Chapter title |
Bioinformatic Analysis of Chloroplast Gene Expression and RNA Posttranscriptional Maturations Using RNA Sequencing
|
---|---|
Chapter number | 19 |
Book title |
Plastids
|
Published in |
Methods in molecular biology, January 2018
|
DOI | 10.1007/978-1-4939-8654-5_19 |
Pubmed ID | |
Book ISBNs |
978-1-4939-8653-8, 978-1-4939-8654-5
|
Authors |
Bastien Malbert, Guillem Rigaill, Veronique Brunaud, Claire Lurin, Etienne Delannoy, Malbert, Bastien, Rigaill, Guillem, Brunaud, Veronique, Lurin, Claire, Delannoy, Etienne |
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. |
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