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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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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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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Green algae and plants, including green stems and unripe fruit, harbor specialized organelles called chloroplasts to carry out photosynthesis. They coordinate both stages of photosynthesis — the light-dependent reactions and the light-independent reactions. The light-dependent reactions use sunlight to release oxygen and produce chemical energy in the form of ATP and NADPH, and the light-independent reactions capture CO2 and use ATP and NADPH to produce sugar.
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Related Experiment Video

Updated: Jul 21, 2025

High-Throughput Robotically Assisted Isolation of Temperature-sensitive Lethal Mutants in Chlamydomonas reinhardtii
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Context and Mutation in Gymnosperm Chloroplast DNA.

Brian R Morton1

  • 1Department of Biology, Barnard College, Columbia University, 3009 Broadway, New York, NY 10027, USA.

Genes
|July 29, 2023
PubMed
Summary

Chloroplast DNA mutation rates are influenced by surrounding DNA bases in gymnosperms, similar to flowering plants. This context-dependency impacts the evolutionary dynamics of chloroplast genomes.

Area of Science:

  • Genomics
  • Molecular Evolution
  • Plant Biology

Background:

  • Mutation and repair processes in chloroplast genomes are known to be context-dependent.
  • Flanking DNA bases (at least three on each side) influence mutation rates at specific sites.

Purpose of the Study:

  • To analyze sequence context and substitution patterns at noncoding and fourfold degenerate coding sites in gymnosperm DNA.
  • To infer substitution direction and generate context-dependent rate matrices.

Main Methods:

  • Analysis of DNA sequences in sets of three to infer substitution direction.
  • Generation of context-dependent rate matrices.
  • Limited analysis to tetranucleotide context due to dataset size.

Main Results:

Keywords:
context dependencygenome evolutionmutation modelplastome

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  • Significant contextual effects on mutation patterns were observed in gymnosperm DNA.
  • These patterns show similarities to those found in angiosperms.
  • Evidence suggests these effects influence underlying mutation/repair dynamics.

Conclusions:

  • The study extends the understanding of complex mutation patterns in plastome lineages.
  • Context-dependent mutation dynamics significantly affect chloroplast genome evolution.
  • Findings highlight conserved mutation patterns across different plant lineages.