Spongiisocius variivoransTs


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)
Cannonical 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 variivoransTs
Parent
Spongiisocius

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
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

Metadata

Outside links and data sources
Search sequences
Local history
Registered by
Thomas, Torsten over 1 year ago
Submitted by
Thomas, Torsten 8 months ago
Curators
Endorsed by
Palmer, Marike 8 months ago
Validated by
Palmer, Marike 8 months ago

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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