Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches

Evaluation of two novel barcodes for species recognition of opportunistic pathogens in Fusarium

(2016) Abdullah M.S. Al-Hatmi et al.   Fungal Biology

Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi

(2016) Hans-Peter Grossart et al.   Fungal Ecology

Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi

(2016) Brian P. Looney et al.   MOLECULAR ECOLOGY

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences

(2016) Vinita Deshpande et al.   MYCOLOGIA

DNA barcoding and taxonomy: dark taxa and dark texts

(2016) Roderic D. M. Page   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)

(2016) Scott Federhen et al.   Standards in Genomic Sciences

Identifying and Naming Plant-Pathogenic Fungi: Past, Present, and Future

(2015) Pedro W. Crous et al.   Annual Review of Phytopathology

Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life

(2015) Bryn T. M. Dentinger et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

How will the ‘molecular revolution’ contribute to biological recording?

(2015) Lori Lawson Handley   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Biodiversity and succession of mycobiota associated to agricultural lignocellulosic waste-based composting

(2015) Juan Antonio López-González et al.   BIORESOURCE TECHNOLOGY

Genomics and the making of yeast biodiversity

(2015) Chris Todd Hittinger et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

High speciation rate at temperate latitudes explains unusual diversity gradients in a clade of ectomycorrhizal fungi

(2015) Santiago Sánchez-Ramírez et al.   EVOLUTION

Rapid identification of clinical members of Fusarium fujikuroi complex using MALDI-TOF MS

(2015) Abdullah MS Al-Hatmi et al.   Future Microbiology

Mycobiome: Approaches to analysis of intestinal fungi

(2015) Jie Tang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database—the quality controlled standard tool for routine identification of human and animal pathogenic fungi

(2015) Laszlo Irinyi et al.   MEDICAL MYCOLOGY

Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi

(2015) Martin Ryberg   MOLECULAR ECOLOGY

Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae (Ascomycota)

(2015) Steven D. Leavitt et al.   MOLECULAR ECOLOGY

Therpb2gene represents a viable alternative molecular marker for the analysis of environmental fungal communities

(2015) Tomáš Větrovský et al.   Molecular Ecology Resources

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

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

(2015) J.B. Stielow et al.   PERSOONIA

Application of the Phylogenetic Species Concept to Wallemia sebi from House Dust and Indoor Air Revealed by Multi-Locus Genealogical Concordance

(2015) Hai D. T. Nguyen et al.   PLoS One

Diversity of Marine-Derived Fungal Cultures Exposed by DNA Barcodes: The Algorithm Matters

(2015) Nikos Andreakis et al.   PLoS One

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform

(2015) Hyun S. Gweon et al.   Methods in Ecology and Evolution

Fungi Identify the Geographic Origin of Dust Samples

(2015) Neal S. Grantham et al.   PLoS One

Molecular Detection of 10 of the Most Unwanted Alien Forest Pathogens in Canada Using Real-Time PCR

(2015) Josyanne Lamarche et al.   PLoS One

Photobiont selectivity leads to ecological tolerance and evolutionary divergence in a polymorphic complex of lichenized fungi

(2014) Lucia Muggia et al.   ANNALS OF BOTANY

Clustering of fungal community internal transcribed spacer sequence data obscures taxonomic diversity

(2014) Naomichi Yamamoto et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular analysis shows that soil fungi from ancient semi-natural woodland exist in sites converted to non-native conifer plantations

(2014) Jethro Johnson et al.   FORESTRY

Use of gene sequence analyses and genome comparisons for yeast systematics

(2014) C. P. Kurtzman   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Rich and cold: diversity, distribution and drivers of fungal communities in patterned-ground ecosystems of the North American Arctic

(2014) I. Timling et al.   MOLECULAR ECOLOGY

Towards the unification of sequence-based classification and sequence-based identification of host-associated microorganisms

(2014) Joshua R. Herr et al.   NEW PHYTOLOGIST

Type material in the NCBI Taxonomy Database

(2014) Scott Federhen   NUCLEIC ACIDS RESEARCH

Endemism and functional convergence across the North American soil mycobiome

(2014) J. M. Talbot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single macrolichen constitutes hundreds of unrecognized species

(2014) R. Lucking et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

Known Knowns, Known Unknowns, Unknown Unknowns and Unknown Knowns in DNA Barcoding: A Comment on Dowton et al.

