Editor: Jan Dijksterhuis
The ITS region as a target for characterization of fungal communities using emerging sequencing technologies
Article first published online: 1 MAY 2009
© 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved
FEMS Microbiology Letters
Volume 296, Issue 1, pages 97–101, July 2009
How to Cite
Nilsson, R. H., Ryberg, M., Abarenkov, K., Sjökvist, E. and Kristiansson, E. (2009), The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. FEMS Microbiology Letters, 296: 97–101. doi: 10.1111/j.1574-6968.2009.01618.x
- Issue published online: 1 JUN 2009
- Article first published online: 1 MAY 2009
- Received 13 December 2008; accepted 7 April 2009.Final version published online 1 May 2009.
- massively parallel sequencing;
- community profiling;
- sequence identification
The advent of new high-throughput DNA-sequencing technologies promises to redefine the way in which fungi and fungal communities – as well as other groups of organisms – are studied in their natural environment. With read lengths of some few hundred base pairs, massively parallel sequencing (pyrosequencing) stands out among the new technologies as the most apt for large-scale species identification in environmental samples. Although parallel pyrosequencing can generate hundreds of thousands of sequences at an exceptional speed, the limited length of the reads may pose a problem to the species identification process. This study explores whether the discrepancy in read length between parallel pyrosequencing and traditional (Sanger) sequencing will have an impact on the perceived taxonomic affiliation of the underlying species. Based on all 39 200 publicly available fungal environmental DNA sequences representing the nuclear ribosomal internal transcribed spacer (ITS) region, the results show that the two approaches give rise to quite different views of the diversity of the underlying samples. Standardization of which subregion from the ITS region should be sequenced, as well as a recognition that the composition of fungal communities as depicted through different sequencing methods need not be directly comparable, appear crucial to the integration of the new sequencing technologies with current mycological praxis.