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.

• Ecogenome
• fungal classification
• fungi
• identification
• ITS

Acknowledgments

Development of the DOE SFA ITS training set was supported by the US Department of Energy, Office of Science, Biological and Environmental Research Division through a Science Focus Area grant to CRK ( 2009LANLF260). The RDP is supported by the Office of Science (Biological and Environmental Research), US Department of Energy ( DE-FG02-99ER62848, DE-SC0010715 and DE-FC02-07ER64494). The initial development of the Warcup training set was supported by the CSIRO office of the chief executive through an OCE honors scholarship awarded to Vinita Deshpande.

We thank Kessy Abarenkov for providing the UNITE dataset.