The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes
Language English Country Germany Media print-electronic
Document type Journal Article, Research Support, Non-U.S. Gov't, Review
- MeSH
- RNA Editing genetics MeSH
- Genome, Mitochondrial genetics MeSH
- Mitochondria genetics MeSH
- Plants genetics MeSH
- Sequence Analysis, RNA methods MeSH
- Transcriptome genetics MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
We review current studies of plant mitochondrial transcriptomes performed by RNA-seq, highlighting methodological challenges unique to plant mitochondria. We propose ways to improve read mapping accuracy and sensitivity such as modifying a reference genome at RNA editing sites, using splicing- and ambiguity-competent aligners, and masking chloroplast- or nucleus-derived sequences. We also outline modified RNA-seq methods permitting more accurate detection and quantification of partially edited sites and the identification of transcription start sites on a genome-wide scale. The application of RNA-seq goes beyond genome-wide determination of transcript levels and RNA maturation events, and emerges as an elegant resource for the comprehensive identification of editing, splicing, and transcription start sites. Thus, improved RNA-seq methods customized for plant mitochondria hold tremendous potential for advancing our understanding of plant mitochondrial evolution and cyto-nuclear interactions in a broad array of plant species.
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