ArticleBMC genomics2007
Separating the effects of mutation and selection in producing DNA skew in bacterial chromosomes.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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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.
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Who cites it
18 citing papers in PubMed, 26 citations in OpenAlex.
- Mitochondrial Genome Variations and Possible Adaptive Implications in Some Tephritid Flies (Diptera, Tephritidae).International journal of molecular sciences · 2025Article
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- Substitution rate heterogeneity across hexanucleotide contexts in noncoding chloroplast DNA.G3 (Bethesda, Md.) · 2022Article
- Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups.Journal of molecular evolution · 2022Article
- Novel metrics for quantifying bacterial genome composition skews.BMC genomics · 2018Article
- The Divided Bacterial Genome: Structure, Function, and Evolution.Microbiology and molecular biology reviews : MMBR · 2017Review
- The Impact of Selection at the Amino Acid Level on the Usage of Synonymous Codons.G3 (Bethesda, Md.) · 2017Article
- A novel skew analysis reveals substitution asymmetries linked to genetic code GC-biases and PolIII a-subunit isoforms.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Codon Adaptation of Plastid Genes.PloS one · 2016Article
- DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes.Current genomics · 2012Article
- Measures of compositional strand bias related to replication machinery and its applications.Current genomics · 2012Article
- Atypical at skew in Firmicute genomes results from selection and not from mutation.PLoS genetics · 2011Article
- Chromosomal rearrangements formed by rrn recombination do not improve replichore balance in host-specific Salmonella enterica serovars.PloS one · 2010Article
- Article
- Testing for selection on synonymous sites in plant mitochondrial DNA: the role of codon bias and RNA editing.Journal of molecular evolution · 2010Article
- Measurements of spontaneous rates of mutations in the recent past and the near future.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2010Review
- Article
- Genome rhetoric and the emergence of compositional bias.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMany bacterial chromosomes display nucleotide asymmetry, or skew, between the leading and lagging strands of replication. Mutational differences between these strands result in an overall pattern of skew that is centered about the origin of replication. Such a pattern could also arise from selection coupled with a bias for genes coded on the leading strand. The relative contributions of selection and mutation in producing compositional skew are largely unknown.
resultsWe describe a model to quantify the contribution of mutational differences between the leading and lagging strands in producing replication-induced skew. When the origin and terminus of replication are known, the model can be used to estimate the relative accumulation of G over C and of A over T on the leading strand due to replication effects in a chromosome with bidirectional replication arms. The model may also be implemented in a maximum likelihood framework to estimate the locations of origin and terminus. We find that our estimations for the origin and terminus agree very well with the location of genes that are thought to be associated with the replication origin. This indicates that our model provides an accurate, objective method of determining the replication arms and also provides support for the hypothesis that these genes represent an ancestral cluster of origin-associated genes.
conclusionThe model has several advantages over other methods of analyzing genome skew. First, it quantifies the role of mutation in generating skew so that its effect on composition, for example codon bias, can be assessed. Second, it provides an objective method for locating origin and terminus, one that is based on chromosome-wide accumulation of leading vs lagging strand nucleotide differences. Finally, the model has the potential to be utilized in a maximum likelihood framework in order to analyze the effect of chromosome rearrangements on nucleotide composition.
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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.