Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences

By D. Hibbett, Anders W. Ohman, Dylan Glotzer, Mitchell Nuhn, P. Kirk, R. Henrik Nilsson. 2011

356 citations recorded by the source corpus.

Subfields: Cell Biology, Ecology, Evolution, Behavior and Systematics, Plant Science

View Paper: https://www.semanticscholar.org/paper/3afd4786c4a9a682e5a232351b985a9d57860a2a

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Citations in the corpus

Phylogeny and taxonomy of meristematic rock-inhabiting black fungi in the Dothideomycetes based on multi-locus phylogenies (2014, background): “Recently, the nuclear ribosomal internal transcribed spacer (ITS) region was designated the official barcode for fungi (Schoch et al. 2012) since it has a long history of use as a molecular marker for species-level identification in ecological and taxonomic studies of fungi (Hibbett et al. 2011).”
New primers to amplify the fungal ITS2 region--evaluation by 454-sequencing of artificial and natural communities. (2012, background): “Sequencing of environmental samples indicates that a significant fraction of fungal diversity remains to be discovered and described (Hibbett et al., 2011), and by relying on primers that were developed based on limited information on primer site variation, there is a risk that important novel branc”
Top 50 most wanted fungi (2016, neutral): “100,000 formally described species (Hibbett et al. 2011).”
Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. (2012, methodology): “As a result, most sampling sites and habitats host a much greater fungal diversity than the above-ground view offered by fruiting bodies would lead the observer to believe (Porter et al. 2008; Hibbett et al. 2011).”
Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizal fungi from phylum to species level. (2012, background): “Standardized MOTUs are a goal for the classification of unknown fungal species from environmental samples (Hibbett et al., 2011), but care has to be taken that the units indeed are based on coherent taxonomic levels (Hawksworth et al., 2011).”
Synthesis of phylogeny and taxonomy into a comprehensive tree of life (2014, background): “Metagenomic studies routinely reveal numerous OTUs that cannot be assigned to named species (37, 38).”
High-Coverage ITS Primers for the DNA-Based Identification of Ascomycetes and Basidiomycetes in Environmental Samples (2012, background): “Some fungi-specific primers such as ITS1-F and ITS4-B are widely used in DNA barcoding of various environmental samples (reviewed in [23]), although their low coverage of fungal taxa is expected to preclude comprehensive analyses of fungal diversity and community structures [39] (Table 3, Fig.”
Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data (2013, background): “1 5% of the estimated 1 5 million species of fungi (Hibbett et al. 2011), and the public fungal ITS sequences come in very different degrees of coverage of the region (Nilsson et al.”
A first comprehensive census of fungi in soil reveals both hyperdiversity and fine-scale niche partitioning (2014, background): “Many taxonomically described fungi have no corresponding molecular barcode sequence available (Hibbett et al. 2011).”
Improving ITS sequence data for identification of plant pathogenic fungi (2014, background): “Similarly, more than half of all public fungal ITS sequences are not annotated to the level of species, and most of these carry little or no taxonomic annotation save, e.g., “Uncultured fungus” (cf. Hibbett et al. 2011).”
Towards a unified paradigm for sequence‐based identification of fungi (2013, background): “The nuclear ribosomal internal transcribed spacer (ITS) region has a long history of use as a molecular marker for species-level identification in ecological and taxonomic studies of fungi (Hibbett et al. 2011).”