ArticlePLoS genetics2011
Atypical at skew in Firmicute genomes results from selection and not from mutation.
Article in PLoS genetics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 43 citations in OpenAlex.
- Rapid GC content evolution in rice through GC-biased gene conversion and selection for translation efficiency.Nature communications · 2026Article
- Purine bias in bacterial genes is driven by runaway transcription.Nature microbiology · 2026Article
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Phylogenetic Reassessment of Murinae Inferred from the Mitogenome of the Monotypic GenusBiology · 2025Article
- High Nucleotide Skew Palindromic DNA Sequences Function as Potential Replication Origins due to their Unzipping Propensity.Journal of molecular evolution · 2024Article
- Selection on synonymous sites: the unwanted transcript hypothesis.Nature reviews. Genetics · 2024Review
- Article
- Comparative Mitogenome Analysis of Gerbils and the Mitogenome Phylogeny of Gerbillinae (Rodentia: Muridae).Biochemical genetics · 2022Article
- An investigation of codon usage pattern analysis in pancreatitis associated genes.BMC genomic data · 2022Article
- Reply to: Testing the adaptive hypothesis of lagging-strand encoding in bacterial genomes.Nature communications · 2022Article
- Unusual mammalian usage of TGA stop codons reveals that sequence conservation need not imply purifying selection.PLoS biology · 2022Article
- SkewDB, a comprehensive database of GC and 10 other skews for over 30,000 chromosomes and plasmids.Scientific data · 2022Article
- Codon Usage Bias Correlates With Gene Length in Neurodegeneration Associated Genes.Frontiers in neuroscience · 2022Article
- Using multi-layer perceptron to identify origins of replication in eukaryotes via informative features.BMC bioinformatics · 2021Article
- Causes and Consequences of Purifying Selection on SARS-CoV-2.Genome biology and evolution · 2021Article
- Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias.Molecular biology and evolution · 2021Article
- Evidence for Strong Mutation Bias toward, and Selection against, U Content in SARS-CoV-2: Implications for Vaccine Design.Molecular biology and evolution · 2021Article
- Phylogeny and evolution ofPeerJ · 2021Article
- Geographic Variation ofFrontiers in genetics · 2021Article
- iterb-PPse: Identification of transcriptional terminators in bacterial by incorporating nucleotide properties into PseKNC.PloS one · 2020Article
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The second parity rule states that, if there is no bias in mutation or selection, then within each strand of DNA complementary bases are present at approximately equal frequencies. In bacteria, however, there is commonly an excess of G (over C) and, to a lesser extent, T (over A) in the replicatory leading strand. The low G+C Firmicutes, such as Staphylococcus aureus, are unusual in displaying an excess of A over T on the leading strand. As mutation has been established as a major force in the generation of such skews across various bacterial taxa, this anomaly has been assumed to reflect unusual mutation biases in Firmicute genomes. Here we show that this is not the case and that mutation bias does not explain the atypical AT skew seen in S. aureus. First, recently arisen intergenic SNPs predict the classical replication-derived equilibrium enrichment of T relative to A, contrary to what is observed. Second, sites predicted to be under weak purifying selection display only weak AT skew. Third, AT skew is primarily associated with largely non-synonymous first and second codon sites and is seen with respect to their sense direction, not which replicating strand they lie on. The atypical AT skew we show to be a consequence of the strong bias for genes to be co-oriented with the replicating fork, coupled with the selective avoidance of both stop codons and costly amino acids, which tend to have T-rich codons. That intergenic sequence has more A than T, while at mutational equilibrium a preponderance of T is expected, points to a possible further unresolved selective source of skew.
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