ArticleProceedings. Biological sciences2017
Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error.
Article in Proceedings. Biological sciences, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed, 93 citations in OpenAlex.
- Article
- Effect of copper and nickel exposure on ribosomal DNA variation in Daphnia pulex mutation accumulation lines.G3 (Bethesda, Md.) · 2025Article
- Unraveling the Evolutionary Patterns of GenusBiology · 2025Article
- Molecular Identification and Genotyping ofArchives of Razi Institute · 2025Article
- The Ribosomal Operon Database: A Full-Length rDNA Operon Database Derived From Genome Assemblies.Molecular ecology resources · 2025Article
- Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing.G3 (Bethesda, Md.) · 2024Article
- VESPA: an optimized protocol for accurate metabarcoding-based characterization of vertebrate eukaryotic endosymbiont and parasite assemblages.Nature communications · 2024Article
- Insights into freshwater ciliate diversity through high throughput DNA metabarcoding.FEMS microbes · 2024Article
- Mock community experiments can inform on the reliability of eDNA metabarcoding data: a case study on marine phytoplankton.Scientific reports · 2023Article
- Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms.ISME communications · 2023Article
- Ciliate Morpho-Taxonomy and Practical Considerations before Deploying Metabarcoding to Ciliate Community Diversity Surveys in Urban Receiving Waters.Microorganisms · 2022Review
- Planktonic microbial communities from microbialite-bearing lakes sampled along a salinity-alkalinity gradient.Limnology and oceanography · 2022Article
- Integrative studies on three new freshwaterMarine life science & technology · 2022Article
- Insights into the phylogeny of the ciliate of class Colpodea based on multigene data.Ecology and evolution · 2022Article
- The Effects of Breed and Residual Feed Intake Divergence on the Abundance and Active Population of Rumen Microbiota in Beef Cattle.Animals : an open access journal from MDPI · 2022Article
- Coupling between Ribotypic and Phenotypic Traits of Protists across Life Cycle Stages and Temperatures.Microbiology spectrum · 2021Article
- New contributions to the phylogeny of the ciliate class Heterotrichea (Protista, Ciliophora): analyses at family-genus level and new evolutionary hypotheses.Science China. Life sciences · 2021Article
- Taxonomy and Molecular Phylogeny of Two New Urostylid Ciliates (Protozoa: Ciliophora) From Chinese Wetlands and Establishment of a New Genus.Frontiers in microbiology · 2021Article
- New contributions to two ciliate genera (Ciliophora, Heterotrichea) based on morphological and molecular analyses, with description of a new Gruberia species.BMC microbiology · 2020Article
- Comparative Studies on the Polymorphism and Copy Number Variation of mtSSU rDNA in Ciliates (Protista, Ciliophora): Implications for Phylogenetic, Environmental, and Ecological Research.Microorganisms · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Small subunit ribosomal DNA (SSU rDNA) is widely used for phylogenetic inference, barcoding and other taxonomy-based analyses. Recent studies indicate that SSU rDNA of ciliates may have a high level of sequence variation within a single cell, which impacts the interpretation of rDNA-based surveys. However, sequence variation can come from a variety of sources including experimental errors, especially the mutations generated by DNA polymerase in PCR. In the present study, we explore the impact of four DNA polymerases on sequence variation and find that low-fidelity polymerases exaggerate the estimates of single-cell sequence variation. Therefore, using a polymerase with high fidelity is essential for surveys of sequence variation. Another source of variation results from errors during amplification of SSU rDNA within the polyploidy somatic macronuclei of ciliates. To investigate further the impact of SSU rDNA copy number variation, we use a high-fidelity polymerase to examine the intra-individual SSU rDNA polymorphism in ciliates with varying levels of macronuclear amplification:
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.