title: Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences.
abstract: Fungi are key organisms in many ecological processes and communities. Rapid and low cost surveys of the fungal members of a community can be undertaken by isolating and sequencing a taxonomically informative genomic region, such as the ITS (internal transcribed spacer), from DNA extracted from a metagenomic sample, and then classifying these sequences to determine which organisms are present. This paper announces the availability of the Warcup ITS training set and shows how it can be used with the Ribosomal Database Project (RDP) Bayesian Classifier to rapidly and accurately identify fungi using ITS sequences. The classifications can be down to species level and use conventional literature-based mycological nomenclature and taxonomic assignments.
authors.affiliation: School of Information Technologies, University of Sydney, Sydney, New South Wales, 2006, Australia.
authors.forename: Vinita
authors.initials: V
authors.lastname: Deshpande
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48823.
authors.forename: Qiong
authors.initials: Q
authors.lastname: Wang
authors.affiliation: CSIRO, North Ryde, New South Wales, 2113, Australia.
authors.forename: Paul
authors.initials: P
authors.lastname: Greenfield
authors.affiliation: School of Physical Sciences, University of Tasmania, Sandy Bay, Tasmania, 7005; School of Information Technologies, University of Sydney, Sydney, New South Wales, 2006, Australia.
authors.forename: Michael
authors.initials: M
authors.lastname: Charleston
authors.affiliation: Department of Biological Sciences, Western Illinois University, Macomb, Illinois 61455.
authors.forename: Andrea
authors.initials: A
authors.lastname: Porras-Alfaro
authors.affiliation: Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545.
authors.forename: Cheryl R
authors.initials: CR
authors.lastname: Kuske
authors.affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 48823.
authors.forename: James R
authors.initials: JR
authors.lastname: Cole
authors.affiliation: CSIRO, North Ryde, New South Wales, 2113, Australia.
authors.forename: David J
authors.initials: DJ
authors.lastname: Midgley
authors.affiliation: CSIRO, North Ryde, New South Wales, 2113, Australia nai.tran-dinh@csiro.au.
authors.forename: Nai
authors.initials: N
authors.lastname: Tran-Dinh
mesh_terms: D001499:Bayes Theorem; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000737:chemistry / Q000235:genetics; D066264:Datasets as Topic; D005658:Fungi / Q000145:classification* / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer
keywords: Ecogenome; ITS; fungal classification; fungi; identification