Hopanoidiivorans cymbastelae^Ts

Citation

Formal styling

Hopanoidiivorans cymbastelae^Ts 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: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 cymbastelae^Ts

Parent

Hopanoidiivorans gtdb

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

• BioSample: SAMN31047467

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

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Last modified about 1 month ago

Metadata

Outside links and data sources

• GTDB Genome: GCA_028283145.1
• GTDB Tree: s__Hopanoidiivorans cymbastelae
• Global Biodiversity Information Facility (GBIF)
• Wikispecies: Hopanoidiivorans cymbastelae (see reference source)

Search sequences

• Seach in NCBI Nucleotide

Local history

• This name was last modified over 1 year ago
• Submission process status
• Quality checks before valid publication

Registered by

Thomas, Torsten about 2 years ago

Submitted by

Thomas, Torsten over 1 year ago

Curators

• Rodriguez-R, Luis M
• Palmer, Marike

Endorsed by

Palmer, Marike over 1 year ago

Validated by

Palmer, Marike over 1 year ago

Date of priority

2023-08-25 02:22 PM (UTC)