The genus Hebeloma in the alpine belt of the Carpathians including two new species

Between 2002 and 2012 regular visits to the Carpathians were made and a number of Hebeloma spp. were collected from the alpine area. In total 44 collections were made that represent 11 species, two of which, Hebeloma grandisporum and H oreophilum, are described here as new. Of the 11 species, four (H alpinum, H marginatulum and the two species described as new) are known only from alpine or Arctic habitats. Hebeloma dunense and H mesophaeum are commonly found in, but not restricted to, alpine habitats. The other five species (H aanenii, H laterinum, H naviculosparum, H vaccinum, H velutipes) are usually found in lowland or boreal habitats. Hebeloma naviculosporum is reported for the first time from the alpine zone and H alpinum for the first time as growing with Helianthemum. All but two species (H alpinum, H marginatulum) are reported for the first time from the Carpathian alpine zone. In this paper we discuss the habitat, the 11 recorded species and give detailed descriptions of the two new species, both morphologically and molecularly. A key for Hebeloma species from sect. Hebeloma occurring in Arctic-alpine habitats is provided

A multi-gene phylogeny of Lactifluus (Basidiomycota, Russulales) translated into a new infrageneric classification of the genus

Infrageneric relations of the genetically diverse milkcap genus Lactifluus (Russulales, Basidiomycota) are poorly known. Currently used classification systems still largely reflect the traditional, mainly morphological, characters used for infrageneric delimitations of milkcaps. Increased sampling, combined with small-scale molecular studies, show that this genus is underexplored and in need of revision. For this study, we assembled an extensive dataset of the genus Lactifluus, comprising 80 % of all known species and 30 % of the type collections. To unravel the infrageneric relationships within this genus, we combined a multi-gene molecular phylogeny, based on nuclear ITS, LSU, RPB2 and RPB1, with a morphological study, focussing on five important characteristics (fruit body type, presence of a secondary velum, colour reaction of the latex/context, pileipellis type and presence of true cystidia). Lactifluus comprises four supported subgenera, each containing several supported clades. With extensive sampling, ten new clades and at least 17 new species were discovered, which highlight the high diversity in this genus. The traditional infrageneric classification is only partly maintained and nomenclatural changes are proposed. Our morphological study shows that the five featured characteristics are important at different evolutionary levels, but further characteristics need to be studied to find morphological support for each clade. This study paves the way for a more detailed investigation of biogeographical history and character evolution within Lactifluus

Fibre caps across Europe: type studies and 11 new species of Inocybe (Agaricales, Basidiomycota)

Based on detailed morphological and genetic investigation, 11 new species of Inocybe (I. abdita, I. alcis, I. carissima, I. cryptica, I. culicis, I. mecoana, I. mortenii, I. orioli, I. rangiferi, I. sepiana and I. turfae) are described. Six of the new species are smooth-spored and five are nodulose-spored. The new species are compared to 18 type specimens, all of which are described here and for seven of which (partial) ITS sequences have been generated. For six species, namely I. griseovelata, I. lacera, I. soluta, I. subcarpta, I. tarda and I. transitoria, a lectotype, epitype or neotype was selected, and a description and a figure plate are provided for each of them. Based on our studies, we are convinced that I. albofibrillosa and I. striatorimosa are synonymous with I. soluta, while I. aurantioumbonata is synonymous with I. tarda. Furthermore, we affirm that I. longicystis is synonymous with I. stellatospora. All of the new species are supported by phylogenetic analyses. In summary, we here describe as new, verify the taxonomic status of, or provide or corroborate morphological concepts for 29 species of Inocybe. alpha taxonomy, epitypification, Inocybaceae, Inocybe, molecular systematics, neotypification nrITS, nrLSU, RPB2, type studies.Fibre caps across Europe: type studies and 11 new species of Inocybe (Agaricales, Basidiomycota)publishedVersio

The UniProt-GO Annotation database in 2011

The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data se

One fungus, which genes?: development and assessment of universal primers for potential secondary fungal DNA barcodes

The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1-D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial beta-tubulin II (TUB2); iv) gamma-actin (ACT); v) translation elongation factor 1-alpha (TEF1 alpha); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5-6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1 alpha. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1 alpha, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail

The Amsterdam Declaration on Fungal Nomenclature

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19–20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented

A new species of <I>Hericium</I> from Sikkim Himalaya (India)

Hericium bharengense is described as new to science from subtropical to temperate forests in the West district of Sikkim. The intricate hymenophoral branching pattern, presence of moderately long spines, size and ornamentation pattern of basidiospores separate it from the allied species H. abietis, H. coralloides and H. erinaceus. Its phylogenetic position within the genus Hericium is supported by rDNA sequences in the ITS gene region. Macro- and micromorphological characters are described and illustrated; its relations to other allied species are discussed.</p