Genome-wide comparison of ribosome occupancy on maize chloroplast mRNAs following light-to-dark and dark-to-light shifts of green seedlings.

<p>(A) Light shift regimes used for this analysis. Seedlings were grown for 8 days in 12-h light/12-h dark cycles and subjected to the indicate light shifts on day 9. (B) Ratio of signal in the light to dark following short-term light shifts at dawn and midday. Values reflect the relative abundance of ribosome footprints (Ribo-seq) or RNA (RNA-seq) mapping to each ORF in light <i>versus</i> dark. Ribo-seq/RNA-seq values reflect the number of ribosomes per mRNA (ribosome density) in light <i>versus</i> dark. The values are the mean ± SEM from three replicate datasets. Genes are grouped according to their function rather than their genomic position. Genes for which mRNA levels could not be measured with confidence are marked with asterisks. These include very short ORFs and intron-containing genes, as explained in [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007555#pgen.1007555.ref017" target="_blank">17</a>]. (C) Comparison of ribosome density on chloroplast ORFs after 12 hours in the dark (dawn) and 7 hours in the light (midday).