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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 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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The Anatomy of Chloroplasts01:08

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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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A Guide to the Chloroplast Transcriptome Analysis Using RNA-Seq.

Elena J S Michel1,2, Amber M Hotto1, Susan R Strickler1

  • 1Boyce Thompson Institute, Ithaca, NY, USA.

Methods in Molecular Biology (Clifton, N.J.)
|July 11, 2018
PubMed
Summary
This summary is machine-generated.

This study introduces ChloroSeq, a new bioinformatics pipeline for analyzing chloroplast RNA metabolism. It enables detailed study of organellar gene expression, splicing, and RNA editing, improving our understanding of nucleus-organelle interactions.

Keywords:
ChloroSeqChloroplastLeaf developmentOrganellesRNA-Seq

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Area of Science:

  • Plant molecular biology
  • Bioinformatics
  • Genomics

Background:

  • High-throughput RNA sequencing (RNA-Seq) has generated extensive plant genomic data since 2007.
  • Organellar transcriptomes are frequently overlooked in standard RNA-Seq data analysis.

Purpose of the Study:

  • To develop a bioinformatics pipeline, ChloroSeq, for systematic analysis of chloroplast RNA metabolism.
  • To provide a user manual for ChloroSeq implementation.
  • To facilitate the study of nucleus-organelle cross talk through simultaneous transcriptome analysis.

Main Methods:

  • Development of the ChloroSeq bioinformatics pipeline.
  • Alignment of quality-controlled RNA-Seq data to a reference genome.
  • Measurement of genome expression levels, splicing, and RNA editing efficiencies.
  • Integration with the Tuxedo suite (TopHat, Cufflinks) for combined organellar and nuclear transcriptome analysis.
  • Utilizing R commands for data visualization.

Main Results:

  • ChloroSeq enables systematic analysis of chloroplast RNA metabolism.
  • The pipeline quantifies expression, splicing, and RNA editing efficiencies.
  • Simultaneous analysis of organellar and nuclear transcriptomes is achievable.
  • Publication-quality figures can be generated from ChloroSeq outputs.
  • Pipeline effectiveness demonstrated using Arabidopsis thaliana leaf development data.

Conclusions:

  • ChloroSeq facilitates comprehensive organellar transcriptome analysis.
  • The pipeline enhances understanding of nucleus-organelle communication.
  • ChloroSeq is a valuable tool for plant molecular biology research.