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Hopanoidiivorans cymbastelaeTs

Citation

Formal styling
Hopanoidiivorans cymbastelaeTs 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:23657

Nomenclature

Rank
Species
Syllabication
cym.bas.te'lae
Etymology
N.L. gen. n. cymbastelae, from the sponge genus Cymbastela
Nomenclatural type
NCBI Assembly: GCA_028283145.1
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
A highly host-specific sponge ymbiont, found so far exclusively in C. coralliophila. Predicted capacity to produce hopanoids. 
Classification
Bacteria » Actinomycetota » Acidimicrobiia » Acidimicrobiales » Hopanoidiivorantaceae » Hopanoidiivorans » Hopanoidiivorans cymbastelaeTs
Parent
Hopanoidiivorans

Genomics

Accession
NCBI Assembly:GCA_028283145.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 87.18%
  • Contamination: 0.0%
  • Quality: 87.18
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 20 amino acids
Sequencing depth
22.0 ×
Source
Other features
  • G+C Content: 53.65%
  • Coding Density: 89.97%
  • Codon Table: 11
  • N50: 41,524 bp
  • Contigs: 90
  • Largest Contig: 92,812 bp
  • Assembly Length: 2,332,150 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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