PROJECT INFORMATION
GOLD Project ID
Gp0442586  
Project Name
Haloferax mediterranei R-4  
Other Names
  
Legacy GOLD ID
  
NCBI BioProject Name Haloferax mediterranei R-4 genome sequencing
NCBI BioProject Accession PRJNA412908
NCBI Locus Tag
  
NCBI BioSample Accession SAMN11356524
PI
Added By JGI automated process on 2019-08-14
Last Modified By
Project Comments
  
Project Status
incomplete  
Project Relevance Evolution
Sequencing Center University of Maryland (USA)
Collaborating Institute
  
Funding Agency
  
Project Description
Haloferax mediterranei R-4 genome sequencing  
Is JGI Project
No  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
JGI Data Utilization Status
  
JGI Award DOI
Genome Publications
  
Other Publications
  
Ignored Publications
  
Unassigned Publications Genome research 8(11):1131-41 Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome?

Saline systems HaloWeb: the haloarchaeal genomes database.

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Experientia 49(6-7):482-6 Identification and analysis of the gas vesicle gene cluster on an unstable plasmid of Halobacterium halobium.

Microbiol Resour Announc sp. Strain JOR-1, an Extremely Halophilic Archaeon from the Dead Sea.

Gene 102(1):117-22 Structure and organization of the gas vesicle gene cluster on the Halobacterium halobium plasmid pNRC100.

Microbiol Resour Announc 10(34):e0061921 Complete Genome and Methylome Analysis of the Box-Shaped Halophilic Archaeon Haloarcula sinaiiensis ATCC 33800.

Proceedings of the National Academy of Sciences of the United States of America Genome sequence of Halobacterium species NRC-1.

Microbiol Resour Announc Species, Haloarcula marismortui and Haloferax mediterranei.

Microbiol Resour Announc Genome Sequence and Methylation Pattern of Haloterrigena salifodinae BOL5-1, an Extremely Halophilic Archaeon from a Bolivian Salt Mine.

Extremophiles 24(1):31-41 Extremophilic models for astrobiology: haloarchaeal survival strategies and pigments for remote sensing.

Gene 119(1):131-6 Genetic transformation of a halophilic archaebacterium with a gas vesicle gene cluster restores its ability to float.

Journal of bacteriology 175(3):684-92 The rightward gas vesicle operon in Halobacterium plasmid pNRC100: identification of the gvpA and gvpC gene products by use of antibody probes and genetic analysis of the region downstream of gvpC.

Plasmid 65(2):77-101 The information transfer system of halophilic archaea.

Proceedings of the National Academy of Sciences of the United States of America 114(47):12530-12535 Key amino acid residues conferring enhanced enzyme activity at cold temperatures in an Antarctic polyextremophilic β-galactosidase.

Journal of bacteriology 175(15):4584-96 Minimal replication origin of the 200-kilobase Halobacterium plasmid pNRC100.

Molecular microbiology 1(3):365-70 A plasmid-encoded gas vesicle protein gene in a halophilic archaebacterium.

Saline systems On the origin of prokaryotic "species": the taxonomy of halophilic Archaea.

BMC genomics The core and unique proteins of haloarchaea.

Standards in genomic sciences 11(1):70 Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34.

Microbiol Resour Announc 10(28):e0052021 sp. GSL-19.

Microbiol Resour Announc 10(48):e0104521 sp. Strain BOL4-2, Isolated and Cultured from Salar de Uyuni, Bolivia.

Microbiol Resour Announc sp. Strain BOL3-1, the First Haloarchaeon Isolated and Cultured from Salar de Uyuni, Bolivia.

Proceedings of the National Academy of Sciences of the United States of America 85(18):6861-5 High-frequency mutations in a plasmid-encoded gas vesicle gene in Halobacterium halobium.

Microbiol Resour Announc Genome Sequences and Methylation Patterns of Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, Two Extremely Halophilic Archaea from a Bolivian Salt Mine.

BMC biotechnology Cloning, overexpression, purification, and characterization of a polyextremophilic β-galactosidase from the Antarctic haloarchaeon Halorubrum lacusprofundi.

