JSONPDF

Hopanoidiivorans cymbastelaeTs

Citation

Formal styling
Hopanoidiivorans cymbastelaeTs corrig. Nguyen et al., 2023
Effective publication
Nguyen et al., 2023
Corrigendum
In SeqCode Registry from “Hopanoidivorans cymbastelae” (sic)
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:v1sky3wb (validated)
Canonical 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 gtdb
Pseudonyms
  • Hopanoidivorans cymbastelae (Original, corrected name)

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
Last modified 6 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
About 3 years ago by Thomas, Torsten
Submitted
Over 2 years ago by Thomas, Torsten
Curators
Endorsed
Over 2 years ago by Palmer, Marike
Validated
Over 2 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


© 2022-2025 The SeqCode Initiative
  All information contributed to the SeqCode Registry is released under the terms of the Creative Commons Attribution (CC BY) 4.0 license
seqco.de/r:v1sky3wb