Rhodoluna miladensis


Citation

Formal styling
Rhodoluna miladensis 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:48729

Nomenclature

Rank
Species
Syllabication
mi.la.den'sis
Etymology
N.L. fem. adj. miladensis, pertaining to Lake Milada (Czechia), the isolation source of the type strain.
Nomenclatural type
NCBI Assembly: GCA_965234705.1
Reference strain
Strain sc|0038944: MiE-23b Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type strain is Rhodoluna miladensis MiE-23b (GCA_965234705.1), isolated from 5 m depth from Lake Milada, Czechia (date: 2019-10-15), via high-throughput dilution to extinction cultivation. MiE-23b has a genome size of 1.28 Mbp with a genomic GC content of 50.2%, contains 3 rRNA genes and 40 tRNAs. The genome is complete, consisting of a circular chromosome. The genome contains genes encoding rhodopsins but lacks the biosynthetic pathway for retinal biosynthesis. No genes for flagella or pilus assembly and chemotaxis were annotated. Pathways for the biosynthesis of all amino acids except for methionine and histidine were predicted. Further, pathways for riboflavin, pyridoxal, coenzyme A, and menaquinone were identified. The closest cultivated relative is Rhodoluna lacicola MWH-Ta8 (GCF_000699505), with an average amino acid identity of 65.06% and average nucleotide identity of 67.72%. Current GTDB classification (R220): d__Bacteria; p__Actinomycetota; c__Actinomycetia; o__Actinomycetales; f__Microbacteriaceae; g__Rhodoluna; s__. 
Classification
Bacteria » Actinomycetota » Actinomycetes » Micrococcales » Microbacteriaceae » Rhodoluna » Rhodoluna miladensis
Parent
Rhodoluna

Genomics

Accession
NCBI Assembly:GCA_965234705.1
Cultures
Strain sc|0038944
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 97.48%
  • Contamination: 0.0%
  • Quality: 97.48
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
898.3 ×
Source
Other features
  • G+C Content: 50.2%
  • Coding Density: 94.7%
  • Codon Table: 11
  • N50: 1,287,838 bp
  • Contigs: 1
  • Largest Contig: 1,287,838 bp
  • Assembly Length: 1,287,838 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 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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seqco.de/r:opjv7zsc