ArticlePLoS biology2011
Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences.
Article in PLoS biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 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
83 citing papers in PubMed, 175 citations in OpenAlex.
- Genetic Variation and Phylogenetic Analysis of Indonesian Sugarcane (Tropical life sciences research · 2026Article
- Host MiRNA responses during different waves of SARS-CoV-2: diagnostic implications of miR-19a-3p, miR-374b-5p, miR-15b-5p, and miR-320a-5p expression.BMC infectious diseases · 2026Article
- Chloroplast Genome of Arisaema takesimense: Comparative Genomics and Phylogenetic Insights into the Arisaema.Biochemical genetics · 2026Article
- Comparative chloroplast genomics reveals codon usage bias, simple sequence repeat dynamics, and phylogenomic relationships in Urticaceae.Frontiers in plant science · 2026Article
- Genetic constraints on protein loop evolution: out-of-frame stop codons limitFrontiers in molecular biosciences · 2026Article
- Chloroplast genome, an effective strategy for identifying hybrid species, using Dendrobium 'Black Gold' as an example.BMC plant biology · 2025Article
- The Identification of a New GeneGenes · 2025Article
- Evolutionary Insights into the Length Variation of DNA Damage Response Proteins Across Eukaryotes.Genome biology and evolution · 2025Article
- Comparative and phylogenetic analysis of the complete chloroplast genome sequences of Melanoseris cyanea group.Scientific reports · 2025Article
- Are Changes Occurring in Bacterial Taxa Community and Diversity with the Utilization of Different Substrates within SIR Measurements?Microorganisms · 2024Article
- Genetic Variations in theCells · 2024Article
- Comparative and phylogenetic analysis of the complete chloroplast genomes of ten Pittosporum species from East Asia.Functional & integrative genomics · 2024Article
- Plastid genome data provide new insights into the dynamic evolution of the tribe Ampelopsideae (Vitaceae).BMC genomics · 2024Article
- Chloroplast genome structure analysis ofFrontiers in plant science · 2024Article
- The complete chloroplast genome ofMitochondrial DNA. Part B, Resources · 2024Article
- Characteristics and Comparative Analysis of Seven Complete Plastomes ofInternational journal of molecular sciences · 2023Article
- Characteristics of plastid genomes in the genus Ceratostigma inhabiting arid habitats in China and their phylogenomic implications.BMC plant biology · 2023Article
- Extensive characterization of 28 complete chloroplast genomes ofComputational and structural biotechnology journal · 2023Article
- Article
- Comparative analysis of chloroplast genome and new insights into phylogenetic relationships ofFrontiers in plant science · 2023Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The genome-sequencing gold rush has facilitated the use of comparative genomics to uncover patterns of genome evolution, although their causal mechanisms remain elusive. One such trend, ubiquitous to prokarya and eukarya, is the association of insertion/deletion mutations (indels) with increases in the nucleotide substitution rate extending over hundreds of base pairs. The prevailing hypothesis is that indels are themselves mutagenic agents. Here, we employ population genomics data from Escherichia coli, Saccharomyces paradoxus, and Drosophila to provide evidence suggesting that it is not the indels per se but the sequence in which indels occur that causes the accumulation of nucleotide substitutions. We found that about two-thirds of indels are closely associated with repeat sequences and that repeat sequence abundance could be used to identify regions of elevated sequence diversity, independently of indels. Moreover, the mutational signature of indel-proximal nucleotide substitutions matches that of error-prone DNA polymerases. We propose that repeat sequences promote an increased probability of replication fork arrest, causing the persistent recruitment of error-prone DNA polymerases to specific sequence regions over evolutionary time scales. Experimental measures of the mutation rates of engineered DNA sequences and analyses of experimentally obtained collections of spontaneous mutations provide molecular evidence supporting our hypothesis. This study uncovers a new role for repeat sequences in genome evolution and provides an explanation of how fine-scale sequence contextual effects influence mutation rates and thereby evolution.
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.