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454 Pyrosequencing ...
454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
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Tedersoo, L. (author)
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- Nilsson, R. Henrik, 1976 (author)
- Gothenburg University,Göteborgs universitet,Institutionen för växt- och miljövetenskaper,Department of Plant and Environmental Sciences
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Abarenkov, Kessy (author)
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Jairus, Teele (author)
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Sadam, Ave (author)
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Saar, Irja (author)
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Bahram, Mohammad (author)
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Bechem, Eneke (author)
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Chuyong, George (author)
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Kõljalg, Urmas (author)
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(creator_code:org_t)
- 2010-07-15
- 2010
- English.
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In: New Phytologist. - : Wiley. - 0028-646X. ; 188:1, s. 291-301
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Abstract
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- Compared with Sanger sequencing-based methods, pyrosequencing provides orders of magnitude more data on the diversity of organisms in their natural habitat, but its technological biases and relative accuracy remain poorly understood. This study compares the performance of pyrosequencing and traditional sequencing for species’ recovery of ectomycorrhizal fungi on root tips in a Cameroonian rain forest and addresses biases related to multi-template PCR and pyrosequencing analyses. Pyrosequencing and the traditional method yielded qualitatively similar results, but there were slight, but significant, differences that affected the taxonomic view of the fungal community. We found that most pyrosequencing singletons were artifactual and contained a strongly elevated proportion of insertions compared with natural intra- and interspecific variation. The alternative primers, DNA extraction methods and PCR replicates strongly influenced the richness and community composition as recovered by pyrosequencing. Pyrosequencing offers a powerful alternative for the identification of ectomycorrhizal fungi in pooled root samples, but requires careful selection of molecular tools. A well-populated backbone database facilitates the detection of biological and technical artifacts. The pyrosequencing pipeline is available at http://unite.ut.ee/454pipeline.tgz.
Subject headings
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (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 -- Biologisk systematik (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Biological Systematics (hsv//eng)
- NATURVETENSKAP -- Geovetenskap och miljövetenskap -- Annan geovetenskap och miljövetenskap (hsv//swe)
- NATURAL SCIENCES -- Earth and Related Environmental Sciences -- Other Earth and Related Environmental Sciences (hsv//eng)
Keyword
- 454 massively parallel pyrosequencing; artifacts; biodiversity; community structure; ectomycorrizal fungi; Korup National Park; PCR bias
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Tedersoo, L.
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Nilsson, R. Henr ...
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Abarenkov, Kessy
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Jairus, Teele
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Sadam, Ave
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Saar, Irja
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show more...
-
Bahram, Mohammad
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Bechem, Eneke
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Chuyong, George
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Kõljalg, Urmas
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show less...
- About the subject
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Ecology
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Bioinformatics a ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Zoology
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Microbiology
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Biological Scien ...
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and Biological Syste ...
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- NATURAL SCIENCES
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NATURAL SCIENCES
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and Earth and Relate ...
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and Other Earth and ...
- Articles in the publication
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New Phytologist
- By the university
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University of Gothenburg