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.