Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

RNA editing is a widespread post-transcriptional molecular phenomenon that can increase proteomic diversity, by modifying the sequence of completely or partially non-functional primary transcripts, through a variety of mechanistically and evolutionarily unrelated pathways. Editing by base substitution has been investigated in both animals and plants. However, conventional strategies based on directed Sanger sequencing are time-consuming and effectively preclude genome wide identification of RNA editing and assessment of partial and tissue-specific editing sites. In contrast, the high-throughput RNA-Seq approach allows the generation of a comprehensive landscape of RNA editing at the genome level. Short reads from Solexa/Illumina GA and ABI SOLiD platforms have been used to investigate the editing pattern in mitochondria of Vitis vinifera providing significant support for 401 C-to-U conversions in coding regions and an additional 44 modifications in non-coding RNAs. Moreover, 76% of all C-to-U conversions in coding genes represent partial RNA editing events and 28% of them were shown to be significantly tissue specific. Solexa/Illumina and SOLiD platforms showed different characteristics with respect to the specific issue of large-scale editing analysis, and the combined approach presented here reduces the false positive rate of discovery of editing events.