Evaluating the potential of 18S rDNA clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information
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 relati...
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ftawi:oai:epic.awi.de:34189 2023-05-15T15:07:08+02:00 Evaluating the potential of 18S rDNA clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information Wolf, Christian Kilias, Estelle Silvia Metfies, Katja 2014-04-22 application/pdf https://epic.awi.de/id/eprint/34189/ https://epic.awi.de/id/eprint/34189/1/Wolf_et_al_2014_Clone_vs_454.pdf https://hdl.handle.net/10013/epic.43597 https://hdl.handle.net/10013/epic.43597.d001 unknown TAYLOR & FRANCIS AS https://epic.awi.de/id/eprint/34189/1/Wolf_et_al_2014_Clone_vs_454.pdf https://hdl.handle.net/10013/epic.43597.d001 Wolf, C. , Kilias, E. S. and Metfies, K. orcid:0000-0003-3073-8033 (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 <https://doi.org/10.1080/17451000.2013.852685> , hdl:10013/epic.43597 EPIC3Marine Biology Research, TAYLOR & FRANCIS AS, 10(8), pp. 771-780, ISSN: 1745-1000 Article isiRev 2014 ftawi https://doi.org/10.1080/17451000.2013.852685 2021-12-24T15:39:04Z 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. Article in Journal/Newspaper Arctic Southern Ocean Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) Arctic Southern Ocean Marine Biology Research 10 8 771 780 |
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Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) |
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ftawi |
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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. |
format |
Article in Journal/Newspaper |
author |
Wolf, Christian Kilias, Estelle Silvia Metfies, Katja |
spellingShingle |
Wolf, Christian Kilias, Estelle Silvia Metfies, Katja Evaluating the potential of 18S rDNA clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information |
author_facet |
Wolf, Christian Kilias, Estelle Silvia Metfies, Katja |
author_sort |
Wolf, Christian |
title |
Evaluating the potential of 18S rDNA clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information |
title_short |
Evaluating the potential of 18S rDNA clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information |
title_full |
Evaluating the potential of 18S rDNA clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information |
title_fullStr |
Evaluating the potential of 18S rDNA clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information |
title_full_unstemmed |
Evaluating the potential of 18S rDNA clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information |
title_sort |
evaluating the potential of 18s rdna clone libraries to complement pyrosequencing data of marine protists with near full-length sequence information |
publisher |
TAYLOR & FRANCIS AS |
publishDate |
2014 |
url |
https://epic.awi.de/id/eprint/34189/ https://epic.awi.de/id/eprint/34189/1/Wolf_et_al_2014_Clone_vs_454.pdf https://hdl.handle.net/10013/epic.43597 https://hdl.handle.net/10013/epic.43597.d001 |
geographic |
Arctic Southern Ocean |
geographic_facet |
Arctic Southern Ocean |
genre |
Arctic Southern Ocean |
genre_facet |
Arctic Southern Ocean |
op_source |
EPIC3Marine Biology Research, TAYLOR & FRANCIS AS, 10(8), pp. 771-780, ISSN: 1745-1000 |
op_relation |
https://epic.awi.de/id/eprint/34189/1/Wolf_et_al_2014_Clone_vs_454.pdf https://hdl.handle.net/10013/epic.43597.d001 Wolf, C. , Kilias, E. S. and Metfies, K. orcid:0000-0003-3073-8033 (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 <https://doi.org/10.1080/17451000.2013.852685> , hdl:10013/epic.43597 |
op_doi |
https://doi.org/10.1080/17451000.2013.852685 |
container_title |
Marine Biology Research |
container_volume |
10 |
container_issue |
8 |
container_start_page |
771 |
op_container_end_page |
780 |
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1766338704207511552 |