ArticleJournal of molecular evolution2007
Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in bacteria.
Article in Journal of molecular evolution, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed, 77 citations in OpenAlex.
- Development of a Rapid, Culture-Free, Universal Microbial Identification System Using Internal Transcribed Spacer Targeting Primers.The Journal of infectious diseases · 2025Article
- Multi-marker comparative analysis of 18S, ITS1, and ITS2 primers for human gut mycobiome profiling.Frontiers in bioinformatics · 2025Article
- GROND: a quality-checked and publicly available database of full-length 16S-ITS-23S rRNA operon sequences.Microbial genomics · 2024Article
- Harnessing Variabilities in Digital Melt Curves for Accurate Identification of Bacteria.Analytical chemistry · 2023Article
- Human gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model.Microbiome · 2021Article
- Microdiversity and phylogeographic diversification of bacterioplankton in pelagic freshwater systems revealed through long-read amplicon sequencing.Microbiome · 2021Article
- Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?IMA fungus · 2020Article
- Development of a real-time PCR method for the specific detection of the novel pear pathogen Erwinia uzenensis.PloS one · 2019Article
- Early Ongoing Speciation ofFrontiers in microbiology · 2018Article
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- Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum.Nature communications · 2017Article
- Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer.GigaScience · 2017Article
- Barcoding theBioMed research international · 2017Article
- Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms.The ISME journal · 2016Article
- Estimating Divergence Times and Substitution Rates in Rhizobia.Evolutionary bioinformatics online · 2016Article
- Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex.PloS one · 2016Article
- Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12.PloS one · 2015Article
- Article
- Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi.Ecology and evolution · 2013Article
- 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
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Variation in the internal transcribed spacer (ITS) of the rRNA (rrn) operon is increasingly used to infer population-level diversity in bacterial communities. However, intragenomic ITS variation may skew diversity estimates that do not correct for multiple rrn operons within a genome. This study characterizes variation in ITS length, tRNA composition, and intragenomic nucleotide divergence across 155 Bacteria genomes. On average, these genomes encode 4.8 rrn operons (range: 2-15) and contain 2.4 unique ITS length variants (range: 1-12) and 2.8 unique sequence variants (range: 1-12). ITS variation stems primarily from differences in tRNA gene composition, with ITS regions containing tRNA-Ala + tRNA-Ile (48% of sequences), tRNA-Ala or tRNA-Ile (10%), tRNA-Glu (11%), other tRNAs (3%), or no tRNA genes (27%). Intragenomic divergence among paralogous ITS sequences grouped by tRNA composition ranges from 0% to 12.11% (mean: 0.94%). Low divergence values indicate extensive homogenization among ITS copies. In 78% of alignments, divergence is <1%, with 54% showing zero variation and 81% containing at least two identical sequences. ITS homogenization occurs over relatively long sequence tracts, frequently spanning the entire ITS, and is largely independent of the distance (basepairs) between operons. This study underscores the potential contribution of interoperon ITS variation to bacterial microdiversity studies, as well as unequivocally demonstrates the pervasiveness of concerted evolution in the rrn gene family.
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