PROJECT INFORMATION
GOLD Project ID
Gp0102205  
Project Name
Gordonia rubripertincta B-276  
Other Names
  
Legacy ER Project ID
76978  
Legacy GOLD ID
Gi0076978  
NCBI BioProject Name Identification of functional genes by genomic sequencing-based detection of large deletions in Rhodococcus corallinus strain B-276
NCBI BioProject ID 247189
NCBI BioProject Accession PRJDB2535
NCBI Locus Tag
  
NCBI BioSample Accession
PI
Added By JGI automated process on 2014-08-08
Last Modified By
Project Comments
  
Project Status
incomplete  
Project Relevance
  
Sequencing Center University of the Ryukyus
Collaborating Institute
  
Funding Agency
  
Project Description
Bacteria of the genus Rhodococcus (Actinomycetes) have the ability to catabolize various organic compounds and are therefore considered potential genetic resources for applications such as bioremediation. We investigated a next-generation sequencing-based procedure to rapidly identify candidate functional gene(s) from rhodococci on the basis of their frequent genome recombination. The Rhodococcus corallinus strain B-276 and its alkene monooxygenase (AMO) gene cluster were the focus of our investigation. Firstly, 2 types of cultures of the R. corallinus strain B-276 were prepared, one of which was supplied with propene, which requires AMO genes for its assimilation, whereas the other was supplied with glucose as the sole energy source. The latter culture was anticipated to have a lower gene frequency of AMO genes because of their deletion during cultivation. We then conducted whole genome shotgun sequencing of the genomic DNA extracted from both cultures. Next, all sequence data were pooled and assembled into contiguous sequences (contigs). Finally, the abundance of each contig was quantified in order to detect contigs that were highly biased between the 2 cultures. We identified contigs that were overrepresented by 2 orders of magnitude in the AMO-required culture and successfully identified an AMO gene cluster among these contigs. We propose this procedure as an efficient method for the rapid identification of functional genes in rhodococci.  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
Project Information
  
Database
  
Genome Publications
  
Other Publications
  
PROJECT COMPOSITION
Study Identification of functional genes by genomic sequencing-based detection of large deletions in Rhodococcus corallinus strain B-276
Organism Gordonia rubripertincta B-276
Analysis Projects
  
Number of Analysis Projects 0
Number of DAPs
0  
SEQUENCING INFORMATION
Sequencing Status In progress
Sequencing Quality (MIGS-31)
Finishing Goal
  
Sequencing Comments
  
Sequencing Technology (MIGS-29)
  
Library Method (MIGS-28)
  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0102205
Organism Name
Gordonia rubripertincta B-276  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
ACTINOBACTERIA  
Genus
Gordonia  
Genus Synonyms
  
Species
Gordonia rubripertincta  
Subspecies
  
Species Synonyms
  
Strain
B-276  
Strain Synonyms
  
Serovar-Biovar
  
Culture Collection ID
  
Type Strain
Unknown  
Exemplar DOI
  
Exemplar Name
  
Taxon DOI
  
Biosafety Level
  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 36822
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Actinobacteria  
NCBI Class
Actinobacteria  
NCBI Order
Corynebacteriales  
NCBI Family
Gordoniaceae  
NCBI Genus
Gordonia  
NCBI Species
Gordonia rubripertincta  
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
  
Biotic Relationships
  
Symbiotic Physical Interaction
  
Symbiotic Relationship
  
Symbiont Name
  
Symbiont Taxon ID
  
Cell Arrangements
  
Diseases
  
Known Habitats
  
Metabolisms
  
Phenotypes
  
Energy Sources
  

 

 

  You are going to add the following user to your project, biosample and study.

 

Contact Name/Email:

Do you want to continue?

 

 

  You are going to remove permissions for the following user to your project, biosample and study.

 

Contact Name/Email:

Do you want to continue?

 

 

  Changing the SP visibility will also change visibility on the following items:

 

Do you want to continue with this visibility change?

 

 

  Checking that this Sequencing Project can be made private:

 

Do you want to continue with this visibility change?