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Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21T)

Journal Article · · Standards in Genomic Sciences
DOI:https://doi.org/10.4056/sigs.2114901· OSTI ID:1630577
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  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  6. Helmholtz Centre for Infection Research, Braunschweig (Germany)
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Davis, CA (United States)
  8. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of Queensland, Brisbane, QLD (Australia)
+ Show Author Affiliations
Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum 'Chloroflexi'. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large number of over-represented COGs, particularly genes associated with transposons, causing the genetic redundancy within the genome being considerably larger than expected by chance. This work is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
German Research Foundation (DFG); USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC02-05CH11231; AC05-00OR22725; AC52-07NA27344
OSTI ID:
1630577
Alternate ID(s):
OSTI ID: 1049893
Journal Information:
Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 1 Vol. 5; ISSN 1944-3277
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

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Analysis of microbial communities in heavy metals-contaminated soils using the metagenomic approach journal September 2018
The potential for microbial life in the highest-elevation (>6000 m.a.s.l.) mineral soils of the Atacama region: LIFE ABOVE 6000 METERS journal June 2012
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life journal June 2017
Why prokaryotes have pangenomes journal March 2017
Genome-based classification of micromonosporae with a focus on their biotechnological and ecological potential journal January 2018
Chitosan degradation and associated changes in bacterial community structures in two contrasting soils journal January 2015
PVCbase: an integrated web resource for the PVC bacterial proteomes journal January 2018
Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system journal June 2013
Linking microbial communities to ecosystem functions: what we can learn from genotype–phenotype mapping in organisms journal March 2020
Description of Thermogemmatispora carboxidivorans sp. nov., a carbon-monoxide-oxidizing member of the class Ktedonobacteria isolated from a geothermally heated biofilm, and analysis of carbon monoxide oxidation by members of the class Ktedonobacteria journal April 2014
Thermosporothrix narukonensis sp. nov., belonging to the class Ktedonobacteria, isolated from fallen leaves on geothermal soil, and emended description of the genus Thermosporothrix journal June 2016
Dictyobacter vulcani sp. nov., belonging to the class Ktedonobacteria, isolated from soil of the Mt Zao volcano journal March 2020
Draft Genome Sequence of Thermogemmatispora onikobensis NBRC 111776 T , an Aerial Mycelium- and Spore-Forming Thermophilic Bacterium Belonging to the Class Ktedonobacteria journal October 2016
Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305T), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae journal January 2014
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling journal January 2013
Geochemical and Metagenomic Characterization of Jinata Onsen, a Proterozoic-Analog Hot Spring, Reveals Novel Microbial Diversity including Iron-Tolerant Phototrophs and Thermophilic Lithotrophs journal January 2019
Novel LanT Associated Lantibiotic Clusters Identified by Genome Database Mining journal March 2014
Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica journal March 2015
Genome Features and Secondary Metabolites Biosynthetic Potential of the Class Ktedonobacteria journal April 2019
Microbial Communities of Polymetallic Deposits’ Acidic Ecosystems of Continental Climatic Zone With High Temperature Contrasts journal July 2019
Effect of the environment on horizontal gene transfer between bacteria and archaea journal January 2017

Figures / Tables (13)

Figure 1(p. 4)figure Figure 1
Figures 2a and 2b(p. 4)figure Figures 2a and 2b
Table 1(p. 5)table Table 1
Table 2(p. 6)table Table 2
Figure 3(p. 7)figure Figure 3
Table 3(p. 7)table Table 3
Table 4(p. 8)table Table 4
Figure 4(p. 9)figure Figure 4
Figure 5(p. 10)figure Figure 5
Figure 6(p. 11)figure Figure 6
Table 5(p. 11)table Table 5
Figure 7(p. 12)figure Figure 7
Figure 8(p. 13)figure Figure 8

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Chloroflexi
GEBA
Gram-positive
Ktedonobacteraceae
aerobic
broken-stick distribution
entropy
filamentous
heterotrophic
moderately acidophilic
non-motile
sporulating
transposon