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The ITS region as a target for characterization of fungal communities using emerging sequencing technologies

R. Henrik Nilsson ; Martin Ryberg ; Kessy Abarenkov ; Elisabet Sjökvist ; Erik Kristiansson (Institutionen för matematiska vetenskaper, matematisk statistik ; Zoologiska institutionen)
FEMS Microbiology Letters (03781097). Vol. 296 (2009), 1, p. 97-101.
[Artikel, refereegranskad vetenskaplig]

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.

Nyckelord: massively parallel sequencing, community profiling, sequence identification



Denna post skapades 2009-06-05.
CPL Pubid: 94739

 

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Institutioner (Chalmers)

Institutionen för växt- och miljövetenskaper (2006-2011)
Institutionen för matematiska vetenskaper, matematisk statistik (2005-2016)
Zoologiska institutionen (1954-2011)

Ämnesområden

Molekylärbiologi
Mikrobiologi
Morfologi
Bioinformatik och systembiologi
Biologisk systematik

Chalmers infrastruktur