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A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.
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Most DNA resides in the nucleus of a cell. However, some organelles in the cell cytoplasm⁠—such as chloroplasts and mitochondria⁠—also have their own DNA. These organelles replicate their DNA independently of the nuclear DNA of the cell in which they reside. Non-nuclear inheritance describes the inheritance of genes from structures other than the nucleus.
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Substitution rate heterogeneity across hexanucleotide contexts in noncoding chloroplast DNA.

Brian R Morton1

  • 1Department of Biology, Barnard College, Columbia University, New York, NY 10027, USA.

G3 (Bethesda, Md.)
|June 14, 2022
PubMed
Summary
This summary is machine-generated.

Chloroplast DNA substitution rates vary significantly based on the surrounding DNA sequence context. This context influences mutation types and evolutionary trajectories, impacting sequence analysis and natural selection studies.

Keywords:
chloroplast DNAcontextgenome evolutionmutationsubstitution model

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Area of Science:

  • Molecular Evolution
  • Genomics
  • Bioinformatics

Background:

  • Noncoding chloroplast DNA sequences exhibit variable substitution rates.
  • Understanding these variations is crucial for accurate evolutionary analyses.

Purpose of the Study:

  • To investigate the influence of hexanucleotide context on DNA substitution rates.
  • To analyze rate heterogeneity and transition:transversion bias across different contexts.

Main Methods:

  • Analysis of substitution rates in relation to the 3 bases flanking each side of the substitution site (hexanucleotide context).
  • Examination of A+T content, purine/pyrimidine arrangement, and strand skew.
  • Statistical control for nucleotide proximity to the substitution site.

Main Results:

  • Observed over 100-fold variation in substitution rates among contexts, especially for A and T.
  • Identified a >200-fold variation in transition:transversion bias, consistent with a CpG effect.
  • Demonstrated correlation between A+T content, strand arrangement, and rate variation.
  • Showed that the third and fourth nucleotides from the substitution site significantly influence dynamics.

Conclusions:

  • Noncoding DNA sites evolve differently depending on their context.
  • Substitution dynamics are more complex than previously assumed.
  • Context-dependent substitution matrices are valuable for sequence analysis, including natural selection studies.