title: The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes.
abstract: 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.
authors.affiliation: Institute of Experimental Botany v.v.i, Academy of Sciences of the Czech Republic, Rozvojova 263, Prague, 16502, Czech Republic.
authors.forename: James D
authors.initials: JD
authors.lastname: Stone
authors.forename: Helena
authors.initials: H
authors.lastname: Storchova
mesh_terms: D054629:Genome, Mitochondrial / Q000235:genetics; D008928:Mitochondria / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D017393:RNA Editing / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome / Q000235:genetics*