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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Yilmaz, Pelin Kottmann, Renzo Pruesse, Elmar Quast, Christian Glöckner, Frank Oliver |
| Spatial Coverage | Atlantic Ocean Pacific Ocean |
| Description | Country affiliation: Germany Author Affiliation: Yilmaz P ( Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359 Bremen, Germany.) |
| Abstract | As an evolutionary marker, 23S ribosomal RNA (rRNA) offers more diagnostic sequence stretches and greater sequence variation than 16S rRNA. However, 23S rRNA is still not as widely used. Based on 80 metagenome samples from the Global Ocean Sampling (GOS) Expedition, the usefulness and taxonomic resolution of 23S rRNA were compared to those of 16S rRNA. Since 23S rRNA is approximately twice as large as 16S rRNA, twice as many 23S rRNA gene fragments were retrieved from the GOS reads than 16S rRNA gene fragments, with 23S rRNA gene fragments being generally about 100bp longer. Datasets for 16S and 23S rRNA sequences revealed similar relative abundances for major marine bacterial and archaeal taxa. However, 16S rRNA sequences had a better taxonomic resolution due to their significantly larger reference database. Reevaluation of the specificity of previously published PCR amplification primers and group specific fluorescence in situ hybridization probes on this metagenomic set of non-amplified 23S rRNA sequences revealed that out of 16 primers investigated, only two had more than 90% target group coverage. Evaluations of two probes, BET42a and GAM42a, were in accordance with previous evaluations, with a discrepancy in the target group coverage of the GAM42a probe when evaluated against the GOS metagenomic dataset. |
| File Format | HTM / HTML |
| ISSN | 07232020 |
| Issue Number | 6 |
| Volume Number | 34 |
| e-ISSN | 16180984 |
| Journal | Systematic and Applied Microbiology |
| Language | English |
| Publisher | Elsevier |
| Publisher Date | 2011-09-01 |
| Publisher Place | Germany |
| Access Restriction | One Nation One Subscription (ONOS) |
| Subject Keyword | Discipline Microbiology Aquatic Organisms Classification Metagenome Genetics Rna, Ribosomal, 23s Analysis Seawater Microbiology Atlantic Ocean Base Sequence Oceans And Seas Pacific Ocean Phylogeny Rna, Ribosomal, 16s Chemistry Journal Article Research Support, Non-u.s. Gov't |
| Content Type | Text |
| Resource Type | Article |
| Subject | Ecology, Evolution, Behavior and Systematics Microbiology Applied Microbiology and Biotechnology |
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