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  Comparative Sequence Analysis and Oligonucleotide Probe Design Based on 23S rRNA Genes of Aphaproteobacteria from North Sea Bacterioplankton

Peplies, J., Glöckner, F., Amann, R., & Ludwig, W. (2004). Comparative Sequence Analysis and Oligonucleotide Probe Design Based on 23S rRNA Genes of Aphaproteobacteria from North Sea Bacterioplankton. Systematic and Applied Microbiology, 27, 573-580.

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Datensatz-Permalink: https://hdl.handle.net/21.11116/0000-0001-D1AD-0 Versions-Permalink: https://hdl.handle.net/21.11116/0000-0007-9271-4
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Peplies4.pdf (Verlagsversion), 165KB
 
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 Urheber:
Peplies, J.1, Autor           
Glöckner, F.O.1, Autor           
Amann, R.2, Autor           
Ludwig, W., Autor
Affiliations:
1Microbial Genomics Group, Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481697              
2Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Max Planck Society, ou_2481696              

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 Zusammenfassung: Almost complete 23S rRNA gene sequences were obtained from 11 Alphaproteobacteria isolated from marine surface water of the German Bight. Five of the strains belong to the "marine alpha" group, a phylogenetic cluster which encompasses members of the genus Roseobacter and closely related bacteria. Phylogenetic sequence analysis based on 52 published as well as unpublished complete 23S rDNA sequences from Alphaproteobacteria including the newly obtained was in general consistent with the 16S rRNA gene sequence-derived phylogeny. 16S and 23S rRNA based phylogenies both showed a distinct cluster for strains associated with the "marine alpha" group. The suitability of both markers for the design of oligonucleotide probes targeting selected groups of Alphaproteobacteria was systematically evaluated and compared in silico. Six clusters of sequences covering different phylogenetic levels as well as two strains were selected in a case study. To compensate for the quantitative difference in the two data sets, the 16S rRNA dataset was truncated to sequences with an equivalent in the 23S rRNA data set. Our results show, that the overall number of phylogenetically redundant probes available could be more than doubled by extending probe design to the 23S rRNA. For small clusters of high sequence similarity and single strains, up to 8 times more discriminating binding sites were provided by the 23S rRNA.

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Sprache(n): eng - English
 Datum: 2004-12-01
 Publikationsstatus: Erschienen
 Seiten: 8
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 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: eDoc: 230497
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Titel: Systematic and Applied Microbiology
  Andere : System. Appl. Microbiol.
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: Stuttgart : Urban & Fischer
Seiten: - Band / Heft: 27 Artikelnummer: - Start- / Endseite: 573 - 580 Identifikator: ISSN: 0723-2020
CoNE: https://pure.mpg.de/cone/journals/resource/954928582871