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ASM21779v1

Organism name:
Thermodesulfatator indicus DSM 15286 (bacteria)
Taxonomy check:
OK
Infraspecific name:
Strain: DSM 15286
BioSample:
SAMN02232057
BioProject:
PRJNA40057
Submitter:
US DOE Joint Genome Institute (JGI-PGF)
Date:
2011/06/10
Assembly type:
na
Assembly level:
Complete Genome
Genome representation:
full
RefSeq category:
representative genome
Relation to type material:
assembly from type material
GenBank assembly accession:
GCA_000217795.1 (latest)
RefSeq assembly accession:
GCF_000217795.1 (latest)
RefSeq assembly and GenBank assembly identical:
yes
Assembly method:
Newbler v. 2.3
Genome coverage:
30x
Sequencing technology:
454/Illumina

IDs: 291998 [UID] 289058 [GenBank] 291998 [RefSeq]

See Genome Information for Thermodesulfatator indicus

History (Show revision history)

Comment

URL -- http://www.jgi.doe.gov
jgi Project ID: 4085567
Source DNA and organism available from Hans-Peter Klenk at the German Collection of Microorganisms and Cell Cultures (DSMZ) (hans-peter.klenk@dsmz.de)
Contacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)
 David Bruce (microbe@cuba.jgi-psf.org)
Whole genome sequencing and draft assembly at JGI-PGF
Finishing done ... by JGI-LANL
Annotation by JGI-ORNL and JGI-PGF
The JGI and collaborators endorse the principles for the distribution and use of large scale sequencing data adopted by the larger genome sequencing community and urge users of this data to follow them. It is our intention to publish the work of this project in a timely fashion and we welcome collaborative interaction on the project and analysis.
(http://www.genome.gov/page.cfm?pageID=10506376)  more

Genome-Annotation-Data

##Genome-Annotation-Data-START##
Annotation Provider::NCBI RefSeq
Annotation Date::04/18/2022 12:40:31
Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Method::Best-placed reference protein set; GeneMarkS-2+
Annotation Software revision::6.1
Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
Genes (total)::2,279
CDSs (total)::2,219
Genes (coding)::2,199
CDSs (with protein)::2,199
Genes (RNA)::60
rRNAs::2, 2, 2 (5S, 16S, 23S)
complete rRNAs::2, 2, 2 (5S, 16S, 23S)
tRNAs::50
ncRNAs::4
Pseudo Genes (total)::20
CDSs (without protein)::20
Pseudo Genes (ambiguous residues)::0 of 20
Pseudo Genes (frameshifted)::3 of 20
Pseudo Genes (incomplete)::16 of 20
Pseudo Genes (internal stop)::3 of 20
Pseudo Genes (multiple problems)::2 of 20
CRISPR Arrays::3
##Genome-Annotation-Data-END##

MIGS-Data

##MIGS-Data-START##
investigation_type::bacteria_archaea
project_name::Thermodesulfatator indicus CIR29812, DSM 15286
collection_date::April 2001
lat_lon::-25.316667 70.033355
depth::2420
alt_elev::Missing
country::Indian Ocean
environment::Deep sea, Hydrothermal vent, Marine
num_replicons::1
ref_biomaterial::DSM 15286, JCM 11887
biotic_relationship::Free living
trophic_level::Chemolithoautotroph
rel_to_oxygen::Anaerobe
isol_growth_condt::14742485
sequencing_meth::WGS
assembly::Newbler v. 2.3 (pre-release)
finishing_strategy::Finished
GOLD Stamp ID::Gi02944
Type Strain::Yes
Greengenes ID::52699
Isolation Site::Deep-sea hydrothermal vent site at the Kairei vent field on the Central Indian Ridge Indian Ocean
Isolation Comments::isolated by H. Moussard
Cell Shape::Rod-shaped
Motility::Motile
Sporulation::Nonsporulating
Temperature Range::Thermophile
Temperature Optimum::70C
pH::6.25
Gram Staining::Gram-
Diseases::None
##MIGS-Data-END##

Global statistics

Total sequence length2,322,224
Total ungapped length2,322,224
Total number of chromosomes and plasmids1

Supplemental Content

PubMed articles for this assembly

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Global assembly definition

Download the full sequence report
Click on the table row to see sequence details in the table to the right
Assembly Unit Name
Primary Assembly
Assembly Unit: Primary Assembly (GCF_000217805.1)
Molecule nameGenBank sequenceRefSeq sequence
Chromosome CP002683.1=NC_015681.1

Assembly statistics

MoleculeTotal
Length
Chromosome 2,322,224

Assembly QA

Taxonomy Check Data

Declared organism

Organism nameSpecies name
Thermodesulfatator indicus DSM 15286Thermodesulfatator indicus

Best-matching type-strain assembly for declared species

AssemblyOrganism nameType category
samena

Best-matching type-strain assembly

AssemblySpecies nameType category
GCA_001642325.1Thermodesulfatator autotrophicustype

Average Nucleotide Identity (ANI) data

ANIQuery coverageSubject coverage
Declared typenanana
Best-match type81.7525.8726.45

ANI result

Taxonomy check statusBest match statusComment
OKbelow-threshold-mismatchAssembly is the type-strain, mismatch is within genus and expected
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