Figure 5. Ribosomal proteins and components of the translation apparatus are potently and coordinately up-regulated at the translation and mRNA level.

(A–B) PCA was performed separately on (A) mRNA and (B) RPF abundance datasets consisting of normalized counts for four-way orthologs in individual samples (one dataset for each replicate and condition). Factor loadings on the first two principal components are plotted for each sample. (C) MA plots of mRNA and RPF expression overlaid with transcripts corresponding to non-ribosomal translation factors (red), ribosomal protein genes (blue), and non translation-related genes highly-weighted on the first principal component (yellow). Data is shown for C. elegans and C. remanei; C. briggsae and C. brenneri show highly similar patterns (Fig. S5). (D–E) Violin plots [31] of fold changes for (D) ribosomal protein genes and (E) non-ribosomal translation factors in mRNA-seq (gold) and RPF (blue) data. White dots indicate medians, box edges represent the interquartile range, and the colored region and curve shows the probability density function. Significance is derived from two-tailed t-tests.