Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons

By Silvia G. Acinas, L. Marcelino, V. Klepac‐Ceraj, M. Polz. Journal of Bacteriology, 2004

644 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/b0e491ab573aef142a7124aeb5c22d63b69c0a66

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Citations in the corpus

UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing (2016, background): “An Exact ZOTU is probably correct, though it could be an error that reproduces a sequence found in the database (this is more likely that it might appear as explained in the discussion of chimera filtering below).”
Deciphering the effects of nitrogen, phosphorus, and temperature on cyanobacterial bloom intensification, diversity, and toxicity in western Lake Erie (2019, background): “Read counts can provide an inaccurate measure of cell abundances, as multiple copies of a gene may be present in a genome and copy numbers can differ between species and within species (Acinas et al. 2004).”
Use of 16S rRNA and rpoB Genes as Molecular Markers for Microbial Ecology Studies (2006, background): “These large inserts form secondary structures (3) suggestive of a functional role in the ribosome.”
Conservative Fragments in Bacterial 16S rRNA Genes and Primer Design for 16S Ribosomal DNA Amplicons in Metagenomic Studies (2009, background): “In prokaryotes, the 16S ribosomal RNA (rRNA) genes are essential and occur in at least one copy in a genome [1].”
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics (2015, background): “…pitfalls are low resolution at the species level (Petrosino et al., 2009; Nalbantoglu et al., 2014), a range in gene copy number in many species (Acinas et al., 2004), horizontal transfer of 16S rRNA genes (Schouls et al., 2003; Bodilis et al., 2012), and the fact that < 0.1% of the total…”
The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses (2013, background): “incidence of horizontal gene transfer was proposed to be the potential cause [5].”
The Functional Significance of Ribosomal (r)DNA Variation: Impacts on the Evolutionary Ecology of Organisms (2005, background): “In a survey of 76 bacterial genomes, Acinas et al. (2004) found that the maximum number of rDNA operons was 15 and the minimum, and most common, was 1.”
Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics (2014, neutral): “based analysis that target a single variable region of the 16S rRNA gene [46,47].”
Deciphering microbial interactions and detecting keystone species with co-occurrence networks (2014, background): “In addition genomes with several gene copies may have non-identical copies and this intragenomic heterogeneity (Acinas et al., 2004; Sun et al., 2013) can lead to counting one species as several species.”
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. (2014, background): “Species belonging to Thermoanaerobacter and Caldicellulosiruptor are known to display higher intercistronic variation among multiple 16S rRNA gene copies (Acinas et al., 2004; Pei et al., 2010).”
PCR-Induced Sequence Artifacts and Bias: Insights from Comparison of Two 16S rRNA Clone Libraries Constructed from the Same Sample (2005, background): “5 rRNA operons per genome [2]), these 12 TABLE 1.”
Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. (2005, background): “Although this problem is present with prokaryotes for which copy number varies between 1 (for example in the typical photosynthetic picoplankton genus Prochlorococcus [44]) and 13 (for example in Bacillus cereus [45]), this range is much wider in eukaryotes.”
Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance (2012, methodology): “Hierarchical clustering (complete linkage) of communities from the microbiome of a human (subject F1-3 in [13]) based on phylogenetic similarity (weighted UniFrac distance metric) for observed relative gene abundances gi (A) and for estimated organismal relative abundances n̂i (B).”
Novel and Unexpected Prokaryotic Diversity in Water and Sediments of the Alkaline, Hypersaline Lakes of the Wadi An Natrun, Egypt (2007, background): “While it is possible that this increased abundance could be an artifact of multiple rrn copy number which is common among the low G + C Gramtype-positive group [3], no clones affiliated with either the Halanaerobiales or the Clostridiales were retrieved from Lake Hamra water.”