.Peer reviewe

Tidying up international nucleotide sequence databases

Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi