Tabrizicola rara


Citation

Formal styling
Tabrizicola rara 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:48735

Nomenclature

Rank
Species
Syllabication
ra'ra
Etymology
L. fem. adj. rara, sporadic or uncommon, referring to the sporadic isolation and recovery from disparate sources of members of this species
Nomenclatural type
NCBI Assembly: GCA_965234505.1
Reference strain
Strain sc|0038956: LH-M10 Lookup StrainInfo
Nomenclatural status
Validly published under the SeqCode

Taxonomy

Description
Type strain is Tabrizicola rara LH-M10 (GCA_965234505.1), isolated from 50 m depth from Lake Lugano, Switzerland (date: 2019-11-05), via high-throughput dilution to extinction cultivation. LH-M10 has a genome size of 4.2 Mbp with a genomic GC content of 62.8%, contains 4 rRNA genes and 48 tRNAs. The genome is a high-quality draft consisting of 22 contigs. The genome contains the complete Calvin cycle for carbon fixation via RuBisCO. Genes for flagellar assembly were annotated in the genome. Pathways for urea and taurine degradation, glycolate oxidation and the biosynthesis of all amino acids were predicted. Further, pathways for riboflavin, coenzyme A, cobalamin, and heme biosynthesis were identified. The closest cultivated relative is Rhodobacter thermarum YIM 73036 (GCF_003574395.1; Basonym: Tabrizicola thermarum Khan et al. 2019), with an average amino acid identity of 75.7% and average nucleotide identity of 77.1%. Current GTDB classification (R220): d__Bacteria; p__Pseudomonadota; c__Alphaproteobacteria; o__Rhodobacterales; f__Rhodobacteraceae; g__Tabrizicola; s__Tabrizicola sp903917595.
Classification
Bacteria » Pseudomonadota » Alphaproteobacteria » Rhodobacterales » Paracoccaceae » Tabrizicola » Tabrizicola rara
Parent
Tabrizicola

Genomics

Accession
NCBI Assembly:GCA_965234505.1
Cultures
Strain sc|0038956
Type
Isolate Genome
Estimated Quality Metrics
  • Completeness: 93.28%
  • Contamination: 0.0%
  • Quality: 93.28
Ribosomal and transfer RNA genes
  • 2 16S rRNAs (up to 100.0%)
  • 1 23S rRNA (up to 100.0%)
  • tRNAs for 19 amino acids
Sequencing depth
214.0 ×
Source
Other features
  • G+C Content: 62.8%
  • Coding Density: 90.99%
  • Codon Table: 11
  • N50: 861,778 bp
  • Contigs: 22
  • Largest Contig: 1,334,515 bp
  • Assembly Length: 4,167,651 bp
  • Ambiguous Assembly Fraction: 9.6e-05%
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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