Planktophila grossartii


Citation

Formal styling
Planktophila grossartii Salcher et al., 2025
Effective publication
Salcher et al., 2025
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:o5wsiwof (validated)
Canonical URL
https://seqco.de/i:49103 Copy

Nomenclature

Rank
Species
Syllabication
gros.sar.ti'i
Etymology
N.L. masc. gen. n. grossartii, named after the German scientist Hans-Peter Grossart, who greatly contributed to the ecological characterization of freshwater Actinomycetota.
Nomenclatural type
NCBI Assembly: GCA_965234365.1
Reference strain
Strain sc|0038786: RE-3 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type species is Planktophila grossartii RE-3 (GCA_965234365.1), isolated from 0.5 m depth from the Římov reservoir, Czechia (date: 2019-04-23), via high-throughput dilution to extinction cultivation. RE-3 has a genome size of 1.4 Mbp with a genomic GC content of 48.8 %, 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 taurine degradation and the biosynthesis of all amino acids except for histidine were predicted. Further, pathways for riboflavin, pyridoxal, coenzyme A, NAD, and menaquinone biosynthesis were identified. The closest cultivated relative is Actinobacteria bacterium IMCC25003 (GCA_002284855.1) with an average nucleotide identity of 90.33%. Current GTDB classification (R220): d__Bacteria; p__Actinomycetota; c__Actinomycetia; o__Nanopelagicales; f__Nanopelagicaceae; g__Planktophila; s__Planktophila sp009701085. 
Classification
Bacteria » Actinomycetota » Actinomycetes » Nanopelagicales » Nanopelagicaceae » Planktophila » Planktophila grossartii
Parent
Planktophila

Genomics

Accession
NCBI Assembly:GCA_965234365.1
Cultures
Strain sc|0038786
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 99.16%
  • Contamination: 2.52%
  • Quality: 86.56
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
1130.0 ×
Source
Other features
  • G+C Content: 48.8%
  • Coding Density: 95.2%
  • Codon Table: 11
  • N50: 1,440,005 bp
  • Contigs: 1
  • Largest Contig: 1,440,005 bp
  • Assembly Length: 1,440,005 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, but as the genome consists of a circular chromosome, it should be complete without any contamination.
Automated checks
Complete

Last modified 3 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
11 months ago by Salcher, Michaela M
Submitted
5 months ago by Salcher, Michaela M
Curators
Endorsed
3 months ago by Rodriguez-R, Luis M
Validated
14 days ago by Rodriguez-R, Luis M
Date of priority
2025-08-28 03:23 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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