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.
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Acknowledgments
We are grateful to Daniel B Sloan for reading and commenting on this manuscript. This work originated in the framework of the project “Integration of the experimental and population biology using new methods of interdisciplinary issues-the way to excellence with young scientists,” Reg.No.: CZ.1.07/2.3.00/30.0048, funded by the European Social Fund (ESF) and the state budget of Czech Republic through the Operational Programme Education for Competitiveness (OPEC). It was further supported by the grant of the Grant Agency of the Czech Republic P506/12/1359 to H.S.
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Stone, J.D., Storchova, H. The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes. Mol Genet Genomics 290, 1–9 (2015). https://doi.org/10.1007/s00438-014-0905-6
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DOI: https://doi.org/10.1007/s00438-014-0905-6