ArticleBMC genomics2009
Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 34 citations in OpenAlex.
- Extensive spontaneous genome reduction in Paraburkholderia sabiae.Scientific reports · 2026Article
- On the origins and variation of nucleotide skews of archaeal genomes.Frontiers in microbiology · 2026Article
- Distinct Expansion of Group II Introns During Evolution of Prokaryotes and Possible Factors Involved in Its Regulation.Frontiers in microbiology · 2022Article
- Evolutionary History of Mitochondrial Genomes in Discoba, Including the Extreme Halophile Pleurostomum flabellatum (Heterolobosea).Genome biology and evolution · 2021Article
- Article
- Reconsidering plasmid maintenance factors for computational plasmid design.Computational and structural biotechnology journal · 2019Review
- Accelerated Laboratory Evolution Reveals the Influence of Replication on the GC Skew in Escherichia coli.Genome biology and evolution · 2018Article
- Euclidean Distance Analysis Enables Nucleotide Skew Analysis in Viral Genomes.Computational and mathematical methods in medicine · 2018Article
- Optimization of amino acid replacement costs by mutational pressure in bacterial genomes.Scientific reports · 2017Article
- Three novel bacteriophages isolated from the East African Rift Valley soda lakes.Virology journal · 2016Article
- Codon Adaptation of Plastid Genes.PloS one · 2016Article
- Multiple Factors Drive Replicating Strand Composition Bias in Bacterial Genomes.International journal of molecular sciences · 2015Article
- Isolation of a minireplicon of the plasmid pG6303 of Lactobacillus plantarum G63 and characterization of the plasmid-encoded Rep replication protein.Journal of genetics · 2015Article
- The mitochondrial genomes of the glaucophytes Gloeochaete wittrockiana and Cyanoptyche gloeocystis: multilocus phylogenetics suggests a monophyletic archaeplastida.Genome biology and evolution · 2014Article
- Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: a new appraisal.BMC genomics · 2014Article
- DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes.Current genomics · 2012Article
- A blueprint for a mutationist theory of replicative strand asymmetries formation.Current genomics · 2012Article
- Measures of compositional strand bias related to replication machinery and its applications.Current genomics · 2012Article
- Validation of bacterial replication termination models using simulation of genomic mutations.PloS one · 2012Article
- A large scale comparative genomic analysis reveals insertion sites for newly acquired genomic islands in bacterial genomes.BMC microbiology · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDue to their bi-directional replication machinery starting from a single finite origin, bacterial genomes show characteristic nucleotide compositional bias between the two replichores, which can be visualised through GC skew or (C-G)/(C+G). Although this polarisation is used for computational prediction of replication origins in many bacterial genomes, the degree of GC skew visibility varies widely among different species, necessitating a quantitative measurement of GC skew strength in order to provide confidence measures for GC skew-based predictions of replication origins.
resultsHere we discuss a quantitative index for the measurement of GC skew strength, named the generalised GC skew index (gGCSI), which is applicable to genomes of any length, including bacterial chromosomes and plasmids. We demonstrate that gGCSI is independent of the window size and can thus be used to compare genomes with different sizes, such as bacterial chromosomes and plasmids. It can suggest the existence of different replication mechanisms in archaea and of rolling-circle replication in plasmids. Correlation of gGCSI values between plasmids and their corresponding host chromosomes suggests that within the same strain, these replicons have reproduced using the same replication machinery and thus exhibit similar strengths of replication strand skew.
conclusionsgGCSI can be applied to genomes of any length and thus allows comparative study of replication-related mutation and selection pressures in genomes of different lengths such as bacterial chromosomes and plasmids. Using gGCSI, we showed that replication-related mutation or selection pressure is similar for replicons with similar machinery.
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.