Figure 2

Overview of the translational landscape. A) Ribosome footprint and mRNA edgeR-normalized RPK for all genes, including pseudogenes, are shown. Each panel includes all biological replicates for a given stage, which are shown in different shades. The box outlines the genes with <50 RPK, the dotted box is enlarged in panel B; and the circle marks a set of genes with high mRNA read counts but relatively lower ribosome read counts that is referred to in the text. B) Illustration of large differences in ribosome association with mRNAs expressed to similar levels in PCF sample 2. Note that the x-axis is linear and the y-axis is log₂. C) Expression levels of pseudogenes, VSG genes and T. brucei specific genes in PCF. The boxed area (<50 RPK) is comprised mostly of pseudogenes (cyan dots) and VSG genes (pink dots) and a subset of the T. brucei specific genes (blue dots). D) The cluster of genes with reduced translation efficiency corresponds to structural components of the cytosolic ribosome (green dots).