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Stand Genomic Sci. 2013 Dec 15;9(2):334-50. doi: 10.4056/sigs.4448212. eCollection 2013 Dec 20.

Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens.

Author information

1
Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany.
2
Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
3
Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
4
Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
5
Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
6
DOE Joint Genome Institute, Walnut Creek, California, USA.
7
Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA.
8
HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.

Abstract

Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T) possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.

KEYWORDS:

Anaerobic; Rhodobacteraceae; Rhodobacterales; motile; rod-shaped; secondary metabolites; tropodithietic acid

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