Zwartia lucis


Citation

Formal styling
Zwartia lucis 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:48725

Nomenclature

Rank
Species
Syllabication
lu'cis
Etymology
L. fem. adj. lucis, of light, referring to the presence of light driven proton pumps (rhodopsins) in the type strain.
Nomenclatural type
NCBI Assembly: GCA_965234455.1
Reference strain
Strain sc|0038968: GE-14 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type strain is Zwartia lucis GE-14 (GCA_965234455.1), isolated from 5 m depth from Greifensee, Switzerland (date: 2019-04-03), via high-throughput dilution to extinction cultivation. GE-14 has a genome size of 3.7 Mbp with a genomic GC content of 50.9%, contains 6 rRNA genes and 41 tRNAs. The genome is a high-quality draft consisting of 7 contigs. In contrast to other Zwartia sp., the genome contains genes encoding rhodopsins and the biosynthetic pathway for retinal biosynthesis. No genes for flagellar or pilus assembly and chemotaxis were annotated. Pathways for nitrate reduction, cyanate, urea and taurine degradation, thiosulfate oxidation (Sox pathway), glycolate and methane/alkanesulfonate oxidation, and the biosynthesis of all amino acids were predicted. Further, pathways for thiamine, riboflavin, pantothenate, coenzyme A, THF, ubiquinone, and heme biosynthesis were identified. The closest cultivated relative is Zwartia panacis strain KCTC42751 (GCF_030410395.1), with an average amino acid identity of 82.1% and average nucleotide identity of 77.6%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Gammaproteobacteria; o__Burkholderiales; f__Burkholderiaceae; g__Zwartia; s__.
Classification
Bacteria » Pseudomonadota » Betaproteobacteria » Burkholderiales » Alcaligenaceae » Zwartia » Zwartia lucis
Parent
Zwartia

Genomics

Accession
NCBI Assembly:GCA_965234455.1
Cultures
Strain sc|0038968
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 93.28%
  • Contamination: 0.84%
  • Quality: 89.08
Ribosomal and transfer RNA genes
  • 2 16S rRNAs (up to 100.0%)
  • 2 23S rRNAs (up to 100.0%)
  • tRNAs for 19 amino acids
Sequencing depth
442.0 ×
Source
Other features
  • G+C Content: 50.9%
  • Coding Density: 92.94%
  • Codon Table: 11
  • N50: 896,894 bp
  • Contigs: 7
  • Largest Contig: 1,346,872 bp
  • Assembly Length: 3,677,725 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 polished 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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