ArticleGenetics2006
Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition.
Article in Genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
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- Solanum aculeatissimum and Solanum torvum chloroplast genome sequences: a comparative analysis with other Solanum chloroplast genomes.BMC genomics · 2024Article
- The Construction of lncRNA/circRNA-miRNA-mRNA Networks Reveals Functional Genes Related to Growth Traits inInternational journal of molecular sciences · 2024Article
- Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers.Journal of molecular evolution · 2023Article
- CDMAP/CDVIS: context-dependent mutation analysis package and visualization software.G3 (Bethesda, Md.) · 2023Article
- Substitution rate heterogeneity across hexanucleotide contexts in noncoding chloroplast DNA.G3 (Bethesda, Md.) · 2022Article
- Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations.G3 (Bethesda, Md.) · 2022Article
- Context-Dependent Substitution Dynamics in Plastid DNA Across a Wide Range of Taxonomic Groups.Journal of molecular evolution · 2022Article
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- Genetic Diversity and Population Structure of aFrontiers in plant science · 2019Article
- Compositional bias coupled with selection and mutation pressure drives codon usage inFood science and biotechnology · 2018Article
- Genome re-sequencing, SNP analysis, and genetic mapping of the parental lines of a commercial FBreeding science · 2018Article
- Codon usage vis-a-vis start and stop codon context analysis of three dicot species.Journal of genetics · 2018Article
- Contributions of Zea mays subspecies mexicana haplotypes to modern maize.Nature communications · 2017Article
- Transcriptome Analysis and Differential Gene Expression on the Testis of Orange Mud Crab, Scylla olivacea, during Sexual Maturation.PloS one · 2017Article
- On the Causes of Evolutionary Transition:Transversion Bias.Molecular biology and evolution · 2016Article
- Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus.BMC genomics · 2015Article
- CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea.Database : the journal of biological databases and curation · 2015Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We examine variation in mutation dynamics across a single genome (Zea mays ssp. mays) in relation to regional and flanking base composition using a data set of 10,472 SNPs generated by resequencing 1776 transcribed regions. We report several relationships between flanking base composition and mutation pattern. The A + T content of the two sites immediately flanking the mutation site is correlated with rate, transition bias, and GC --> AT pressure. We also observe a significant CpG effect, or increase in transition rate at CpG sites. At the regional level we find that the strength of the CpG effect is correlated with regional A + T content, ranging from a 1.7-fold increase in transition rate in relatively G + C-rich regions to a 2.6-fold increase in A + T-rich regions. We also observe a relationship between locus A + T content and GC --> AT pressure. This regional effect is in opposition to the influence of the two immediate neighbors in that GC --> AT pressure increases with increasing locus A + T content but decreases with increasing flanking base A + T content and may represent a relationship between genome location and mutation bias. The data indicate multiple context effects on mutations, resulting in significant variation in mutation dynamics across the genome.
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Registered trials
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