Evidence map›Paper›PMID 25197486›Full record

ArticleStandards in genomic sciences2014

Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring.

Markus Göker, Stefan Spring, Carmen Scheuner, Iain Anderson, Ahmet Zeytun, Matt Nolan, Susan Lucas, Hope Tice, Tijana Glavina Del Rio, Jan-Fang Cheng and 26 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Standards in genomic sciences, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.1field-weighted citation impact, top 44% of its field
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

2 citing papers in PubMed, 8 citations in OpenAlex.

  1. Article
  2. Article
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

36 authors at 8 institutions in 5 countries.

Markus GökerLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Stefan SpringLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Carmen ScheunerLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Iain AndersonDOE Joint Genome Institute, Walnut Creek, California, USA.
Ahmet ZeytunDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Matt NolanDOE Joint Genome Institute, Walnut Creek, California, USA.
Susan LucasDOE Joint Genome Institute, Walnut Creek, California, USA.
Hope TiceDOE Joint Genome Institute, Walnut Creek, California, USA.
Tijana Glavina Del RioDOE Joint Genome Institute, Walnut Creek, California, USA.
Jan-Fang ChengDOE Joint Genome Institute, Walnut Creek, California, USA.
Cliff HanDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Roxanne TapiaDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Lynne A GoodwinDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Sam PitluckDOE Joint Genome Institute, Walnut Creek, California, USA.
Konstantinos LioliosDOE Joint Genome Institute, Walnut Creek, California, USA.
Konstantinos MavromatisDOE Joint Genome Institute, Walnut Creek, California, USA.
Ioanna PaganiDOE Joint Genome Institute, Walnut Creek, California, USA.
Natalia IvanovaDOE Joint Genome Institute, Walnut Creek, California, USA.
Natalia MikhailovaDOE Joint Genome Institute, Walnut Creek, California, USA.
Amrita PatiDOE Joint Genome Institute, Walnut Creek, California, USA.
Amy ChenBiological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Krishna PalaniappanBiological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Miriam LandDOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Loren HauserDOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Yun-Juan ChangDOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Cynthia D JeffriesDOE Joint Genome Institute, Walnut Creek, California, USA ; Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.
Manfred RohdeHZI - Helmholtz Centre for Infection Research, Braunschweig, Germany.
John C DetterDOE Joint Genome Institute, Walnut Creek, California, USA ; Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA.
Tanja WoykeDOE Joint Genome Institute, Walnut Creek, California, USA.
James BristowDOE Joint Genome Institute, Walnut Creek, California, USA.
Jonathan A EisenDOE Joint Genome Institute, Walnut Creek, California, USA ; University of California Davis Genome Center, Davis, California, USA.
Victor MarkowitzBiological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Philip HugenholtzDOE Joint Genome Institute, Walnut Creek, California, USA ; Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia.
Nikos C KyrpidesDOE Joint Genome Institute, Walnut Creek, California, USA ; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
Hans-Peter KlenkLeibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
Alla LapidusTheodosius Dobzhansky Center for Genome Bionformatics, St. Petersburg State University, St. Petersburg, Russia ; Algorithmic Biology Lab, St. Petersburg Academic University, St. Petersburg, Russia.
Joint Genome Institute · USLeibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures · DELawrence Berkeley National Laboratory · USLos Alamos National Laboratory · USOak Ridge National Laboratory · USHelmholtz Centre for Infection Research · DESt Petersburg University · RUUniversity of California, Davis · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3(T) is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Indexed as

anaerobicchemoorganotrophicGEBAmotileouter sheath-like structuresolfataric springthermophilicThermotogaceae

Identifiers

PMID25197486
PMCPMC4148951
OpenAlexW2159892301

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.