ArticlePloS one2009
Diversity of 23S rRNA genes within individual prokaryotic genomes.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed, 73 citations in OpenAlex.
- Laboratory strategies for the identification of Burkholderia species: From classical phenotyping to advanced genomic and proteomic approaches.Antonie van Leeuwenhoek · 2026Review
- Different phytoplankton distributions and assembly processes in marine water masses with contrasting nutrient conditions.BMC microbiology · 2025Article
- Article
- Genetic Markers ofCurrent issues in molecular biology · 2024Article
- Harnessing the intragenomic variability of rRNA operons to improve differentiation of Vibrio species.Scientific reports · 2024Article
- Comparative genomics ofFrontiers in microbiology · 2024Article
- RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing.Frontiers in microbiology · 2023Article
- Sugarcane Genotypes with Contrasting Biological Nitrogen Fixation Efficiencies Differentially Modulate Nitrogen Metabolism, Auxin Signaling, and Microorganism Perception Pathways.Plants (Basel, Switzerland) · 2022Article
- New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia.International journal of microbiology · 2022Review
- Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics.Frontiers in microbiology · 2022Review
- The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation.RNA biology · 2021Review
- µgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria.Scientific reports · 2020Article
- Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing.NAR genomics and bioinformatics · 2020Article
- Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum.Nature communications · 2017Article
- Macrolide Resistance in the Syphilis Spirochete, Treponema pallidum ssp. pallidum: Can We Also Expect Macrolide-Resistant Yaws Strains?The American journal of tropical medicine and hygiene · 2015Article
- Differentiation of non-pylori Helicobacter species based on PCR-restriction fragment length polymorphism of the 23S rRNA gene.World journal of microbiology & biotechnology · 2014Article
- Prevalence and molecular analyses of hemotrophic Mycoplasma spp. (hemoplasmas) detected in sika deer (Cervus nippon yesoensis) in Japan.The Journal of veterinary medical science · 2014Article
- Article
- Structure of rrn operons in pathogenic non-cultivable treponemes: sequence but not genomic position of intergenic spacers correlates with classification of Treponema pallidum and Treponema paraluiscuniculi strains.Journal of medical microbiology · 2013Article
- Development of a broad-range 23S rDNA real-time PCR assay for the detection and quantification of pathogenic bacteria in human whole blood and plasma specimens.BioMed research international · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundThe concept of ribosomal constraints on rRNA genes is deduced primarily based on the comparison of consensus rRNA sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept within organisms with multiple rRNA operons. METHODOLOGY/PRINCIPAL
findingsUsing the 23S rRNA gene as an example, we analyzed the diversity among individual rRNA genes within a genome. Of 184 prokaryotic species containing multiple 23S rRNA genes, diversity was observed in 113 (61.4%) genomes (mean 0.40%, range 0.01%-4.04%). Significant (1.17%-4.04%) intragenomic variation was found in 8 species. In 5 of the 8 species, the diversity in the primary structure had only minimal effect on the secondary structure (stem versus loop transition). In the remaining 3 species, the diversity significantly altered local secondary structure, but the alteration appears minimized through complex rearrangement. Intervening sequences (IVS), ranging between 9 and 1471 nt in size, were found in 7 species. IVS in Deinococcus radiodurans and Nostoc sp. encode transposases. T. tengcongensis was the only species in which intragenomic diversity >3% was observed among 4 paralogous 23S rRNA genes. CONCLUSIONS/SIGNIFICANCE: These findings indicate tight ribosomal constraints on individual 23S rRNA genes within a genome. Although classification using primary 23S rRNA sequences could be erroneous, significant diversity among paralogous 23S rRNA genes was observed only once in the 184 species analyzed, indicating little overall impact on the mainstream of 23S rRNA gene-based prokaryotic taxonomy.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.