PROJECT INFORMATION
GOLD Project ID
Gp0025985  
Project Name
Chitinophagaceae bacterium JGI 0001013-J17  
Other Names
  
Legacy ER Project ID
29580  
Legacy GOLD ID
Gi22082  
NCBI BioProject Name Chitinophagaceae bacterium JGI 0001013-J17
NCBI BioProject ID 183557
NCBI BioProject Accession PRJNA183557
NCBI Locus Tag
G081  
NCBI BioSample Accession SAMN02441087
PI Susannah Tringe
Added By JGI automated process on 2012-09-25
Last Modified By JGI automated process on 2018-10-08
Project Comments
  
Project Status
Permanent Draft  
Project Relevance
  
Sequencing Center DOE Joint Genome Institute (JGI) (USA)
Collaborating Institute
  
Funding Agency U.S. Department of Energy (DOE) (USA)
Project Description
Rhizosphere Grand Challenge Single Cell Sequencing. The goal of this project is to comprehensively characterize the genomes of microorganisms found in the rhizosphere and endosphere of Arabidopsis thaliana. Organisms for study have been targeted based on their reproducible association with one or more Arabidopsis genotypes grown in natural soil. To obtain genomes from both culturable and unculturable fractions of the Arabidopsis microbiome, rhizosphere and endosphere samples were disaggregated and individual cells sorted by flow cytometry and amplified by MDA, then microbes of interest were identified by 16S rRNA sequencing and their whole genomes sequenced. Genomic sequences will be analyzed for genes participating in the plant-microbe symbiosis.  
Is JGI Project
Yes  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
JGI Portal Download Raw Sequence Data
Project Information
  
Database
  
Genome Publications
  
Other Publications
  
SRA Experiment
  
PROJECT COMPOSITION
Study Rhizosphere Grand Challenge Single Cell Sequencing
Organism Chitinophagaceae bacterium JGI 0001013-J17
Analysis Projects Combined assembly of Chitinophagaceae endophytes JGI 0001054
Chitinophagaceae bacterium JGI 0001013-J17 (unscreened)
Number of Analysis Projects 2
Number of DAPs
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31) Level 1: Standard Draft
Finishing Goal Level 1: Standard Draft
Sequencing Comments
  
Sequencing Technology (MIGS-29) Illumina HiSeq 2500
Illumina HiSeq 2000
Library Method (MIGS-28)
Illumina Regular Fragment, 300bp, Plates  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
39  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0025985
Organism Name
Chitinophagaceae bacterium JGI 0001013-J17  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
BACTEROIDETES  
Genus
  
Genus Synonyms
  
Species
Chitinophagaceae bacterium JGI 0001013-J17  
Subspecies
  
Species Synonyms
  
Strain
JGI 0001013-J17  
Strain Synonyms
  
Serovar/Cultivar
  
Culture Collection ID
  
Type Strain
Unknown  
Exemplar DOI
  
Exemplar Name
  
Taxon DOI
  
Biosafety Level
  
Organism Comments
  
Cultured
No  
Culture Type
  
Organism Type
Natural  
Uncultured Type
Single Cell  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 1268323
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Bacteroidetes  
NCBI Class
Chitinophagia  
NCBI Order
Chitinophagales  
NCBI Family
Chitinophagaceae  
NCBI Genus
  
NCBI Species
Chitinophagaceae bacterium JGI 0001013-J17  
ISOLATION CLASSIFICATION
Ecosystem
  
Ecosystem Category
  
Ecosystem Type
  
Ecosystem Subtype
  
Specific Ecosystem
  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID
GENERAL PROPERTIES
Oxygen Requirement
  
Cell Shape
  
Motility
  
Sporulation
  
Temperature Range
  
Temperature Optimum
  
Salinity
  
pH
  
Cell Diameter
  
Cell Length
  
Color
  
Gram Staining
Gram-  
Biotic Relationships
  
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements
  
Diseases
  
Known Habitats
  
Metabolisms
  
Phenotypes
  
Energy Sources
  

 

 

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