Spongiisocius variivorans^Ts

Citation

Formal styling

Spongiisocius variivorans^Ts Nguyen et al., 2023

Effective publication

Nguyen et al., 2023

SeqCode status

Valid (SeqCode)

Register List

seqco.de/r:v1sky3wb (validated)

Canonical URL

https://seqco.de/i:23655

Nomenclature

Rank

Species

Syllabication

va.ri.i.vo'rans

Etymology

L. masc. adj. varius, diverse; L. pres. part. vorans, eating; N.L. masc. adj. variivorans, one with diversified eating

Nomenclatural type

NCBI Assembly: GCA_028279005.1

Nomenclatural status

Validly published under the SeqCode

Taxonomy

Description

Symbiont associated with 31 sponge species. Predicted to be capable of utilizing multiple different types of electron donors, including sn-glycerol 3-phosphate, (S)-hydroxyglutarate, (S)-lactate, (S)-2-hydroxybutanoate, choline, glycolate, and FADH2. 

Classification

Bacteria » Actinomycetota » Acidimicrobiia » Spongiisociales » Spongiisociaceae » Spongiisocius » Spongiisocius variivorans^Ts

Parent

Spongiisocius gtdb

Genomics

Accession

NCBI Assembly:GCA_028279005.1

Type

Metagenome-Assembled Genome (MAG)

Estimated Quality Metrics

• Completeness: 83.16%
• Contamination: 1.79%
• Quality: 74.21

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

14.0 ×

Source

• BioSample: SAMN31047461

Other features

• G+C Content: 66.16%
• Coding Density: 89.74%
• Codon Table: 11
• N50: 6,607 bp
• Contigs: 443
• Largest Contig: 31,777 bp
• Assembly Length: 2,595,325 bp
• Ambiguous Assembly Fraction: 0.0%

Submitter comments

Completeness and contamination were assessed with CheckM v1.1.0 using a lineage-specific workflow.
This symbiont is from a sponge and we have seen previously seen that sponge-associated genomes which are closed (i.e. single, circular contig) have completeness estimates that are below the 90% threshold. For example, we have one completed MAG (2000x coverage, Q>50) for a sponge symbiont and gotten the following completeness estimates:
CheckM: 91 % complete

CheckM2: 81 % complete

Busco v5: 74 % complete

Clearly all pipelines are wrong and substantially underestimate the completeness. I believe this is also the case for this organisms.

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_028279005.1
• GTDB Tree: s__Spongiisocius variivorans
• Global Biodiversity Information Facility (GBIF)
• Wikispecies: Spongiisocius variivorans (see reference source)

Search sequences

• Seach in NCBI Nucleotide

Local history

• This name was last modified over 1 year ago
• Submission process status
• Quality checks before valid publication

Registered by

Thomas, Torsten about 2 years ago

Submitted by

Thomas, Torsten over 1 year ago

Curators

• Rodriguez-R, Luis M
• Palmer, Marike

Endorsed by

Palmer, Marike over 1 year ago

Validated by

Palmer, Marike over 1 year ago

Date of priority

2023-08-25 02:22 PM (UTC)