Fig. 7

Evaluation of mammalian editing sites in Xenopus. A Assessment of 58 conserved mammalian ADAR targets in X. laevis. The mammalian targets were lifted over from both the human and mouse genome assemblies and those that could not be converted were largely found in non-coding regions. Additionally, one mammalian site could give rise to two lifted over positions in X. laevis because the human sequence mapped to one homeolog while the mouse sequence mapped to the other homeolog. B Assessment of 58 conserved mammalian ADAR targets in X. tropicalis. C Nucleotide identity of genomic loci in X. laevis that had been successfully converted from our recently published list of human coding sites. D Nucleotide identity of genomic loci in X. tropicalis that had been successfully converted from our recently published list of human coding sites. E Pie chart summarizing our analysis of the 1517 human coding sites in X. laevis. F Pie chart summarizing our analysis of the 1517 human coding sites in X. tropicalis. G Self-organizing map of editing rates in the MHT study. Each row is a different vertebrate conserved coding site, while each column is a different developmental stage of X. laevis. H Self-organizing map of editing rates in the JBL study. Each row is a different vertebrate conserved coding site, while each column is a different developmental stage of X. tropicalis. I Scatterplots showing the modification rates of human coding sites and the corresponding lifted over positions in X. laevis. Sites found in genes with conflicting symbols between the two species or with insufficient sequencing coverage were omitted. Dotted lines indicate 10% difference in editing between human and Xenopus. J Scatterplots showing the modification rates of human coding sites and the corresponding lifted over positions in X. tropicalis. K Scatterplots showing the modification rates of conserved coding sites in two adult tissues of human and X. laevis. Each plotted site was covered by at least 10 sequencing reads per sample. L Scatterplots showing the maximum editing levels of coding DNA sequence (CDS)-targeted genes in human and their counterparts in X. laevis. M Scatterplots showing the maximum editing levels of CDS-targeted genes in human and their counterparts in X. tropicalis. Some well-known ADAR substrates were edited in human and both Xenopus species, such as transcripts encoding subunits of the glutamate receptor. However, several well-characterized mammalian ADAR targets were not edited in both frogs, such as the serotonin 5-HT2C receptor. N Alignment of partial COG3 protein sequences from human, X. laevis, and X. tropicalis, with the targeted amino acid residues boxed in black. Notably, the cog3 gene was differentially edited between the three species. The first editing event occurs only in X. laevis and is silent as there is no change in amino acid, while the second editing event is a conserved mammalian ADAR target and converts an isoleucine codon to a valine codon. Curiously, the second site is edited at much lower levels in Xenopus