Puniceispirillum marinum^Ts

Citation

Formal styling

Puniceispirillum marinum^Ts Oh et al., 2010 (valid 2024)

Effective publication

Oh et al., 2010

SeqCode status

Valid (SeqCode)

Register List

seqco.de/r:1s9xy0s7 (validated)

Canonical 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 marinum^Ts

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

• BioSample: SAMN02603472

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

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Last modified about 1 month ago

Metadata

Outside links and data sources

• GTDB Genome: GCA_000024465.1
• GTDB Tree: s__Puniceispirillum marinum
• Global Biodiversity Information Facility (GBIF)
• Wikispecies: Puniceispirillum marinum (see reference source)

Search sequences

• Seach in NCBI Nucleotide

Local history

• This name was last modified 8 months ago
• Submission process status
• Quality checks before valid publication

Registered by

Chuvochina, Maria over 1 year ago

Submitted by

Chuvochina, Maria 9 months ago

Curators

• Rodriguez-R, Luis M (genomics)
• Palmer, Marike (nomenclature)

Validated by

Rodriguez-R, Luis M 8 months ago

Date of priority

2024-03-28 05:13 AM (UTC)