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Pelagibacter malawiensis

Citation

Formal styling
Pelagibacter malawiensis corrig. Fernandes et al., 2025
Effective publication
Fernandes et al., 2025
Corrigendum
In SeqCode Registry from “Pelagibacter malawensis” (sic)
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:gnukuc44 (validated)
Canonical URL
https://seqco.de/i:49883

Nomenclature

Rank
Species
Syllabication
ma.la.wi.en'sis
Etymology
N.L. masc. adj. malawiensis, pertaining to Lake Malawi, the origin of the metagenome-assembled genome
Nomenclatural type
NCBI Assembly: GCA_965235955.1
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type genome is Pelagibacter malawiensis N-Mw13-23nov23-053 (GCA_965235955.1), a metagenome-assembled genome (MAG) assembled from 5 m depth from Lake Malawi, Malawi (date: 2023-11-23). N-Mw13-23nov23-053 has a genome size of 1 Mbp with a genomic GC content of 29.4%, contains 3 rRNA genes and 28 tRNAs. The genome is of high quality, consisting of 7 contigs, with a completeness of 99.5%, contamination of 0.5% and strain heterogeneity of 0% as assessed with checkM. The metagenome was assembled with FLYE from combined long-and short-read sequencing (Oxford Nanopore and Illumina NovaSeq). The closest cultivated relatives are ‘Candidatus Pelagibacter ubique SAR11 HTCC9022 (GCF_000472565.1), with an average amino acid identity of 75% and average nucleotide identity of 76.4% and ‘Candidatus Pelagibacter ubique SAR11 HTCC7211 (GCF_000155895.1), with an AAI of 74.2% and an ANI of 76.4%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Pelagibacterales; f__Pelagibacteraceae; g__Pelagibacter; s__Pelagibacter sp016870175.
Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Pelagibacterales » Pelagibacteraceae » Pelagibacter » Pelagibacter malawiensis
Parent
Pelagibacter
Pseudonyms
  • Pelagibacter malawensis (Original, corrected name)

Genomics

Accession
NCBI Assembly:GCA_965235955.1
Type
Metagenome-Assembled Genome (MAG)
Estimated Quality Metrics
  • Completeness: 99.5%
  • Contamination: 0.5%
  • Quality: 97.0
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
28.3273 ×
Source
Other features
  • G+C Content: 29.4%
  • Coding Density: 93.71%
  • Codon Table: 11
  • N50: 946,070 bp
  • Contigs: 8
  • Largest Contig: 946,070 bp
  • Assembly Length: 1,246,959 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
This is a metagenome-assembled genome (MAG) that was assembled with FLYE v2.9.1-b1780 (settings: --nano-corr –meta –no-alt-contigs) from combined long- and short-read sequencing (Oxford Nanopore and Illumina NovaSeq). Contigs ≥3 kbp were used for hybrid binning (tetranucleotide frequencies and coverage data using cross-mapping of reads gained from the same lake, i.e., 12 samples in the case of Lake Malawi) using MaxBin-2.2.7, MetaBAT and MetaBAT2 and DAS Tool-1.1.3 to combine their predictions. Bins were manually curated and CheckM v1.1.3 was used to estimate bin completeness, contamination, and strain heterogeneity. rRNA genes were predicted with barrnap v0.9, tRNA genes were predicted with tRNAscan v1.4.
Automated checks
Complete
See additional details
Last modified 4 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
8 months ago by Salcher, Michaela M
Submitted
3 months ago by Salcher, Michaela M
Curators
Validated
2 months ago by Rodriguez-R, Luis M
Date of priority
2025-08-28 03:13 PM (UTC)

Publications
1

Citation Title
Fernandes et al., 2025, Nature Microbiology Ecophysiology and global dispersal of the freshwater SAR11-IIIb genus Fontibacterium
Effective publication


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seqco.de/r:gnukuc44