JSON

Genome sc|0000339

Name

Poriferisocius anaerobius

Database

NCBI Assembly

Accession

GCA_028278785.1

Genomics

Accession
NCBI Assembly:GCA_028278785.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 85.9%
  • Contamination: 4.27%
  • Quality: 64.55
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 80.0%)
  • 0 23S rRNAs
  • tRNAs for 20 amino acids
Sequencing depth
11.0 ×
Source
Other features
  • G+C Content: 65.92%
  • Coding Density: 91.44%
  • Codon Table: 11
  • N50: 9,022 bp
  • Contigs: 302
  • Largest Contig: 48,813 bp
  • Assembly Length: 2,243,157 bp
  • Ambiguous Assembly Fraction: 0.0029%
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.

We have not be able to reconstruct a better 16S rRNA gene sequence, but phylogenetic placement of the 16S rRNA gene is robust (see Nguyen et al., 2023).
Automated checks
Complete
Last modified 10 months ago

Sample Metadata

BioSample entries
Date
Collection Date: 2014-06
Location
Lat Lon: 18° 48′ 58″ S, 147° 37′ 59″ E
View map of sampling locations
Toponym
Geo Loc Name: Australia: Davies Reef, Great Barrier Reef
Environment
Sample Type: metagenomic assembly
Isolation Source: sponge tissue, high temperature high CO2 • sponge tissue
Env Broad Scale: coral reef [ENVO:00000150]
Env Local Scale: coral reef [ENVO:00000150]
Env Medium: sponge
Other
Host: Rhopaloeides odorabile
Package
Biosamplemodel: MIMAG.host-associated • Metagenome or environmental
All retrieved samples
Metadata retrieved 10 months ago


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