Spongiisocius variivoransTs


Citation

Formal styling
Spongiisocius variivoransTs Nguyen et al., 2023
Proposed by
Nguyen et al., 2023
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
  • 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

Metadata

Outside links and data sources
Search sequences
Local history
Registered by
torstenthomas 12 months ago
Submitted by
torstenthomas about 1 month ago
Endorsed by
MarikePalmer about 1 month ago
Validated by
MarikePalmer about 1 month ago

Publications (1)

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



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