Genome sc|0001493


Database

NCBI Assembly

Accession

GCA_900290375.1

Genomics

Accession
NCBI Assembly:GCA_900290375.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 98.0%
  • Contamination: 3.9%
  • Quality: 78.5
Ribosomal and transfer RNA genes
  • 1 16S rRNA (up to 100.0%)
  • 1 23S rRNA (up to 77.0%)
  • tRNAs for 20 amino acids
Source
Other features
  • G+C Content: 42.6%
  • Coding Density: 82.2%
  • Codon Table: 11
  • N50: 11,065 bp
  • Contigs: 971
  • Largest Contig: 94,466 bp
  • Assembly Length: 5,321,430 bp
  • Ambiguous Assembly Fraction: 0.027%
Submitter comments
Sampling of peat soil from the acidic peatland Schlöppnerbrunnen II (Germany), DNA-stable isotope probing (DNA-SIP), total nucleic acid extraction, metagenome sequencing and assembly, and coverage-based binning were described previously (5, 16, 29). In brief, DNA from native peat soil (10- to 20-cm depth) and DNA pooled from 16 13C-enriched fractions (density, 1.715 to 1.726 g ml−1) of a previous DNA-SIP experiment with soil from the same site (16) was sequenced using the Illumina HiSeq 2000 system. DNA-SIP was performed after a 120-day incubation (again, 10- to 20-cm depth) that was periodically amended with small dosages of sulfate and first a mixture of unlabeled formate, acetate, propionate, and lactate for 2 weeks and thereafter a mixture of 13C-labeled formate, acetate, propionate, and lactate (all in the lower-micromolar range) (16). Raw reads were quality filtered, trimmed, and coassembled (native soil, 385 million reads; DNA-SIP, 576 million reads) using the CLC Genomics Workbench 5.5.1 (CLC Bio). Differential coverage binning was applied to extract the Desulfosporosinus metagenome-assembled genome (MAG) (75). As expected (16), the Desulfosporosinus MAG was of low abundance in the native soil with an average coverage of 0.026 while enriched in the SIP sample with an average coverage of 34 (detailed per scaffold in Table S1b). A side effect of sequencing a DNA-SIP sample is an apparent G+C content skew, which was normalized arbitrarily to improve binning using the following formula (29, 76): (coverage/G+C content9) × 1015.
Scaffolds containing the 16S and 23S rRNA genes were successfully identified using paired-end linkage data (75). Completeness, contamination, and strain heterogeneity were estimated using CheckM 1.0.6 (77).
Phylogenomic analysis of the Desulfosporosinus MAG was based on a concatenated set of 34 phylogenetically informative marker genes as defined by reference 77 and the Bayesian phylogeny inference method PhyloBayes using the CAT-GTR model (78). 16S rRNA gene-based phylogeny was inferred using the ARB SILVA database r126 as a reference (79), the SINA aligner (80), and the substitution model testing and maximum likelihood treeing method IQ-TREE (81). Pairwise 16S rRNA gene sequence identities were calculated with T-Coffee 11 (82). Pairwise average nucleic and amino acid identities (ANI and AAI, respectively) (37) between protein-encoding genes of the Desulfosporosinus MAG and reference genomes were calculated as described previously (29).
Automated checks
Complete

Sample Metadata

Date
Collection Date: 2010-09-21
Location
Lat Lon: 50.131881 N 11.881046 E
Toponym
Geo Loc Name: Germany: Schloeppnerbrunnen fen II, Fichtel Mountains, northeastern Bavaria
Environment
Env Material: peat soil
Env Biome: fen
Other
Ph: 5-Apr
Depth: 0.1-0.2 m
Rel To Oxygen: anaerobe
Package
Ncbi Submission Package: MIGS.ba.soil.5.0
Biosamplemodel: MIGS/MIMS/MIMARKS.soil
All retrieved samples

Metadata retrieved 5 months ago


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