(2014) Rupert A. Collins et al.   SYSTEMATIC BIOLOGY

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

(2014) C. L. Schoch et al.   Database-The Journal of Biological Databases and Curation

An Illumina metabarcoding pipeline for fungi

(2014) Miklós Bálint et al.   Ecology and Evolution

What’s for dinner? Undescribed species of porcini in a commercial packet

(2014) Bryn T.M. Dentinger et al.   PeerJ

The Genera of Fungi: fixing the application of type species of generic names

(2014) Pedro W. Crous et al.   IMA Fungus

From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

(2013) Andrea Porras-Alfaro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

A three-gene phylogeny of the Mycena pura complex reveals 11 phylogenetic species and shows ITS to be unreliable for species identification

(2013) Christoffer B. Harder et al.   Fungal Biology

The oldest sequenced fungal specimen

(2013) David L. HAWKSWORTH   LICHENOLOGIST

Host plant genus-level diversity is the best predictor of ectomycorrhizal fungal diversity in a Chinese subtropical forest

(2013) Cheng Gao et al.   MOLECULAR ECOLOGY

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

Non-concerted ITS evolution in fungi, as revealed from the important medicinal fungus Ophiocordyceps sinensis

(2013) Yi Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary consequences of putative intra-and interspecific hybridization in agaric fungi

(2013) Karen W. Hughes et al.   MYCOLOGIA

Toward genome-enabled mycology

(2013) David S. Hibbett et al.   MYCOLOGIA

Topographic diversity of fungal and bacterial communities in human skin

(2013) Keisha Findley et al.   NATURE

Fungal systematics: is a new age of enlightenment at hand?

(2013) David S. Hibbett et al.   NATURE REVIEWS MICROBIOLOGY

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Filling Gaps in Biodiversity Knowledge for Macrofungi: Contributions and Assessment of an Herbarium Collection DNA Barcode Sequencing Project

(2013) Todd W. Osmundson et al.   PLoS One

Genomic Treasure Troves: Complete Genome Sequencing of Herbarium and Insect Museum Specimens

(2013) Martijn Staats et al.   PLoS One

A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System

(2013) Sujeevan Ratnasingham et al.   PLoS One

Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi

(2013) Daniel L. Lindner et al.   Ecology and Evolution

BioNames: linking taxonomy, texts, and trees

(2013) Roderic D.M. Page   PeerJ

Miocene divergence, phenotypically cryptic lineages, and contrasting distribution patterns in common lichen-forming fungi (Ascomycota: Parmeliaceae)

(2012) Steven D. Leavitt et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

DNA barcoding as a new tool for food traceability

(2012) Andrea Galimberti et al.   FOOD RESEARCH INTERNATIONAL

Now you see it, now you don’t: The challenge of detecting, monitoring and conserving ectomycorrhizal fungi

(2012) Sietse van der Linde et al.   Fungal Ecology

Comparison of two DNA sequence-based typing schemes for the Fusarium solani Species Complex and proposal of a new consensus method

(2012) Anne Debourgogne et al.   JOURNAL OF MICROBIOLOGICAL METHODS

DNA-based identification of lichen-forming fungi: can publicly available sequence databases aid in lichen diversity inventories of Mount Cameroon (West Africa)?

(2012) Elizabeth Ayuk OROCK et al.   LICHENOLOGIST

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

Evaluating the effects of terrestrial ecosystems, climate and carbon dioxide on weathering over geological time: a global-scale process-based approach

(2012) L. L. Taylor et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transoceanic Dispersal and Subsequent Diversification on Separate Continents Shaped Diversity of the Xanthoparmelia pulla Group (Ascomycota)

(2012) Guillermo Amo de Paz et al.   PLoS One

Differences in Soil Fungal Communities between European Beech (Fagus sylvatica L.) Dominated Forests Are Related to Soil and Understory Vegetation

(2012) Tesfaye Wubet et al.   PLoS One

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hidden Killers: Human Fungal Infections

(2012) G. D. Brown et al.   Science Translational Medicine

The Effect of Geographical Scale of Sampling on DNA Barcoding

(2012) J. Bergsten et al.   SYSTEMATIC BIOLOGY

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

Distribution and drivers of ectomycorrhizal fungal communities across the North American Arctic

(2012) I. Timling et al.   Ecosphere

The Fungi: 1, 2, 3 … 5.1 million species?

