Evidence map›Paper›PMID 24501652›Full record

ArticleStandards in genomic sciences2013

Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis.

Marco Dogs, Hazuki Teshima, Jörn Petersen, Anne Fiebig, Olga Chertkov, Hajnalka Dalingault, Amy Chen, Amrita Pati, Lynne A Goodwin, Patrick Chain and 11 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Standards in genomic sciences, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

21 authors.

Marco DogsInstitute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany .
Hazuki TeshimaLos Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Jörn PetersenLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Anne FiebigLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Olga ChertkovLos Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Hajnalka DalingaultLos Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Amy ChenBiological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Amrita PatiDOE Joint Genome Institute, Walnut Creek, California, USA.
Lynne A GoodwinLos Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA.
Patrick ChainDOE Joint Genome Institute, Walnut Creek, California, USA.
John C DetterLos Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA.
Natalia IvanovaDOE Joint Genome Institute, Walnut Creek, California, USA.
Alla LapidusDOE Joint Genome Institute, Walnut Creek, California, USA.
Manfred RohdeHZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.
Sabine GronowLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Nikos C KyrpidesDOE Joint Genome Institute, Walnut Creek, California, USA.
Tanja WoykeDOE Joint Genome Institute, Walnut Creek, California, USA.
Meinhard SimonInstitute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany .
Markus GökerLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Hans-Peter KlenkLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Thorsten BrinkhoffInstitute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany .

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

TF-218(T) is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218(T) contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218(T) possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.

Indexed as

facultative anaerobeindigoidineMarine microbiologyRhodobacteraceaeRoseobacter clade

Identifiers

PMID24501652
PMCPMC3910554

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