Puniceispirillum marinumTs


Citation

Formal styling
Puniceispirillum marinumTs Oh et al., 2010 (valid 2024)
Effective publication
Oh et al., 2010
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:1s9xy0s7 (validated)
Cannonical URL
https://seqco.de/i:189

Nomenclature

Rank
Species
Syllabication
ma.ri'num
Etymology
L. neut. adj. marinum, marine
Nomenclatural type
NCBI Assembly: GCA_000024465.1
Reference strain
IMCC 1322
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
The description is the same as given by Oh et al., 2010:
"“Candidatus Puniceispirillum marinum” IMCC1322 is expected to be a metabolic generalist carrying functional genes for utilizing resourceful sunlight, DMSP, CO, and C1 compounds in the surface ocean. Such metabolic potential of strain IMCC1322, the first cultured representative of the SAR116 clade, might reflect ecological niches for even more dominant marine bacterioplankton clades SAR11, Roseobacter, and SAR86."
Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Puniceispirillales » Puniceispirillaceae » Puniceispirillum » Puniceispirillum marinumTs
Parent
Puniceispirillum gtdb

Genomics

Accession
NCBI Assembly:GCA_000024465.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 99.94%
  • Contamination: 0.15%
  • Quality: 99.19
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 19 amino acids
Sequencing depth
46.0 ×
Source
Other features
  • G+C Content: 48.85%
  • Coding Density: 91.12%
  • Codon Table: 11
  • N50: 2,753,527 bp
  • Contigs: 1
  • Largest Contig: 2,753,527 bp
  • Assembly Length: 2,753,527 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
The information about genome coverage was received from the original authors via personal communication (see below). From: s-jkim@kordi.re.kr, Hyun-Myung Oh

Accoding to Dr. Kwon at kiost (kkkwon@kiost.ac.kr) abi 3730 xl sequencing coverage was 2x from 4,512-clone genomic library and the additional pyrosequencing runs were done 3 times.
I could not get raw reads from pyrosequencing, I expect not more that 100k reads per 454 run.
Since Macrogen reported tens of thounsand reads per 454 run, and they did it three times to get more than 40 phred score, the following calculation would make sense ! 
100k * 3 run * 400 bp / 2.7 Mbp = 44.44 x
So our final decision on the genomic coverage of the completeted genome of IMCC1322 should be 46 folds.
 
Automated checks
Complete
See additional details

Metadata

Outside links and data sources
Search sequences
Local history
Registered by
Chuvochina, Maria about 1 year ago
Submitted by
Chuvochina, Maria 3 months ago
Curators
Validated by
Rodriguez-R, Luis M about 2 months ago
Date of priority
2024-03-28 05:13 AM (UTC)

Publications
3

Citation Title
Lee, Oh, 2024, Journal of Microbiology Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322
Lee et al., 2019, Journal of Microbiology Isolation, cultivation, and genome analysis of proteorhodopsin-containing SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322
Oh et al., 2010, Journal of Bacteriology Complete Genome Sequence of “ Candidatus Puniceispirillum marinum” IMCC1322, a Representative of the SAR116 Clade in the Alphaproteobacteria
Effective publication



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