Biochim. Biophys. Acta 505(3-4):215-78 Bacteriorhodopsin and the purple membrane of halobacteria.

Astrobiology 18(4):412-418 An Antarctic Extreme Halophile and Its Polyextremophilic Enzyme: Effects of Perchlorate Salts.

Journal of bacteriology 173(12):3933 Structure of the gas vesicle plasmid in Halobacterium halobium inversion isomers, inverted repeats, and insertion sequences.

PloS one 8(3):e58587 Amino acid substitutions in cold-adapted proteins from Halorubrum lacusprofundi, an extremely halophilic microbe from antarctica.

Nucleic acids research 17(19):7785-93 Analysis of insertion mutants reveals two new genes in the pNRC100 gas vesicle gene cluster of Halobacterium halobium.

Journal of bacteriology 176(24):7646-52 Wild-type gas vesicle formation requires at least ten genes in the gvp gene cluster of Halobacterium halobium plasmid pNRC100.

SRA Experiment
 
SRA Experiment Id SRX5765065  (Link to NCBI )
Experiment Title SMRTHmeBP
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name HmeBP9_50
Library Layout SINGLE
Library Instrument PAC_BIO_RS_II
 
SRA Experiment Id SRX5765066  (Link to NCBI )
Experiment Title SMRTHme
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Hme
Library Layout SINGLE
Library Instrument PAC_BIO_RS_II
PROJECT COMPOSITION
Study Origin of Prokaryotic Species: Haloarchaeal Genomes Sequencing Project
Organism Haloferax mediterranei R-4
Analysis Projects
  
Number of Analysis Projects (AP) 0
Number of Derived Analyis Projects (DAP)
0  
SEQUENCING INFORMATION
Sequencing Status In progress
Sequencing Quality (MIGS-31)
Finishing Goal
Contamination Screening Input
  
DNA Amplification Method
  
Single Cell Lysis Protocol
  
Single Cell Lysis Approach
  
Sequencing Comments
  
DNA Amplification Kit
  
Sequencing Technology (MIGS-29)
  
Library Method (MIGS-28)
  
Library Layout
  
Library Screening Method
  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0035222
Organism Name
Haloferax mediterranei R-4  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
ARCHAEAL  
Phylogeny
EURYARCHAEOTA-HALOBACTERIA  
Genus
Haloferax  
Genus Synonyms
  
Species
Haloferax mediterranei  
Subspecies
  
Species Synonyms
  
Strain
R-4  
Strain Synonyms
  
Serovar/Cultivar
  
Culture Collection ID
ATCC 33500  
Type Strain
Unknown  
Exemplar DOI
10.1601/ex.279  
Exemplar Name
Haloferax mediterranei  
Taxon DOI
10.1601/tx.311  
Biosafety Level
1  
Organism Comments
set to private during organism consolidation, candidate for deletion  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 523841
NCBI Superkingdom
Archaea  
NCBI Kingdom
  
NCBI Phylum
Euryarchaeota  
NCBI Class
Halobacteria  
NCBI Order
Haloferacales  
NCBI Family
Haloferacaceae  
NCBI Genus
Haloferax  
NCBI Species
Haloferax mediterranei  
ISOLATION CLASSIFICATION
Ecosystem
Environmental  
Ecosystem Category
Aquatic  
Ecosystem Type
Non-marine Saline and Alkaline  
Ecosystem Subtype
Salt crystallizer ponds  
Specific Ecosystem
Unclassified  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID D11107
GENERAL PROPERTIES
Oxygen Requirement
Aerobe  
Cell Shape
Disc-shaped  
Motility
Motile  
Sporulation
  
Temperature Range
Mesophile  
Salinity
Halophile  
pH
  
Cell Diameter
  
Cell Length
  
Color
  
Gram Staining
Gram-  
Biotic Relationships Free living
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements
  
Diseases
  
Known Habitats
  
Metabolisms
  
Phenotypes
  
Energy Sources
  

 

 

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