Planktophila warneckei


Citation

Formal styling
Planktophila warneckei Salcher et al., 2025
Effective publication
Salcher et al., 2025
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:opjv7zsc (validated)
Canonical URL
https://seqco.de/i:48741

Nomenclature

Rank
Species
Syllabication
war.ne.cke'i
Etymology
N.L. masc. gen. n. warneckei, of Warnecke, named after the deceased German scientist Falk Warnecke, who intensively worked on the ecology of freshwater Planktophila
Nomenclatural type
NCBI Assembly: GCA_965234675.1
Reference strain
Strain sc|0038946: RE-8 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type strain is Planktophila warneckii RE-8 (GCA_965234675.1), isolated from 0.5 m depth from the Římov reservoir, Czechia (date: 2019-04-23), via high-throughput dilution to extinction cultivation. RE-8 has a genome size of 1.4 Mbp with a genomic GC content of 46.2%, contains 3 rRNA genes and 38 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins. No genes for flagella or pilus assembly and chemotaxis were annotated. Pathways for the biosynthesis of all amino acids except for histidine were predicted. Further, pathways for riboflavin, pyridoxal, coenzyme A, and menaquinone biosynthesis were identified. The closest cultivated relative is Actinobacteria bacterium IMCC26103 (GCA_002284875.1), with an average amino acid identity of 72.2% and average nucleotide identity of 70.96%. Current GTDB classification (R220): d__Bacteria; p__Actinomycetota; c__Actinomycetia; o__Nanopelagicales; f__Nanopelagicaceae; g__Planktophila; s__.
Classification
Bacteria » Actinomycetota » Actinomycetes » Nanopelagicales » Nanopelagicaceae » Planktophila » Planktophila warneckei
Parent
Planktophila

Genomics

Accession
NCBI Assembly:GCA_965234675.1
Cultures
Strain sc|0038946
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 100.0%
  • Contamination: 2.52%
  • Quality: 87.4
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
1117.3 ×
Source
Other features
  • G+C Content: 46.2%
  • Coding Density: 95.33%
  • Codon Table: 11
  • N50: 1,409,984 bp
  • Contigs: 1
  • Largest Contig: 1,409,984 bp
  • Assembly Length: 1,409,984 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Genome of a culture that was harvested by filtration on 0.22 µm filters; DNA was extracted with the Quiagen MagAttract HMW DNA kit. Sequencing was done with Illuminia Novaseq 6000, trimming of reads with BBMap v36.x, assembly with SPAdes v3.12.0. The genome was manually curated to a circular chromosome in Geneious 10 by repeated rounds of read mapping. Completeness and contamination were assessed with CheckM.
Automated checks
Complete

Last modified 6 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
Over 1 year ago by Layoun, Paul
Submitted
7 months ago by Layoun, Paul
Curators
Endorsed
5 months ago by Rodriguez-R, Luis M
Validated
3 months ago by Valero Tebar, Juan
Date of priority
2025-08-28 03:27 PM (UTC)

Publications
1

Citation Title
Salcher et al., 2025, Nature Communications Bringing the uncultivated microbial majority of freshwater ecosystems into culture
Effective publication



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