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Additional file 5: of Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae

Table of essential positions for RNA recognition in the PPRs of CLB19 and the corresponding RNA targets. (XLSX 40 kb

Additional file 2: of Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae

Phylogeny of the RARE1 orthologs in angiosperms. Shown is a Maximum Likelihood tree (see Methods). (PDF 468 kb

Additional file 3: of Expected and unexpected evolution of plant RNA editing factors CLB19, CRR28 and RARE1: retention of CLB19 despite a phylogenetically deep loss of its two known editing targets in Poaceae

Phylogeny of the CLB19 orthologs in angiosperms. Shown is a Maximum Likelihood tree (see Methods). (PDF 78 kb

Additional file 3: of Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0

Alignment prediction output. An example for the output of a multiple-query alignment for different references. (DOCX 79 kb

Additional file 4: of Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0

TargetScan of Editing environment. An example illustrating the use of TargetScan to identify nucleotide bias in the immediate environment of editing sites in position -4 to +3 as discussed in the text. (DOCX 87 kb

Additional file 1: of Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0

Multiple sequence input. An example for multiple query and reference sequence input in PREPACT’s alignment modes as discussed in the text. (DOCX 198 kb

Additional file 2: of Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0

Table of re-checked edits. Verification of additional RNA editing events previously overlooked in editome references. (DOCX 45 kb

Additional file 2: of Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors

Prediction of RNA editing using the BLASTX prediction mode of PREPACT exemplarily shown for the Amborella trichopoda ndhD gene. (DOCX 66 kb

Additional file 2: Figure S1. of Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns – a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles

Comparison of mitochondrial RNA editing sites between monilophytes and lycophytes. The experimentally confirmed editing sites in the genes atp1 and nad5 of the monilophyte species Polypodium cambricum, Dicksonia antarctica and Azolla filiculoides are compared with the respective editing sites deposited in NCBI from the lycophytes Isoetes engelmannii and Selaginella moellendorffii. Only 16 edits are shared between all five taxa. Most of the edits from the two lycophytes are unique to either one species or are shared between the two lycophytes and are therefore most likely independent gains. For the basal lycophyte Phlegmariurus squarrosus only 14 edits (all of the C-to-U type) are found in our cDNA analysis. Three of these edits are shared between all three lycophytes and six between Phlegmariurus and Isoetes. (DOCX 127 kb