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Spongiisocius variivoransTs

This name contravenes at least one rule from the SeqCode, and it's at risk of being rejected:
  • Low genome completeness: The completeness of the type genome should be above 90%

Citation

Formal styling
Spongiisocius variivoransTs 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
Genome sc|0000342 Ts
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 variivoransTs
Parent
Spongiisocius gtdb

Genomics

Accession
NCBI Assembly: GCA_028279005.1 [NCBI | EMBL]
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
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
Last modified about 2 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
Almost 4 years ago by Thomas, Torsten
Submitted
About 3 years ago by Thomas, Torsten
Curators
Endorsed
About 3 years ago by Palmer, Marike
Validated
About 3 years ago by Palmer, Marike
Date of priority
2023-08-25 02:22 PM (UTC)

Publications
1

Citation Title
Nguyen et al., 2023, Systematic and Applied Microbiology Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species
Effective publication


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seqco.de/r:v1sky3wb