Planktophila vernalis


Citation

Formal styling
Planktophila vernalis Neuenschwander et al., 2018 (priority 2025)
Effective publication
Neuenschwander et al., 2018
SeqCode status
Valid (SeqCode)
Register List
seqco.de/r:kv6gij82 (validated)
Canonical URL
https://seqco.de/i:23846

Nomenclature

Rank
Species
Syllabication
ver.na'lis
Etymology
L. fem. adj. vernalis, belonging to spring; referring to high abundances in spring
Nomenclatural type
NCBI Assembly: GCA_002288185.1
Reference strain
Strain sc|0038986: MMS-IIA-15 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type genome is Planktophila vernalis MMS-IIA-15 (GCF_002288185.1), which was isolated via dilution-to-extinction cultivation from Lake Zurich, Switzerland. Curved rods with lengths of 0.43±0.12 μm and diameters of 0.26±0.05 μm. The initial pure culture was lost after a few propagations to fresh medium; no growing culture is available. The initial culture grew well in sterile lake water amended with minimal carbon medium, vitamins and amino acids. Planktophila vernalis MMS-IIA-15 has a genome size of 1.36 Mbp and a genomic GC content of 45.7%. The genome is complete, consisting of a circular chromosome and contains 3 rRNA genes and 39 tRNAs. It is auxotrophic for reduced sulfur sources, serine, and several vitamins (B1, B5, B7, B12) and possesses rhodopsins. Planktophila vernalis can be recognized by the presence of the diagnostic oligonucleotide sequence 5’- AACTACTACCACACCGGTTCG-3’ in the 23S rRNA gene (positions 1420-1441, E. coli numbering). Basis for the assignment is a phylogenomic tree of 476 concatenated protein sequences, phylogenetic analysis of 16S rRNA, 23S rRNA, and rhodopsin genes, as well as average nucleotide and amino acid identities presented in Neuenschwander et al. (2018, ISMEJ, doi: 10.1038/ismej.2017.156). The closest cultivate relatives are Planktophila sp. IMCC19121 (GCA_002284895) and Planktophila limnetica MMS-VB-114 (GCF_002288365.1) with average amino acid identities of 93.1 and 72.1%, respectively, and average nucleotide identities of 89.7 and 71.3%, respectively.
Classification
Bacteria » Actinomycetota » Actinomycetes » Nanopelagicales » Nanopelagicaceae » Planktophila » Planktophila vernalis
Parent
Planktophila gtdb

Genomics

Accession
NCBI Assembly:GCA_002288185.1
Cultures
Strain sc|0038986
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 98.04%
  • Contamination: 0.0%
  • Quality: 98.04
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
800.0 ×
Source
Other features
  • G+C Content: 45.7%
  • Coding Density: 95.32%
  • Codon Table: 11
  • N50: 1,364,004 bp
  • Contigs: 1
  • Largest Contig: 1,364,004 bp
  • Assembly Length: 1,364,004 bp
  • Ambiguous Assembly Fraction: 0.0%
Submitter comments
Genome of a culture with growth arrest. DNA was amplified by MDA (REPLI-g single cell kit) prior to sequencing. Sequencing was done with Illuminia MiSeq (PE250), assembly was done with SPAdes-3.6.2. The genome was manually curated to a circular chromosome in Geneious 7.1.7 by repeated rounds of read mapping, primer design for contig ends and low-coverage regions and sanger sequencing. 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 2 months ago

Metadata

Outside links and data sources
Search sequences
Local history
Registered
Over 2 years ago by Salcher, Michaela M
Submitted
2 months ago by Salcher, Michaela M
Curators
Validated
About 1 month ago by Palmer, Marike
Date of priority
2025-04-30 03:20 PM (UTC)

Publications
1

Citation Title
Neuenschwander et al., 2018, The ISME Journal Microdiversification in genome-streamlined ubiquitous freshwater Actinobacteria
Effective publication



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