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About the Authors:
Todd W. Osmundson
Affiliation: Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
Vincent A. Robert
Affiliation: Centraalbureau voor Schimmelcultures, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands
Conrad L. Schoch
Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
Lydia J. Baker
Affiliation: Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
Amy Smith
Affiliation: Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
Giovanni Robich
Affiliation: Venice Museum of Natural History, Venice, Italy
Luca Mizzan
Affiliation: Venice Museum of Natural History, Venice, Italy
Matteo M. Garbelotto
* E-mail: [email protected]
Affiliation: Forest Pathology and Mycology Laboratory, Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
Introduction
With recent estimates of diversity ranging from approximately 720,000 [1] to over 5.1 million [2] species–of which only approximately 99,000 have been described [3], [4]–the status of Fungi as a poorly known group of organisms is well-established and frequently discussed in the scientific literature [3]. An even larger unknown is the ecology and basic biology of fungal species, both described and undescribed: knowledge of their geographic range, host range, diversity of life cycle stages, and community ecology remains fragmentary.
The ubiquity, high diversity and often cryptic manifestations of fungi frequently necessitate the use of molecular tools for detecting and identifying them in the environment. By far, the most widely used molecular marker for this purpose is the nuclear ribosomal RNA internal transcribed spacer (ITS) region [5], [6]. In recent comparisons, ITS has been demonstrated to outperform other tested markers in terms of overall PCR amplification success, sequencing success, and species resolution for many groups of fungi [5], [7], [8]. In addition, a significant amount of analytical infrastructure, including sequence processing and quality-checking tools as well as curated reference databases, is tailored to this locus [9]–[16]. These features, as well as the momentum provided by the large number of ITS sequences currently in public sequence databases, have led to formal recognition of ITS...