Ryujinia shimokita^Ts

Citation

Formal styling

Ryujinia shimokita^Ts Sun et al., 2025

Effective publication

Sun et al., 2025

SeqCode status

Valid (SeqCode)

Register List

seqco.de/r:zf1yjhk0 (validated)

Canonical URL

https://seqco.de/i:49692

Nomenclature

Rank

Species

Syllabication

shi.mo.ki'ta

Etymology

N.L. fem. n. shimokita, named after the sampling site, the international waters off the Shimokita Peninsula in Japan

Notes

Current usage under both the SeqCode and ICNP would use -ensis/-ense adjectival endings for species epithets derived from geographical names, however, as this name was published in its current form, and the name does not contravene any rules of the SeqCode, the spelling of the name was retained as requested by the authors.

Nomenclatural type

INSDC Nucleotide: BAAGKY000000000.1

Nomenclatural status

Validly published under the SeqCode

Taxonomy

Description

This uncultured species is represented by the genome ‘SP_28H5_5’, whose genome size is 2.0 MB, with the presence of 23S, 16S and 5S rRNA genes. R. shimokita is inferred to have a chemolithotrophic lifestyle, since this species encodes a nearly complete Wood–Ljungdahl (WL) pathway. It also has the potential for a heterotrophic lifestyle with substrate-level phosphorylation through glycolysis, while it lacks most genes for the citrate cycle and beta-oxidation. The type genome does not encode the ability for the oxidoreduction of nitrogen or sulphur compounds. 

Classification

Bacteria » Ryujiniota » Ryujiniia » Ryujiniales » Ryujiniaceae » Ryujinia » Ryujinia shimokita^Ts

Parent

Ryujinia assigned in Sun et al., 2025

Genomics

Accession

INSDC Nucleotide:BAAGKY000000000.1

Type

Metagenome-Assembled Genome (MAG)

Estimated Quality Metrics

• Completeness: 96.99%
• Contamination: 0.65%
• Quality: 93.74

Ribosomal and transfer RNA genes

• 1 16S rRNA (up to 1557.0%)
• 1 23S rRNA (up to 65.0%)
• tRNAs for 19 amino acids

Sequencing depth

85.0 ×

Source

• SRA: DRX300295

Other features

• G+C Content: 41.66%
• Coding Density: 87.34%
• Codon Table: 11
• N50: 42,075 bp
• Contigs: 77
• Largest Contig: 134,155 bp
• Assembly Length: 2,043,533 bp
• Ambiguous Assembly Fraction: 0.0%

Submitter comments

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Automated checks

Complete

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Last modified 3 months ago

Metadata

Outside links and data sources

• Wikispecies: Ryujinia shimokita
• Wikidata: Q136956255

Search sequences

• Seach in NCBI Nucleotide

Local history

• This name was last modified 15 days ago
• Submission process status
• Quality checks before valid publication

Registered

10 months ago and claimed 3 months ago by Rinke, Chris

Submitted

3 months ago by Rinke, Chris

Curators

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

Validated

15 days ago by Palmer, Marike

Date of priority

2025-09-17 07:39 AM (UTC)