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The ITS region as a...
The ITS region as a target for characterization of fungal communities using emerging sequencing technologies
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- Nilsson, R. Henrik, 1976 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för växt- och miljövetenskaper,Department of Plant and Environmental Sciences,University of Gothenburg
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- Ryberg, Martin, 1976 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för växt- och miljövetenskaper,Department of Plant and Environmental Sciences,University of Gothenburg
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Abarenkov, Kessy (författare)
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- Sjökvist, Elisabet, 1982 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för växt- och miljövetenskaper,Department of Plant and Environmental Sciences,University of Gothenburg
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- Kristiansson, Erik, 1978 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för matematiska vetenskaper, matematisk statistik,Zoologiska institutionen,Department of Mathematical Sciences, Mathematical Statistics,Department of Zoology,Chalmers tekniska högskola,Chalmers University of Technology,University of Gothenburg
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(creator_code:org_t)
- 2009
- 2009
- Engelska.
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Ingår i: FEMS Microbiology Letters. - 0378-1097 .- 1574-6968. ; 296:1, s. 97-101
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Abstract
Ämnesord
Stäng
- 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.
Ämnesord
- NATURVETENSKAP -- Biologi -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Zoologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Zoology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
- NATURVETENSKAP -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)
Nyckelord
- massively parallel sequencing
- community profiling
- sequence identification
- massively parallel sequencing
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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