The ITS region as a target for characterization of fungal communities using emerging sequencing technologies
Artikel i vetenskaplig tidskrift, 2009

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.

massively parallel sequencing

community profiling

sequence identification

Författare

R. Henrik Nilsson

Göteborgs universitet

Martin Ryberg

Göteborgs universitet

Kessy Abarenkov

Elisabet Sjökvist

Göteborgs universitet

Erik Kristiansson

Chalmers, Matematiska vetenskaper, matematisk statistik

Göteborgs universitet

FEMS Microbiology Letters

0378-1097 (ISSN)

Vol. 296 1 97-101

Ämneskategorier

Biologisk systematik

Biokemi och molekylärbiologi

Mikrobiologi

Bioinformatik och systembiologi

Zoologi