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Plastids pp 279-294 | Cite as

Bioinformatic Analysis of Chloroplast Gene Expression and RNA Posttranscriptional Maturations Using RNA Sequencing

  • Bastien Malbert
  • Guillem Rigaill
  • Veronique Brunaud
  • Claire Lurin
  • Etienne Delannoy
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1829)

Abstract

Sequencing of total RNA enables the study of the whole plant transcriptome resulting from the simultaneous expression of the three genomes of plant cells (located in the nucleus, mitochondrion and chloroplast). While commonly used for the quantification of the nuclear gene expression, this method remains complex and challenging when applied to organellar genomes and/or when used to quantify posttranscriptional RNA maturations. Here we propose a complete bioinformatical and statistical pipeline to fully characterize the differences in the chloroplast transcriptome between two conditions. Experimental design as well as bioinformatics and statistical analyses are described in order to quantify both gene expression and RNA posttranscriptional maturations, i.e., RNA splicing, editing, and processing, and identify statistically significant differences.

Key words

Chloroplast transcriptome Organellar RNAseq Differentially expressed Splicing Editing Processing 

Notes

Acknowledgments

This work has benefited from a French State grant (LabEx Saclay Plant Sciences-SPS, ANR-10-LABX-0040-SPS), managed by the French National Research Agency under an “Investments for the Future” program (ANR-11-IDEX-0003-02).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Bastien Malbert
    • 1
    • 2
  • Guillem Rigaill
    • 1
    • 2
    • 3
  • Veronique Brunaud
    • 1
    • 2
  • Claire Lurin
    • 1
    • 2
  • Etienne Delannoy
    • 1
    • 2
  1. 1.Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-SaclayGif sur YvetteFrance
  2. 2.Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-CitéGif sur YvetteFrance
  3. 3.Laboratoire de Mathématiques et Modélisation d’Evry, Centre National de la Recherche Scientifique, École Nationale Supérieure d’Informatique pour l’Industrie et l’Entreprise, USC Institut National de la Recherche AgronomiqueUMR 8071, Université d’Evry Val d’EssonneGif sur YvetteFrance

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