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rdf:type |
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lifeskim:mentions |
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pubmed:dateCreated |
2009-11-17
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pubmed:abstractText |
Recent advances in sequencing strategies make possible unprecedented depth and scale of sampling for molecular detection of microbial diversity. Two major paradigm-shifting discoveries include the detection of bacterial diversity that is one to two orders of magnitude greater than previous estimates, and the discovery of an exciting 'rare biosphere' of molecular signatures ('species') of poorly understood ecological significance. We applied a high-throughput parallel tag sequencing (454 sequencing) protocol adopted for eukaryotes to investigate protistan community complexity in two contrasting anoxic marine ecosystems (Framvaren Fjord, Norway; Cariaco deep-sea basin, Venezuela). Both sampling sites have previously been scrutinized for protistan diversity by traditional clone library construction and Sanger sequencing. By comparing these clone library data with 454 amplicon library data, we assess the efficiency of high-throughput tag sequencing strategies. We here present a novel, highly conservative bioinformatic analysis pipeline for the processing of large tag sequence data sets.
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pubmed:commentsCorrections |
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:issn |
1741-7007
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:volume |
7
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
72
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pubmed:dateRevised |
2010-9-27
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pubmed:meshHeading |
pubmed-meshheading:19886985-Animals,
pubmed-meshheading:19886985-Bacteria, Anaerobic,
pubmed-meshheading:19886985-Biodiversity,
pubmed-meshheading:19886985-Ciliophora,
pubmed-meshheading:19886985-Classification,
pubmed-meshheading:19886985-DNA, Bacterial,
pubmed-meshheading:19886985-Eukaryota,
pubmed-meshheading:19886985-Seawater,
pubmed-meshheading:19886985-Sequence Analysis, DNA,
pubmed-meshheading:19886985-Sequence Tagged Sites
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pubmed:year |
2009
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pubmed:articleTitle |
Massively parallel tag sequencing reveals the complexity of anaerobic marine protistan communities.
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pubmed:affiliation |
Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany. stoeck@rhrk.uni-kl.de
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pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, Non-P.H.S.
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