PROJECT INFORMATION
GOLD Project ID
Gp0012874  
Project Name
candidate division WS3 b1dcf5.1.c12  
Other Names
candidate division WS3-b1dcf5.1.c12  
Legacy ER Project ID
6031  
Legacy GOLD ID
Gi0006031  
NCBI BioProject Name Uncultured candidate division WS3 bacterium fosmid clone b1dcf5.1.c12
NCBI BioProject ID
NCBI BioProject Accession
NCBI Locus Tag
  
NCBI BioSample Accession
PI Tanja Woyke
Added By Christian Rinke on 2011-11-01
Last Modified By Supratim Mukherjee on 2016-07-07
Project Comments
Metagenomic data, especially sequence data from large insert clones, are most useful when reasonable inferences about phylogenetic origins of inserts can be made. Often, clones that bear phylotypic markers (usually ribosomal RNA genes) are sought, but sometimes phylogenetic assignments have been based on the preponderance of blast hits obtained with predicted protein coding sequences (CDSs). Here we use a cloning method which greatly enriches for ribosomal RNA-bearing fosmid clones to ask two questions: (i) how reliably can we judge the phylogenetic origin of a clone (that is, its RNA phylotype) from the sequences of its CDSs? and (ii) how much lateral gene transfer (LGT) do we see, as assessed by CDSs of different phylogenetic origins on the same fosmid? We sequenced 12 rRNA containing fosmid clones, obtained from libraries constructed using DNA isolated from Baltimore harbour sediments. Three of the clones are from bacterial candidate divisions for which no cultured representatives are available, and thus represent the first protein coding sequences from these major bacterial lineages. The amount of LGT was assessed by making phylogenetic trees of all the CDSs in the fosmid clones and comparing the phylogenetic position of the CDS to the rRNA phylotype. We find that the majority of CDSs in each fosmid, 57-96%, agree with their respective rRNA genes. However, we also find that a significant fraction of the CDSs in each fosmid, 7-44%, has been acquired by LGT. In several cases, we can infer co-transfer of functionally related genes, and generate hypotheses about mechanism and ecological significance of transfer.  
Project Status
Permanent Draft  
Project Relevance GEBA-Single Cells
Sequencing Center Genome Atlantic (Canada)
Collaborating Institute
  
Funding Agency
  
Project Description
Single cell isolate from sample from sediment in Baltimore's harbor.  
Is JGI Project
  
Project Information Visibility Public
PROJECT TYPE
Specimen Organism
Nucleic Acid DNA
Sequencing Strategy
Whole Genome Sequencing  
EXTERNAL PROJECT LINKS
Project Information
  
Database
  
Genome Publications Environmental microbiology Lateral gene transfer and phylogenetic assignment of environmental fosmid clones.
Other Publications
  
PROJECT COMPOSITION
Study GEBA-MDM
Organism candidate division WS3 b1dcf5.1.c12
Analysis Projects candidate division WS3 b1dcf5.1.c12 (contamination screened)
Number of Analysis Projects 1
Number of DAPs
0  
SEQUENCING INFORMATION
Sequencing Status Complete
Sequencing Quality (MIGS-31) Level 1: Standard Draft
Finishing Goal
  
Sequencing Comments
  
Sequencing Technology (MIGS-29) Sanger
Library Method (MIGS-28)
  
Number Of Reads
  
Read Size
  
Vector
  
GC Percent
62  
Chromosome Count
  
Plasmid Count
  
ORGANISM NAME
GOLD Organism ID Go0012874
Organism Name
candidate division WS3 b1dcf5.1.c12  
Other names (alias, synonyms, short names, common names)
  
Organism Domain
BACTERIAL  
Phylogeny
LATESCIBACTERIA (WS3)  
Genus
  
Genus Synonyms
  
Species
  
Subspecies
  
Species Synonyms
  
Strain
b1dcf5.1.c12  
Strain Synonyms
  
Serovar-Biovar
  
Culture Collection ID
  
Type Strain
No  
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 74015
NCBI Superkingdom
Bacteria  
NCBI Kingdom
  
NCBI Phylum
Candidatus Latescibacteria  
NCBI Class
  
NCBI Order
  
NCBI Family
  
NCBI Genus
  
NCBI Species
  
ISOLATION CLASSIFICATION
Ecosystem
Environmental  
Ecosystem Category
Aquatic  
Ecosystem Type
Marine  
Ecosystem Subtype
Oceanic  
Specific Ecosystem
Sediment  
ORGANISM EXTERNAL REFERENCES
Strain Info ID
Genbank 16S ID
GENERAL PROPERTIES
Oxygen Requirement
Anaerobe  
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 Marine
Sediment
Metabolisms
  
Phenotypes
  
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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