Evolutionary analysis reveals regulatory and functional landscape of coding and non-coding RNA editing
Fig 1
Identification of editing sites and evolution of editing levels.
(A) A tree representing the schematic phylogeny of Drosophila species [43]. All 13 species were used for RNA editing site identification; the 6 species used for editing level evolution analyses are highlighted in orange. D. melanogaster, D.mel; D. simulans, D.sim; D. yakuba, D.yak; D. eugracilis, D.eug; D. takahashii, D.tak; D. ficusphila, D.fic; D. elegans, D.ele; D. kikkawai, D.kik; D. bipectinata, D.bip; D. ananassae, D.ana; D. pseudoobscura, D.pse; D. mojavensis, D.moj; D. virilis, D.vir. The divergence time between D.ele, D.eug, D.fic, D.kik, D.bip and others are unknown; the dotted lines in the tree only represent the topology. The data used for each species are indicated. (B) Venn diagram showing sites reported in this study and three previously published studies. (C) Numbers of sites used for pairwise comparisons between the 6 selected species derived from the RNA-seq, mmPCR-seq and combined sets. Sites covered by ≥50 reads were included. The average numbers of the male and female whole body data are shown. (D) Pairwise comparison of editing levels (male whole body data), with the Spearman’s rho values in red. Sites covered by ≥50 reads were included. A site that was not an ‘A’ at the DNA level was defined as having an editing level of 0%. (E) Editing level divergence distance values (1 –Spearman’s rho) plotted against estimated divergence time for all possible species pairs. The dashed line indicates the linear regression. (F) Neighbor-joining tree with branch lengths inferred using editing level (male whole body data) distance (1- Spearman’s rho) for all pairs of species. Only sites edited in both species were used for analysis.