PROJECT INFORMATION
GOLD Project ID
Gp0023473  
Project Name
Streptococcus pneumoniae TIGR4  
Other Names
  
Legacy ER Project ID
27920  
Legacy GOLD ID
Gc02396, Gi0027920  
NCBI BioProject Name Streptococcus pneumoniae TIGR4
NCBI BioProject ID 76613
NCBI BioProject Accession PRJNA76613
NCBI Locus Tag
H020  
NCBI BioSample Accession SAMN00103527
PI David B. Jaffe
Added By JGI automated process on 2012-07-30
Last Modified By Supratim Mukherjee on 2017-03-29
Project Comments
  
Project Status
Permanent Draft  
Project Relevance Medical
Sequencing Center Broad Institute (USA)
Collaborating Institute
  
Funding Agency
  
Project Description
To test methods for de novo genome assembly using Illumina and Pacific Biosciences shotgun data, microbial genomes with finished reference sequences were selected. Streptococcus pneumoniae TIGR4 was one of these microbial genomes. At least one Pacific Biosciences library (long fragment) and two Illumina libraries (short fragment and jumping) were generated and sequenced. Genomic DNA from Claudette Thompson. Two different genome assemblies are part of this project. The assembly in AKBW00000000 is the complete chromosome assembled from Illumina reads. The assembly in AKVY00000000 is the complete chromosome assembled from reads used to assemble AE005672 plus reads from a different isolate of the strain.  
Is JGI Project
No  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
Project Information
  
Database
  
Genome Publications Genome research 22(11):2270-7 Finished bacterial genomes from shotgun sequence data.

Other Publications
  
SRA Experiment
 
SRA Experiment Id SRX111079
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-42879' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-42879
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 194
 
SRA Experiment Id SRX111078
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-36223' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-36223
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 210
 
SRA Experiment Id SRX110127
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-63275' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-63275
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 202
 
SRA Experiment Id SRX113241
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Pond-52451' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Pond-52451
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 202
 
SRA Experiment Id SRX109958
Experiment Title Whole Genome Sequencing and Assembly
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name LR_59_Spnuemoniae
Library Layout SINGLE
Library Instrument PAC_BIO_RS
 
SRA Experiment Id SRX110130
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-62928' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-62928
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 202
 
SRA Experiment Id SRX109959
Experiment Title Whole Genome Sequencing and Assembly
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name LR_59_Spneumonaie
Library Layout SINGLE
Library Instrument PAC_BIO_RS
 
SRA Experiment Id SRX105406
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-44969' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-44969
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 194
 
SRA Experiment Id SRX105405
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-60829' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-60829
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 210
 
SRA Experiment Id SRX105404
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-36223' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-36223
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 194
 
SRA Experiment Id SRX105403
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA library 'Pond-52451' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Pond-52451
Library Layout SINGLE
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 109
 
SRA Experiment Id SRX105402
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-36223' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-36223
Library Layout PAIRED
Library Instrument ILLUMINA_GENOME_ANALYZER_II
Spot Length 194
 
SRA Experiment Id SRX105401
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-36223' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-36223
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 194
 
SRA Experiment Id SRX105400
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Pond-52451' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Pond-52451
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 210
 
SRA Experiment Id SRX105399
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Pond-52451' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Pond-52451
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 96
 
SRA Experiment Id SRX110129
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-42879' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-42879
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 202
 
SRA Experiment Id SRX105398
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-42879' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-42879
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 210
 
SRA Experiment Id SRX110128
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-36223' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-36223
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 202
 
SRA Experiment Id SRX105397
Experiment Title Illumina whole genome shotgun sequencing of genomic DNA paired-end library 'Solexa-36223' containing sample M167C-T4
Exp Library Strategy WGS
Library Source GENOMIC
Library Selection RANDOM
Library Name Solexa-36223
Library Layout PAIRED
Library Instrument ILLUMINA_HI_SEQ_2000
Spot Length 210
PROJECT COMPOSITION
Study Streptococcus pneumoniae TIGR4
Organism Streptococcus pneumoniae TIGR4
Analysis Projects Streptococcus pneumoniae TIGR4
Number of Analysis Projects 1
Number of DAPs
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31) Level 3: Improved-High-Quality Draft
Finishing Goal
  
Sequencing Comments
  
Sequencing Technology (MIGS-29) Illumina
PacBio RS
Library Method (MIGS-28)
  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
40  
Chromosome Count
1  
Plasmid Count
0  
ORGANISM NAME
GOLD Organism ID Go0000727
Organism Name
Streptococcus pneumoniae TIGR4  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
FIRMICUTES  
Genus
Streptococcus  
Genus Synonyms
  
Species
Streptococcus pneumoniae  
Subspecies
  
Species Synonyms
  
Strain
TIGR4  
Strain Synonyms
  
Serovar/Cultivar
4  
Culture Collection ID
ATCC BAA-334  
Type Strain
Unknown  
Exemplar DOI
  
Exemplar Name
  
Taxon DOI
  
Biosafety Level
2  
Organism Comments
  
Cultured
Yes  
Culture Type
Isolate  
Organism Type
Natural  
Uncultured Type
  
Commercial Strain
  
Commercial Strain Comments
  
ORGANISM TAXONOMY
NCBI Taxonomy ID 170187
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Firmicutes  
NCBI Class
Bacilli  
NCBI Order
Lactobacillales  
NCBI Family
Streptococcaceae  
NCBI Genus
Streptococcus  
NCBI Species
Streptococcus pneumoniae  
ISOLATION CLASSIFICATION
Ecosystem
Host-associated  
Ecosystem Category
Human  
Ecosystem Type
Circulatory system  
Ecosystem Subtype
Blood  
Specific Ecosystem
Unclassified  
ORGANISM EXTERNAL REFERENCES
Strain Info ID 352345
Genbank 16S ID
GENERAL PROPERTIES
Oxygen Requirement
Facultative  
Cell Shape
Coccus-shaped  
Motility
Nonmotile  
Sporulation
Nonsporulating  
Temperature Range
Mesophile  
Temperature Optimum
30 - 35  
Salinity
  
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 Pairs
Chains
Diseases Pneumonia
Meningitis
Otitis media
Known Habitats Host
Nasopharyngeal microflora
Metabolisms
  
Phenotypes Alpha-hemolytic
Pathogen
Energy Sources
  
CYANOBACTERIA METADATA
Filaments
  
Filament Type
  
Differentiated Cells
  
Position Of Heterocysts
  
Cysts
  
Mode Of Reproduction
  
Trichome
  
Trichome Type
  
Carotenoids
  
Pigments
  
Phage Infectivity
  
Phage Type
  
Restriction Enzyme
  
Toxin Production
  
Toxin Type
  
Secondary Metabolites
  
Developmental Cycle
  
Branching
  
Gas Vesicles
  
Gas Vesicle Type
  
Diagnostic Inclusion Body Information
  
Extracellular Structures
  
Bloom Forming
  
Pigment Type
  
Complementary chromatic adaptation (CCA)
  
Medium Types
  

 

 

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