The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes

0446185 - ÚEB 2016 RIV DE eng J - Journal Article
Stone, James D. - Štorchová, Helena
The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes.
Molecular Genetics and Genomics. Roč. 290, č. 1 (2015), s. 1-9. ISSN 1617-4615. E-ISSN 1617-4623
R&D Projects: GA ČR(CZ) GAP506/12/1359
Institutional support: RVO:61389030
Keywords : RNA-seq * Plant mitochondria * Transcriptome
Subject RIV: EF - Botanics
Impact factor: 2.622, year: 2015

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.
Permanent Link: http://hdl.handle.net/11104/0248170