(2011) Meredith Blackwell   AMERICAN JOURNAL OF BOTANY

Goodbye morphology? A paradigm shift in the delimitation of species in lichenized fungi

(2011) H. Thorsten Lumbsch et al.   FUNGAL DIVERSITY

An arctic community of symbiotic fungi assembled by long-distance dispersers: phylogenetic diversity of ectomycorrhizal basidiomycetes in Svalbard based on soil and sporocarp DNA

(2011) József Geml et al.   JOURNAL OF BIOGEOGRAPHY

DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer

(2011) GREGG P. ROBIDEAU et al.   Molecular Ecology Resources

Phylogeny and diversity of Japanese truffles (Tuber spp.) inferred from sequences of four nuclear loci

(2011) Akihiko Kinoshita et al.   MYCOLOGIA

Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

(2011) Daniel L. Lindner et al.   MYCOLOGIA

DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context

(2011) Laura J. Kelly et al.   NEW PHYTOLOGIST

Sequencing the fungal tree of life

(2011) F. Martin et al.   NEW PHYTOLOGIST

Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizal fungi from phylum to species level

(2011) Manuela Krüger et al.   NEW PHYTOLOGIST

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Comparing COI and ITS as DNA Barcode Markers for Mushrooms and Allies (Agaricomycotina)

(2011) Bryn T. M. Dentinger et al.   PLoS One

Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi

(2011) A. Rosling et al.   SCIENCE

Global diversity and distribution of arbuscular mycorrhizal fungi

(2011) Stephanie N. Kivlin et al.   SOIL BIOLOGY & BIOCHEMISTRY

Evolutionary informatics: unifying knowledge about the diversity of life

(2011) Cynthia S. Parr et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2011) David S. Hibbett et al.   Fungal Biology Reviews

Three reasons to re-evaluate fungal diversity ‘on Earth and in the ocean’

(2011) David Bass et al.   Fungal Biology Reviews

Current state and perspectives of fungal DNA barcoding and rapid identification procedures

(2010) Dominik Begerow et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

(2010) Kessy Abarenkov et al.   Evolutionary Bioinformatics

Cryptic speciation in Hymenoscyphus albidus

(2010) V. Queloz et al.   FOREST PATHOLOGY

Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections

(2010) K. O'Donnell et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal

(2010) GREGORY M. BONITO et al.   MOLECULAR ECOLOGY

Multilocus species identification and fungal DNA barcoding: insights from blue stain fungal symbionts of the mountain pine beetle

(2010) AMANDA D. ROE et al.   Molecular Ecology Resources

Multiple origins of high reciprocal symbiotic specificity at an intercontinental spatial scale among gelatinous lichens (Collemataceae, Lecanoromycetes)

(2010) Mónica A.G. Otálora et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)

(2010) M. Öpik et al.   NEW PHYTOLOGIST

Not every fungus is everywhere: scaling to the biogeography of fungal-plant interactions across roots, shoots and ecosystems

(2010) Kabir G. Peay et al.   NEW PHYTOLOGIST

Cyber infrastructure for Fusarium: three integrated platforms supporting strain identification, phylogenetics, comparative genomics and knowledge sharing

(2010) B. Park et al.   NUCLEIC ACIDS RESEARCH

Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics

(2010) A. S. Amend et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Progress towards DNA barcoding of fungi

(2009) KEITH A. SEIFERT   Molecular Ecology Resources

Fungal networks made of humans: UNITE, FESIN, and frontiers in fungal ecology

(2009) Thomas D. Bruns et al.   NEW PHYTOLOGIST

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST

General latitudinal gradient of biodiversity is reversed in ectomycorrhizal fungi

(2009) Leho Tedersoo et al.   NEW PHYTOLOGIST

A Phylogenetic Estimation of Trophic Transition Networks for Ascomycetous Fungi: Are Lichens Cradles of Symbiotrophic Fungal Diversification?

(2009) A. Elizabeth Arnold et al.   SYSTEMATIC BIOLOGY

Mining metadata from unidentified ITS sequences in GenBank: A case study in Inocybe (Basidiomycota)

(2008) Martin Ryberg et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts

(2008) Y. Liu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fruiting body and soil rDNA sampling detects complementary assemblage of Agaricomycotina (Basidiomycota, Fungi) in a hemlock-dominated forest plot in southern Ontario

(2008) TERESITA M. PORTER et al.   MOLECULAR ECOLOGY

Evidence for strong inter- and intracontinental phylogeographic structure in Amanita muscaria, a wind-dispersed ectomycorrhizal basidiomycete

(2008) József Geml et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

How to know unknown fungi: the role of a herbarium

(2008) Patrick M. Brock et al.   NEW PHYTOLOGIST