Additional file 8: of The plastid and mitochondrial genomes of Eucalyptus grandis

Figure S4. Number of predicted C to U editing sites in the mitochondrial and plastid genomes of E. grandis using PREPACT, PREP-suite, and REDITOOLS mRNA editing detection of polyA-selected reads. a. Number of editing sites (y-axis) in E. grandis mitochondrial genes (x-axis) as predicted by PREP-Mt (blue), PREPACT (orange), and evidence from bulked polyA-selected reads from three samples each of eight tissues in E. grandis using REDItools (DNA-RNA algorithm: minimum read depth = 10, minimum amount of reads per editing event = 3) shown in grey. b. Number of editing sites (y-axis) in E. grandis plastid genes (x-axis) as predicted by PREP-Cp (blue), PREPACT (orange), and evidence from polyA-selected reads using REDItools (grey). These figures show that bulked polyA selected reads are sufficient to detect the majority of predicted editing events in land plants, however the read depth lower than would be detected with total RNA sequencing. c. Number of predicted editing sites in common between PREP-Mt, PREPACT, and REDItools in the E. grandis mitochondrial genome. d. Number of predicted editing sites in common between PREP-Cp, PREPACT, and REDItools in the E. grandis plastid genome. (PDF 52 kb