Title |
The application of RNA-seq to the comprehensive analysis of plant mitochondrial transcriptomes
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Published in |
Molecular Genetics and Genomics, September 2014
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DOI | 10.1007/s00438-014-0905-6 |
Pubmed ID | |
Authors |
James D. Stone, Helena Storchova |
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. |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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United States | 1 | 2% |
Uruguay | 1 | 2% |
Italy | 1 | 2% |
Germany | 1 | 2% |
Unknown | 45 | 92% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 14 | 29% |
Student > Ph. D. Student | 11 | 22% |
Student > Master | 7 | 14% |
Student > Doctoral Student | 2 | 4% |
Professor | 2 | 4% |
Other | 8 | 16% |
Unknown | 5 | 10% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 25 | 51% |
Biochemistry, Genetics and Molecular Biology | 11 | 22% |
Medicine and Dentistry | 2 | 4% |
Engineering | 2 | 4% |
Nursing and Health Professions | 1 | 2% |
Other | 3 | 6% |
Unknown | 5 | 10% |