Genome sc|0000339

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

• BioSample: SAMN31047475

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

Sample Metadata

Date

Collection Date: 2014-06

Location

Lat Lon: 18.816 S 147.633 E

Toponym

Geo Loc Name: Australia:Davies Reef

Environment

Sample Type: metagenomic assembly

Isolation Source: sponge microbiome

Env Broad Scale: coral reef [ENVO:00000150]

Env Local Scale: coral reef [ENVO:00000150]

Env Medium: sponge

Other

Host: Rhopaloeides odorabile

Package

Ncbi Submission Package: MIMAG.host-associated.5.0

Biosamplemodel: MIMAG.host-associated

All retrieved samples

• SAMN31047475: MIMAG Metagenome-assembled Genome sample from Candidatus Poriferisocius anaerobius

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Metadata retrieved 10 months ago