Evaluating the potential of 18S rDNA clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information


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Christian.Wolf [ at ] awi.de

Abstract

Sequencing of 18S rDNA clone libraries and 454-pyrosequencing are valuable methods used to describe microbial diversity. The massively parallel 454-pyrosequencing generates vast amounts of ribosomal sequence data and has the potential to uncover more organisms, even rare species. However, the relatively short sequence lengths of ~500 bp are suboptimal for taxonomic annotation and phylogenetic analyses. In this study, we assessed the potential of 18S ribosomal clone libraries to complement corresponding 454-pyrosequencing data with near full-length sequence information. This involved a comparison of protist community compositions in five polar samples suggested by 18S rDNA clone libraries with the corresponding community compositions suggested by 454-pyrosequencing. The study was conducted with four Arctic water samples, focusing on the eukaryotic picoplankton (0.4-3 µm), and with one sample collected in the Southern Ocean, examining the whole size spectrum (>0.4 µm). For all individual samples, the protist community compositions suggested by the two different approaches showed significant similarities. Around 70% of the sequences detected by sequencing of clone libraries were also present in the 454-pyrosequencing data set. However, the clone library sequences reflected only ~20% of the abundant biosphere identified by 454-pyrosequencing and identified ribosomal sequences, that were not detected in the 454-pyrosequencing data sets.



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ISI/Scopus peer-reviewed
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Published
Eprint ID
34189
DOI 10.1080/17451000.2013.852685

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Wolf, C. , Kilias, E. S. and Metfies, K. (2014): Evaluating the potential of 18S rDNA clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information , Marine Biology Research, 10 (8), pp. 771-780 . doi: 10.1080/17451000.2013.852685


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