Fig. 6: RNA-seq and Ribo-seq analyses of chloroplast gene expression.

RNA-seq analysis of chloroplast transcript abundance (a) and Ribo-seq analysis of ribosome footprint abundance (b) in the fpb1, pam68, and lpa1 mutants. Ratios of RNA-seq and Ribo-seq reads in the mutants relative to the wild type (WT) plants for all of the chloroplast PSII genes (For RNA-seq, the psbM gene was excluded because its number of reads is the lowest among PSII genes and is less than 200 in the samples of the first experiment) and of several representative chloroplast genes encoding subunits of other thylakoid protein complexes are shown. The values are the mean with standard deviations from three biological replicates of WT, fpb1, and pam68 (Supplementary Data 2) and the mean with single dots from two replicates of lpa1. The data are expressed as cpRPKM (reads per kilobase in the ORF per million reads mapped to total chloroplast ORFs) and plotted in log₂ scale on the Y-axis. c–e Distribution of ribosome footprints along the psbB ORF in three replicates of WT, fpb1, and pam68 mutant plants. The Y-axis shows the total reads at each position from the three genotypes (upper) or normalized based on the total reads (bottom). TMD-encoding positions on the psbB mRNA are indicated by Arabic numerals. Source data are provided as a Source Data file.