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Fig. 4 | Genome Biology

Fig. 4

From: A large-scale genome and transcriptome sequencing analysis reveals the mutation landscapes induced by high-activity adenine base editors in plants

Fig. 4

Transcriptome-wide ABE-induced off-target mutations. a Number of SNVs and A>G SNVs, and percentage of A>G SNVs in plants harboring SpCas9 (Cas), SpCas9n-TadA8e (rBE46b), and SpCas9n-TadA9 (rBE49b). b Ratios of A>G mutations were calculated for A>G SNV loci detected in lines R49bAG_s2 and R49bAG_s3 and shown in the scatterplot. The Pearson correlation coefficient (r) was also calculated, and the red line is the diagonal line. c A sequence logo derived from edited adenines from all RNA-seq data. Bits account for how much each column is conserved and how much the nucleotide frequencies obtained in the profile differ from those that would have been obtained by aligning oligonucleotides chosen at random. d Boxplot showing ratios of A>G mutations at all RNA A>G SNV loci for plants harboring SpCas9, rBE46b, and rBE49b. A Wilcoxon test was conducted between every plant harboring ABEs versus plants harboring Cas only, and the -log10 p-value is shown. e Bar plot showing the average RPM values of ABEs for plants without RNA mutations and plants with RNA mutations. Each bar represents the mean value, each error bar represents the standard error, and each dot represents the ABE RPM value of each plant. (***) denotes p-value < 0.001 (one-tailed Wilcoxon test). f Ratios of A>G mutations of all A>G RNA SNV loci were calculated for one 49bAG_s2 T0 plant and four 49bAG_s2 T1 plants (left). -log10 p-value of Wilcoxon test on A>G ratios between five 49bAG_s2 plants versus plants harboring SpCas9 (middle). RPMs of ABEs are shown in the bar plot (right). N1 and N2 are T1 49bAG_s2 plants with a T-DNA insertion, while N3 and N4 are T1 49bAG_s2 plants without a T-DNA insertion

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