Names of fungal species with the same epithet applied to different morphs: how to treat them

The abolition of the separate naming of different morphs of the same fungal species in 2011 will inevitably result in many name changes in some genera. The working practices commended here are intended to minimize one category of these changes, that which can arise as a consequence of an author using the epithet of an asexual morph when describing the sexual morph of the same species. We consider that name proposed for the sexual morph in such cases should be treated as a formal error for a new combination and not as a new species, and so be corrected. This is interpreted as applying even where the author indicated that a new species was being described and designated a type. We argue that those formalities were a result of the requirements of the rules then in force, as the author recognized that a morph of a named species was being described, and not a new hitherto unnamed species was being reported - but was barred from making a new combination so used the same epithet for the new morph name instead. Where a type with the sexual morph was designated for the sexual morph, under this interpretation that no longer has nomenclatural status, the type being that of the basionym. The material for the sexual morph indicated as a type, would be available for designation as an epitype, though a modern sequenced sample with both sexual and asexual morphs would be more informative as an epitype in many cases. A proposal to regularize the working practice commended here, and also the converse situation where the sexual morph typified name is the earlier, will be made to the 2017 Shenzhen Congress

Ophiostoma gemellus and Sporothrix variecibatus from mites infesting Protea infructescences in South Africa

Ophiostoma (Ophiostomatales) represents a large genus of fungi mainly known from associations with bark beetles (Curculionidae: Scolytinae) infesting conifers in the northern hemisphere. Few southern hemisphere native species are known, and the five species that consistently occur in the infructescences of Protea spp. in South Africa are ecologically unusual. Little is known about the vectors of Ophiostoma spp. from Protea infructescences, however recent studies have considered the possible role of insects and mites in the distribution of these exceptional fungi. In this study we describe a new species of Ophiostoma and a new Sporothrix spp. with affinities to Ophiostoma, both initially isolated from mites associated with Protea spp. They are described as Ophiostoma gemellus sp. nov. and Sporothrix variecibatus sp. nov. based on their morphology and comparisons of DNA sequence data of the 28S ribosomal, ß-tubulin and internal transcribed spacer (ITS1, 5.8S, ITS2) regions. DNA sequences of S. variecibatus were identical to those of a Sporothrix isolate obtained from Eucalyptus leaf litter in the same area in which S. variecibatus occurs in Protea infructescences. Results of this study add evidence to the view that mites are the vectors of Ophiostoma spp. that colonize Protea infructescences. They also show that DNA sequence comparisons are likely to reveal additional cryptic species of Ophiostoma in this unusual niche

Two new Ophiostoma species from Protea caffra in Zambia

The genus Ophiostoma (Ophiostomatales) has a global distribution and species are best known for their association with bark beetles (Curculionidae: Scolytinae) on conifers. An unusual assemblage of these fungi is closely associated with the African endemic plant genus Protea (Proteaceae). Protea-associated Ophiostoma species are ecologically atypical as they colonise the fruiting structures of various serotinous Protea species. Seven species have been described from this niche in South Africa. It has been speculated that novel species may be present in other African countries where these host plants also occur. This view was corroborated by recent collections of two unknown species from Protea caffra trees in Zambia. In the present study we evaluate the species delineation of these isolates using morphological comparisons with other Protea-associated species, differential growth studies and analyses of DNA sequence data for the β-tubulin and internal transcribed spacer (ITS1, 5.8S, ITS2) regions. As a result, the species O. protea-sedis sp. nov., and O. zambiensis sp. nov. are described here as new. This study brings the number of Protea-associated Ophiostoma species to nine and highlights the need for more inclusive surveys, including additional African countries and hosts, to elucidate species diversity in this uncharacteristic niche

Ophiostoma spp. associated with pine- and spruce-infesting bark beetles in Finland and Russia

The timber and pulp industries of Finland rely heavily on importations from Russia as source of raw timber. These imports raise the risk of accidentally importing forest pests and pathogens, especially bark beetles and their associated fungi, into Finland. Although ophiostomatoid fungi have previously been reported from Finland and Russia, the risks of accidentally moving these fungi has prompted a first survey to compare the diversity of conifer-infesting bark beetles and associated fungi from boreal forests on both sides of the Finnish-Russian border. The aim of the present study was to identify and characterise Ophiostoma species isolated in association with 11 bark beetle species infesting Pinus sylvestris and Picea abies during this survey in the eastern parts of Finland and neighbouring Russia. Fungal isolates were grouped based on morphology and representatives of each morphological group were subjected to DNA sequence comparisons of the internal transcribed spaced region (ITS1, 5.8S, ITS2) and β-tubulin gene region. A total of 15 species of Ophiostoma were identified, including seven known species, five new species, and three species for which the identity remains uncertain. In the O. piceae-complex we identified O. canum, O. floccosum, O. karelicum and O. rachisporum sp. nov., and related to these, some isolates belonging to the European clade of O. minus in the O. minus-complex. Ophiostoma bicolor and O. fuscum sp. nov. were identified in the O. ips-complex, while O. ainoae, O. brunneo-ciliatum, O. tapionis sp. nov. and O. pallidulum sp. nov. were shown to group close to, but not in a strict monophyletic lineage with species of the O. ips-complex. Together with a single O. abietinum-like isolate, the only species that grouped close to the Sporothrix schenckii- O. stenoceras complex, was O. saponiodorum sp. nov

Finding needles in haystacks: Linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Reannotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.B.R. and C.L.S. acknowledge support from the Intramural Research Program of the National Institutes of Health, National Library of MedicinePeer Reviewe

Phylogenomic analysis of a 55.1 kb 19-gene dataset resolves a monophyletic Fusarium that includes the Fusarium solani Species Complex

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user¿s needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option availabl

Three new Graphium species from baobab trees in South Africa and Madagascar

Australia has efficient and visible plant quarantine measures, which through various border controls and survey activities attempt to prevent the entry of unwanted pests and diseases. The ability to successfully perform this task relies heavily on determining what pathogens are present and established in Australia as well as those pathogens that are exotic and threatening. There are detailed checklists and databases of fungal plant pathogens in Australia, compiled, in part, from surveys over many years sponsored by Federal and State programmes. These checklists and databases are mostly specimen-based, which enables validation of records with reference herbarium specimens and sometimes associated cultures. Most of the identifications have been based on morphological examination. The use of molecular methods, particularly the analysis of DNA sequence data, has recently shown that several well-known and important plant pathogenic species are actually complexes of cryptic species. We provide examples of this in the important plant pathogenic genera Botryosphaeria and its anamorphs, Colletotrichum, Fusarium, Phomopsis / Diaporthe and Mycosphaerella and its anamorphs. The discovery of these cryptic species indicates that many of the fungal names in checklists need scrutiny. It is difficult, and often impossible, to extract DNA for sequence analysis from herbarium specimens in order to validate identifications that may now be considered suspect. This validation can only be done if specimens are recollected, re-isolated and subjected to DNA analysis. Where possible, herbarium specimens as well as living cultures are needed to support records. Accurate knowledge of the plant pathogens within Australia’s borders is an essential prerequisite for the effective discharge of plant quarantine activities that will prevent or delay the arrival of unwanted plant pathogens