Omnitrophus fodinae^Ts

Citation

Formal styling

Omnitrophus fodinae^Ts Rinke et al., 2013 (valid 2023)

Effective publication

Rinke et al., 2013

SeqCode status

Valid (SeqCode)

Register List

seqco.de/r:d841ck02 (validated)

Canonical URL

https://seqco.de/i:23567

Nomenclature

Rank

Species

Syllabication

fo.di'nae

Etymology

L. gen. n. fodinae, of a mine, coal mine

Nomenclatural type

NCBI Assembly: GCA_000405945.1

Nomenclatural status

Validly published under the SeqCode

Taxonomy

Description

This species is the type of the genus Omnitrophus. No data on cell size in the species is available. This species is represented by only one medium-quality genome, however, for historical significance, this genome serves as the nomenclatural type for the species. The %GC content of the genome is 49.56%. The estimated genome size is 2.9 Mb, with the available genome estimated to be 65 % complete. The genome available for this species encodes 2 very large ORFs with domains typically implicated in eukaryotic cell adhesion. This organism originated from groundwater sampled at Homestake Mine (Sanford Lab Homestake), South Dakota. The nomenclatural type for the species is the genome GCA_000405945.1.

Notes

• This name was discussed by the community: https://github.com/seq-code/seqcode/discussions/2
• A decision to allow a quality exception for this name was recommended in SeqCode Reconciliation Commission, 2023, Zenodo
• After a period ending on 12 / March / 2024 for the SeqCode Community to express opposition, the exception was granted

Classification

Bacteria » Omnitrophota » Omnitrophia » Omnitrophales » Omnitrophaceae » Omnitrophus » Omnitrophus fodinae^Ts

Parent

Omnitrophus gtdb

Genomics

Accession

NCBI Assembly:GCA_000405945.1

Type

Single-Cell Amplified Genome (SAG)

Estimated Quality Metrics

• Completeness: 65.01%
• Contamination: 0.56%
• Quality: 62.21

Ribosomal and transfer RNA genes

• 1 16S rRNA (up to 100.0%)
• 1 23S rRNA (up to 100.0%)
• tRNAs for 17 amino acids

Source

• SRA: SRX1954861

Other features

• G+C Content: 49.56%
• Coding Density: 93.69%
• Codon Table: 11
• N50: 20,345 bp
• Contigs: 150
• Largest Contig: 75,002 bp
• Assembly Length: 2,037,078 bp
• Ambiguous Assembly Fraction: 0.001%

Submitter comments

Quality metrics were assessed using CheckM v. 2. This genome has lower completeness than suggested by standards but we request lowering of the requirement here, because this is a historical name and allows us to keep the nomenclature for the entire phylum. Despite several attempts at recovering a higher completeness genome from metagenomic data, there has been no other genomes recovered for the genus, thus in order to retain the historical genus through phylum names with the least amount of confusion, we request special consideration for validation with this genome as type. 

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_000405945.1
• GTDB Tree: s__Omnitrophus fodinae
• Global Biodiversity Information Facility (GBIF)
• Wikispecies: Omnitrophus fodinae (see reference source)

Search sequences

• Seach in NCBI Nucleotide

Local history

• This name was last modified 9 months ago
• Submission process status
• Quality checks before valid publication

Registered by

Rinke, Chris about 2 years ago

Submitted by

Rinke, Chris almost 2 years ago

Curators

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

Validated by

Rodriguez-R, Luis M 9 months ago

Date of priority

2023-02-22 12:07 AM (UTC)